How to Use Bioinformatics Databases and Tools to Accelerate Your Research
September 23, 2023Table of Contents
A Guide to Bioinformatics Tools and Databases
Venturing into the vast realm of bioinformatics reveals a spectrum of innovative tools and databases meticulously designed to interpret and analyze biological data. This guide provides a structured exploration into these diverse domains.
Metabolic and enzyme databases
Name | URL | Brief description | Download of Data | Current status |
---|---|---|---|---|
1-CMDb | http://slsdb.manipal.edu/ocm/ | Multi omics associated with one carbon metabolism | Yes | Online |
CaspDB | http://caspdb.sanfordburnham.org | Cleavage sites in proteins collected in Uniprot and their orthologs | No | Offline |
CFam | http://bidd2.nus.edu.sg/cfam | Cluster drugs, bioactive molecules, human metabolites, natural products, patented agents and other molecules | No | Offline |
CIDeR* | http://mips.helmholtz-muenchen.de/cider/ | Information from neurological and metabolic diseases | Yes | Online |
DESTAF | https://www.cbrc.kaust.edu.sa/destaf/ | Metabolism and toxins in diseases and tissues | Yes | Online |
dkNET | https://dknet.org// | Integrated data of Diabetes and Digestive and Kidney Diseases | Yes | Online |
HEMD | http://mdl.shsmu.edu.cn/HEMD/ | Human epigenetic enzymes and chemical modulators | Yes | Online |
HEPATONET1 | http://www.ebi.ac.uk/biomodels-main/MODEL1009150000 | Genome-scale metabolic network of human hepatocytes | No | Online |
HMA | https://metabolicatlas.org/ | Comprehensive human metabolic information as models | Yes | Online |
HumanCyc | https://humancyc.org/ | Human nutrition that associates with a set of metabolic pathways | No | Online |
HMDB* | https://hmdb.ca/ | Human Metabolome Database | Yes | Online |
KinMap | http://www.kinhub.org/kinmap/ | Interactive navigation through human kinome data | Yes | Online |
KinMutRF | http://kinmut2.bioinfo.cnio.es/KinMut2 | Prediction of variants in the human protein kinase superfamily | No | Offline |
metabolicMine | https://www.humanmine.org/humanmine/begin.do | Metabolome profiling and model organisms | Yes | Online |
MetSigDis | http://www.bio-annotation.cn/MetSigDis/ | Metabolite alterations in various diseases | Yes | Offline |
MSEA | https://www.metaboanalyst.ca/ | Enrichment analyses for (primarily human) metabolomic studies | Yes | Online |
NOPdb | http://www.lamondlab.com/NOPdb | Nucleolar proteins identified by mass spectrometry analyses | No | Offline |
PeroxisomeDB | http://www.peroxisomedb.org/ | Peroxisomal proteins, molecular function, metabolic pathway and disorders | Yes | Online |
PhosphoPredict | http://phosphopredict.erc.monash.edu/ | Predict kinase-specific phosphorylation substrates and sites in the human proteome | Yes | Online |
Piphillin | http://piphillin.secondgenome.com/ | Metagenomic data by Direct Inference from Human Microbiomes | Yes | Online |
R spider | http://www.bioprofiling.de/gene_list.html | Pathway analysis from KEGG and Reactome | No | Online |
RegenBase | http://regenbase.org/ | Effect of compounds on enzyme activity and cell growth | Yes | Online |
TSEM | https://hood-price.isbscience.org/research/tsem/ | Tissue specific encyclopedia of metabolism and metabolic models | Yes | Online |
VMH | https://vmh.life/ | Human metabolism and genetics, microbial metabolism, nutrition, and diseases | Yes |
Methylation databases
Name | URL | Brief description | Download of Data | Current status |
---|---|---|---|---|
ANCOGeneDB | https://bioinfo.uth.edu/ancogenedb/ | Epigenomic, enhancers, and expression quantitative trait loci | Yes | Online |
BECon* | https://redgar598.shinyapps.io/BECon/ | Interpreting methylation findings from blood in the context of brain | Yes | Online |
CMS | http://cbbiweb.uthscsa.edu/KMethylomes/ | Analytic functions for cancer methylome datasets | No | Offline |
DBCAT | http://dbcat.cgm.ntu.edu.tw/ | Methylation profiles of DNA alteration in human cancer | Yes | Online |
DiseaseMeth* | http://bio-bigdata.hrbmu.edu.cn/diseasemeth/ | Aberrant methylomes of human diseases | No | Online |
GED | http://gametsepi.nwsuaflmz.com/ | Epigenetic modification of gametogenesis in mammals | Yes | Online |
Geneimprint | http://www.geneimprint.com/site/home | Gene imprinting and which allele is expressed | Yes | Online |
Lnc2Meth | http://bio-bigdata.hrbmu.edu.cn/Lnc2Meth/ | Informs about RNAs and DNA methylation of transcripts | Yes | Online |
MeInfoText | http://bws.iis.sinica.edu.tw:8081/MeInfoText2/ | Gene methylation and cancers, protein-protein interactions, and biological pathways | Yes | Offline |
MethHC | http://methhc.mbc.nctu.edu.tw/ | Focuses on aberrant methylomes of human diseases | No | Offline |
MethylomeDB | http://epigenomics.columbia.edu/methylomedb/index.html | DNA methylation profiles for human and mouse brains | Yes | Offline |
mPod | www.genome.org | Genome-wide tissue-specific DNA methylation profiles | No | Online |
PhenoScanner | http://www.phenoscanner.medschl.cam.ac.uk/ | Methylation and human genotype-phenotype associations | Yes | Online |
ROADMAP | https://egg2.wustl.edu/roadmap/web_portal/index.html | Epigenetic modifications and mRNA expression of human cell types and tissues | Yes | Online |
TCGA | https://www.cancer.gov/ | Cancer methylation and expression | Yes | Online |
TSGene | http://bioinfo.mc.vanderbilt.edu/TSGene/ | Methylation status of tumor suppressor genes | No | Offline |
Regulatory databases
The 29 databases allow to visualize modified ribosomal nucleotides of human and several major model organisms, present resources to the identification of transcription factors, functional elements, cis-regulatory elements, interferon regulated genes, large intergenic non-coding RNAs (lincRNAs) and miRNA regulatory cascades in human diseases, Triplex Target DNA Site (TSS) with genomic regulatory sequences and signals, and RNA binding elements. The data is either from text-mining-assisted workflow, chromatin immunoprecipitation (ChIP), high-throughput datasets, Genome-Wide Association Studies (GWAS), next-generation sequencing techniques and/or predicted by computational models with annotations obtained by expert review of the scientific literature. Gene names, accession numbers, Fasta sequences, ligand ID (e.g., G4L0021), ligand name (e.g., TMPyP4), ligand activity or binding properties (e.g., Cytotoxicity), author name of ligand related literature, Ensembl ID List, tissue or cell type are examples of the possible inputs. Databases for Triplex target DNA sites provide specific search criteria, such as percent guanine content and pyrimidine interruption. The result shows a list of genes, tables, venn diagrams, scatter plot, position weight matrix for a selected motif, navigation across the motifs, and heatmaps with the target elements and biosamples.
Name | URL | Brief description | Download of Data | Current status |
---|---|---|---|---|
ChIPSummitDB | http://summit.med.unideb.hu/summitdb/index.php | ChIP-seq-based data of transcription factor binding sites and the topological arrangements of the proteins | Yes | Online |
CREME | https://creme.dcode.org/ | Cis-regulatory module explorer for the human genome | Yes | Online |
CRUNCH | http://crunch.unibas.ch/crunch/ | ChIP-seq data analysis | Yes | Online |
FirstEF | http://rulai.cshl.org/tools/FirstEF/ | First Exon Finder (FirstEF) is a 5’ terminal exon and promoter prediction program | Yes | Online |
GlycoViewer | http://www.glycoviewer.babs.unsw.edu.au/ | Visualisation tool for representing a set of glycan structures | Yes | Online |
HERVd | https://herv.img.cas.cz/ | Human endogenous retroviruses database | No | Online |
HumCFS | https://webs.iiitd.edu.in/raghava/humcfs/index.html | Human chromosomal fragile sites data | No | Online |
Interferome* | http://interferome.its.monash.edu.au/interferome/home.jspx | Contains type I, II and III interferon (IFN) regulated genes | No | Online |
JASPAR | http://jaspar.genereg.net/ | The high-quality transcription factor binding profile database | Yes | Online |
MANTA | http://manta.cmmt.ubc.ca/manta2/upload | Maps of transcription factor binding sites | Yes | Online |
MAPPER | http://genome.ufl.edu/mapperdb | Multi-genome analysis of positions and patterns of elements of regulation | No | Offline |
MEME Suite | http://meme-suite.org/ | DNA motifs, transcription factor binding sites or protein domain | Yes | Online |
MET | http://veda.cs.uiuc.edu/MET/ | The motif enrichment tool identifies significantly associated sets of genes that share a regulatory motif | Yes | Online |
microDoR | http://reprod.njmu.edu.cn/cgi-bin/microdor/index.py | Predict Human miRNA-mediated gene silencing | Yes | Online |
OsteoporosAtlas | http://biokb.ncpsb.org/osteoporosis/index.php | Regulatory sequences in osteoporosis-related genes | Yes | Online |
PReMod | http://genomequebec.mcgill.ca/PReMod | Predict transcriptional regulatory modules of human genome | Yes | Online |
pseudoMap | http://pseudomap.mbc.nctu.edu.tw/php/index.php | Gathers information about transcribed pseudogenes | No | Offline |
SM-TF | http://zoulab.dalton.missouri.edu/SM-TF/ | Database of small molecule-transcription factor complexes | Yes | Online |
SNP@lincTFBS | http://210.46.85.180:8080/SNP_linc_tfbs/ | SNPs in potential TFBSs of human Large intergenic non-coding RNAs (lincRNAs) | Yes | Offline |
TcoF-DB | https://tools.sschmeier.com/tcof/home/ | Human transcription co-factors and transcription factor interacting proteins | No | Online |
TFBSbank | http://tfbsbank.co.uk/ | Chip-seq data of 585 transcription factors in 5 species | Yes | Online |
TFCat | http://www.tfcat.ca/ | Curated catalog of mouse and human transcription factors | No | Offline |
TFClass | http://tfclass.bioinf.med.uni-goettingen.de/ | Eukaryotic TFs according to their DNA-binding domains | No | Online |
TFCONES | http://tfcones.fugu-sg.org/ | Transcription factor genes and conserved noncoding elements | Yes | Online |
TFM-Explorer | https://bioinfo.lifl.fr/TFM/ | Putative TFBS within a set of upstream regulatory sequences for a given set of genes | Yes | Online |
TMREC | http://www.jianglab.cn/TMREC/ | TF and miRNA regulatorY cascades in human diseases | Yes | Online |
TRANSFAC | http://genexplain.com/transfac/ | Eukaryotic TF, their experimentally-proven binding sites, consensus binding sequences and regulated genes | No | Online |
TTSMI database* | http://ttsmi.bii.a-star.edu.sg/ | Triplex target DNA site mapping and integration database | No | Online |
Alternative splicing databases
In the intricate landscape of bioinformatics, 24 distinctive tools focus on analyzing the effect of alternative splicing on protein interactions and structures within the human genome. These tools delve deep into the consequences of SNVs in intron positions, offering insights into the differential splicing of introns and exons across various species. Many databases, grounded in robust molecular studies and enhanced with machine learning predictions, provide curated catalogs of alternative splicing sites and gene transcripts.
Name | URL | Brief description | Download of Data | Current status |
---|---|---|---|---|
AltExtron | http://bioinformatics.org.au/tools/altExtron/ | Constitutively and alternatively spliced introns and exons, for conservation in mouse. | Yes | Online |
AS-ALPS | http://as-alps.nagahama-i-bio.ac.jp/index.php | Alternative splicing-induced alteration of protein structure | Yes | Online |
ASpedia | http://combio.snu.ac.kr/aspedia/index.html | Alternative splicing encyclopedia with genomic annotation | Yes | Online |
ASPicDB* | http://srv00.recas.ba.infn.it/ASPicDB/ | Alternative splicing pattern of human genes, and functional annotation of predicted isoforms | Yes | Online |
BrainRNA-seq | https://www.brainrnaseq.org/ | Alternative splicing events in cell types | Yes | Online |
DBASS | http://www.dbass.org.uk/ | Splice-site prediction, and definition of auxiliary splicing signals | Yes | Online |
EDAS | http://www.gene-bee.msu.ru/edas/ | EST-derived alternative splicing database | No | Offline |
FAST DB | http://www.genosplice.com/alternative-splicing | Alternative splicing and alteration of splicing regulation | No | Online |
FLJ DB | http://flj.lifesciencedb.jp/top/ | Variations of transcription start site (TSS) and splicing | Yes | Online |
H-DBAS | http://www.h-invitational.jp/h-dbas/ | Human-transcriptome data of alternative splicing | Yes | Online |
HEXEvent | http://hexevent.mmg.uci.edu/cgi-bin/HEXEvent/HEXEventWEB.cgi | Splice events based on EST information | No | Online |
HOLLYWOOD | http://hollywood.mit.edu/hollywood/Login.php | Splicing patterns derived from spliced alignment of cDNAs | Yes | Online |
HSF | http://www.umd.be/HSF3/index.html | Prediction of mutations in splice sites | No | Online |
HYBRIDdb | http://www.primate.or.kr/hybriddb/ | Identify intergenic splicing-mediated gene fusion | No | Offline |
IntSplice | https://www.med.nagoya-u.ac.jp/neurogenetics/IntSplice/ | Predict a splicing consequence of SNV | Yes | Online |
IsoFunc | https://guanlab.ccmb.med.umich.edu/isofunc | A tool for assigning function to protein-coding splice variants | No | Offline |
MiasDB | http://47.88.84.236/Miasdb/index.php | Molecular interactions associated with human splicing | Yes | Online |
NetGene2 | http://www.cbs.dtu.dk/services/NetGene2/ | Splice sites in human, C. elegans and A. thaliana | No | Online |
NetUTR | http://www.cbs.dtu.dk/services/NetUTR/ | Prediction of splice sites in 5′ UTR regions | No | Online |
PALS DB | http://palsdb.ym.edu.tw/ | Collection of Putative Alternative Splicing | No | Offline |
SpliceInfo | http://SpliceInfo.mbc.NCTU.edu.tw/ | Info of exon skipping, 5’ or 3’-alternative splicing and intron retention | Yes | Offline |
SplicePort | http://spliceport.cbcb.umd.edu/ | Splice-site predictions for submitted sequences | No | Online |
SpliceProt | http://bioinfoteam.fiocruz.br/spliceprot/index.php | Alternative spliced variants based on experimental human transcriptomic data | Yes | Online |
TassDB* | http://tassdb2.leibniz-fli.de/ | Search for specific genes or for genes containing tandem splice sites | Yes | Online |
Cancer databases
A collection of 56 specialized databases offers comprehensive insights into various tumor types, human TCRs’ recognition of cancer epitopes, and the impacts of somatic mutations in human cancer. These resources enable meticulous analysis of gene-specific copy numbers in diverse tumors and offer extensive information about cancer cell lines, driver genes, and metastasis, contributing to a deeper understanding of cancer’s multifaceted nature.
Name | URL | Brief description | Download of Data | Current status |
---|---|---|---|---|
MGDB | MGDB | Multiomics catalog of genes involved in melanoma | Yes | Online |
MiRCancer | MiRCancer | Expression profiles in human cancers and curated literature | Yes | Online |
MiTranscriptome | MiTranscriptome | Primary tumor, metastases, and normal or benign adjacent tissues | Yes | Online |
MSGene | MSGene | Comprehensive gene resource for metastasis suppressor | Yes | Online |
MTCTScan | MTCTScan | Mutations affecting cancer drug sensitivity based on genomic profiles | Yes | Online |
NCI ALMANAC | NCI ALMANAC | Information about greater antitumor activity than either agent alone | Yes | Online |
NeXtProt | NeXtProt | Gene expression of genes in hereditary cancers and channelopathies | Yes | Online |
OncoDB.HCC | OncoDB.HCC | Quantitative trait loci of rodent models and human Hepatocellular cancer | Yes | Online |
OncomiRdbB | OncomiRdbB | Data of microRNAs which are known to be deregulated in various cancers | No | Online |
Oncotator | Oncotator | Cancer-specific annotations from public resources | Yes | Offline |
Oncoyeasti | Oncoyeasti | Human homologs of yeast genes in samples of TCGA and CCLE | No | Online |
Pedican | Pedican | Gene expression in pediatric/childhood cancer | Yes | Online |
PepiD | PepiD | Epigenetic data in prostate cancer of human, mouse, and rat | Yes | Offline |
Progenetix | Progenetix | Oncogenomic database that provides copy number aberration data | No | Online |
S-MED | S-MED | miRNA expression in various human sarcoma types | Yes | Online |
SelTarbase | SelTarbase | Collection of human microsatellite instability tumor and cell line | Yes | Online |
TANTIGEN | TANTIGEN | Tumor T cell antigens and validated epitopes for discovered peptides | No | Online |
TCGA Portal* | TCGA Portal* | The cancer genome atlas with multi-omic and clinical data | Yes | Online |
TCRex | TCRex | Predict the recognition of pathogenic & cancer epitopes by human TCR | Yes | Online |
TICdb | TICdb | Gene expression and translocation breakpoints in human tumors | Yes | Offline |
TUMIR | TUMIR | Validated resource of microRNA deregulation in various cancers | Yes | Offline |
UMDTP53db | UMDTP53db | A reference for all scientists working on p53 | Yes | Online |
arrayMap | https://arraymap.org/ | Resource targeting copy number profiling data | Yes | Online |
CGAProject | https://mitelmandatabase.isb-cgc.org/ | Gene expression profiles of normal, precancer, and cancer cells | Yes | Online |
CancerNet | http://bis.zju.edu.cn/CancerNet/ | Contains cancer-specific miRNA and protein-protein interactions | Yes | Online |
CanGEM | http://www.cangem.org/ | Clinical information, transcriptome, genome, and aCGH data | No | Offline |
CanProVar | http://canprovar.zhang-lab.org/index.php | Conservation, protein expression, and domains in cancer data | Yes | Online |
CARGO | http://cargo2.bioinfo.cnio.es/ | Visualize 3D SNPs, and view summarized gene annotation | Yes | Online |
CaSNP | http://cistrome.dfci.harvard.edu/CaSNP/ | Identifying CNAs in cancers and in the human genome | No | Offline |
CCLE* | https://portals.broadinstitute.org/ccle | Cancer cell line encyclopedia with 36 tumor types. | Yes | Online |
CGMD | http://cgmd.in/ | A database of tumor genes and markers with experimental evidence | No | Offline |
ChiTaRS | http://chitars.md.biu.ac.il/ | Data of chimeric RNAs from eight organisms | Yes | Online |
CMS | http://cbbiweb.uthscsa.edu/KMethylomes/ | Gene expression and cancer methylome datasets | No | Offline |
COSMIC | https://cancer.sanger.ac.uk/cosmic | Gene expression and somatic mutations in human cancer | Yes | Online |
CPDB | https://www.library.ucdavis.edu/database/carcinogenic-potencydatabase-cpdb/ | Human exposures to chemicals that cause cancer in rodent tests | No | Online |
DBCAT | http://dbcat.cgm.ntu.edu.tw/ | DataBase of CpG islands with a genome browser | Yes | Online |
DbDEMC | https://www.picb.ac.cn/dbDEMC/ | A database of differentially expressed miRNAs in human cancers | Yes | Online |
dbDEPC | https://www.scbit.org/dbdepc3/index.php | A database with curated cancer proteomics data | Yes | Online |
DBGC | http://bminfor.tongji.edu.cn/dbgc/index.do | Human gastric cancer-related gene expression data | No | Offline |
DiseaseMeth | http://bio-bigdata.hrbmu.edu.cn/diseasemeth/ | Associations between diseases and methylation of specific DNA regions | No | Online |
DriverDB | http://120.110.158.132:8787/driverdbv2/cancer.php | Gene expression and driver gene/mutation identification | Yes | Online |
DSTHO | http://203.199.182.73/gnsmmg/databases/dstho.html | Database of siRNAs Targeted at Human Oncogenes | No | Offline |
GCOD | http://compbio.dfci.harvard.edu/gcod | Microarray data on GeneChip arrays related to human cancers | Yes | Offline |
GEMiCCL | https://www.kobic.kr/GEMICCL/ | Repository of cancer cell lines genotype and expression information. | Yes | Online |
GeneHub-GEPIS | http://www.cgl.ucsf.edu/Research/genentech/genehub-gepis/ | Human and mouse gene expression of normal and cancer tissues | Yes | Online |
GSR | https://popmodels.cancercontrol.cancer.gov/gsr/ | Genetic simulation resources provided by the National Cancer Institute | No | Online |
HCMDB | http://hcmdb.i-sanger.com/index | Human cancer metastasis database with gene expression data | Yes | Online |
HCPIN | http://nmr.cabm.rutgers.edu/hcpin | Gene expression of human cancer with protein interaction network | No | Offline |
HNOCDB | HNOCDB | Methylation and gene expression in Head Neck and Oral Cancer | No | Online |
ISOexpresso | ISOexpresso | Isoform-level gene expression analysis in human cancer | Yes | Online |
MCF10A | MCF10A | Visualizing data from normal and mammary tumors | No | Online |
MeInfoText | MeInfoText | Manual curation of gene methylation-cancer relations | Yes | Offline |
MERAV | MERAV | Gene expression in normal tissues, cancer cell lines, and primary tumors | Yes | Online |
MethHC | MethHC | Expression profiles and methylation of cancers and other diseases | No | Offline |
MethmiRbase | MethmiRbase | Epigenetic regulated miRNA in human cancers | Yes | Online |
Comparative databases
Within comparative databases, 31 unique tools facilitate the identification of genes associated with orthologous phenotypes across species and offer extensive comparative genomic analyses. These tools are crucial for investigating the evolutionary dynamics of genes and provide insights into non-human primate reference transcriptomes and human nonsynonymous SNPs in protein structures and metabolic networks.
Name | URL | Brief description | Download of Data | Current status |
---|---|---|---|---|
EVOG | EVOG | Phylogenetic evolution analysis for genes among species | No | Online |
GALA | GALA | Human-mouse whole-genome alignments and annotations | Yes | Online |
GMO | GMO | Analysis of the gametogenesis genes in human and mouse | Yes | Online |
Gene Set Builder | Gene Set Builder | Gene sets and Homology annotations among species | Yes | Online |
HelmCoP | HelmCoP | Comparative genomic data from plant, animal and human helminths | Yes | Online |
Homophila | Homophila | Links between human diseases and the Drosophila genome | Yes | Online |
Idiographica | Idiographica | Create idiograms of human, mouse, rat, and fruit fly | Yes | Online |
IRView | IRView | Interacting regions in human and mouse proteins | Yes | Online |
LMPD | LMPD | Lipidomics and genomics from several species | Yes | Online |
MANTEIA | MANTEIA | Comparative genomics of human and model organisms | Yes | Online |
MDWeb | MDWeb | Standard molecular dynamics simulations | No | Online |
Metab2MeSH | Metab2MeSH | Annotations of PubChem and Human Metabolome Database | Yes | Online |
MGC | MGC | Collection of cDNA clones for human, mouse, and rat genes | No | Online |
Netview | Netview | Explore the human and mouse gene regulatory networks | Yes | Online |
NHPRTR | NHPRTR | Non-human primate transcriptomes and tissue pools | Yes | Online |
NRED | NRED | Gene expression of long ncRNAs in human and mouse | Yes | Offline |
OpenDOAR | OpenDOAR | Directory of open access repositories, outputs, and resources | No | Online |
PhenoHM | PhenoHM | Identification of genes associated with phenotypes | Yes | Online |
POMO | POMO | Omics relationships and annotations across organisms | No | Offline |
POEDB | POEDB | Orthologous exon regions in human, chimpanzee, and rhesus | No | Offline |
RasMol | RasMol | Molecular graphics visualization tool | No | Online |
ReCGiP | ReCGiP | Providing candidate genes for reproductive researches | Yes | Online |
SQUAT | SQUAT | Analysis tools for human, mouse, and chicken data | No | Offline |
StemMapper | StemMapper | Info of stem cell/progenitor cell types of mouse and human | Yes | Online |
TiSGeD | TiSGeD | Tissue-specific genes of human, mouse, and rat | No | Offline |
TISSUES* | TISSUES* | Gene-tissue associations in human and mammalian models | Yes | Online |
ToppCluster* | ToppCluster* | Comparative enrichment and network analysis of multiple gene lists of human/mammalian organisms | Yes | Online |
TBrowser | TBrowser | Human and mouse molecular interactions | Yes | Offline |
tRFdb | tRFdb | Transfer RNA Fragments of human and model organisms | No | Online |
Vega Browser | Vega Browser | Vertebrate genome annotation | No | Online |
VISTA Browser | VISTA Browser | Experimentally validated human and mouse enhancers | Yes | Online |
Disease-specific and variant-disease association
Exploration uncovers 84 specialized tools and databases related to a spectrum of diseases, from monogenic conditions to complex ailments like Alzheimer’s and Autism. These serve as repositories for human mutations and SNVs, delivering annotated variants and their impacts, and elucidating the clinical significance of variants for a range of conditions, making them indispensable for understanding diverse human diseases.
Name | URL | Brief description | Download of Data | Current status |
Globin Server | http://globin.cse.psu.edu | Experimental data and tools of human hemoglobin mutations | No | Online |
AutDB | http://autism.mindspec.org/autdb/Welcome.do | Genetic variations related to autism spectrum disorders | Yes | Online |
BioAfrica | https://www.krisp.org.za/tools.php | Data of Human Immunodeficiency Virus proteins and other viruses | Yes | Online |
C/VD | http://www.padb.org/cvd/index.html | Compiles multi-omics data of cardiovascular-related traits | No | Online |
ClinVar | https://www.ncbi.nlm.nih.gov/clinvar/ | Interpretations of clinical significance of variants for reported conditions | Yes | Online |
DbAARD | http://genomeinformatics.dce.edu/dbAARD/ | Database of Aging and age-related disorders | Yes | Offline |
DbDNV | http://goods.ibms.sinica.edu.tw/DNVs/ | Data of variants of duplicated gene loci in the human reference genome | Yes | Online |
DbGaP | https://www.ncbi.nlm.nih.gov/gap/ | Archives and distributes the results of genotype-phenotype studies | Yes | Online |
dbPEC | http://ptbdb.cs.brown.edu/dbpec/ | Resource of preeclampsia phenotypes and associated genes | Yes | Offline |
dbSNP | http://www.ncbi.nlm.nih.gov/SNP | Disease-causing clinical mutations as well as neutral polymorphisms | Yes | Online |
dbWGFP | http://bioinfo.au.tsinghua.edu.cn/dbwgfp | Data about whole-genome SNVs and their functional predictions | Yes | Offline |
DECIPHER | https://decipher.sanger.ac.uk/ | Genomic variants and phenotype using Ensembl resources | No | Online |
Denovo-db | http://denovo-db.gs.washington.edu/denovo-db/ | Contains data about human de novo variants | Yes | Online |
DES-Mutation | https://www.cbrc.kaust.edu.sa/des-mutation/mykbase/ | Mutation-focused knowledge-base of Pubmed articles | No | Offline |
DGP | http://maine.ebi.ac.uk:8000/services/dgp | Probability scores for genes being involved in hereditary disease | Yes | Offline |
DGV | http://dgv.tcag.ca/ | Collection of structural variation in the human genome | No | Online |
Digital Ageing Atlas | http://ageing-map.org/ | Integrated data about human ageing changes and pathologies | Yes | Online |
Diseasome | http://www.kobic.kr/diseasome/ | Genetic variation in disease focus on polymorphisms | No | Online |
DisGeNET | https://www.disgenet.org/ | Variant and gene-disease associations in more than 20000 diseases | Yes | Online |
DMDM | http://bioinf.umbc.edu/dmdm/ | Visualization of human coding disease-related mutations and SNPs for each protein domain | Yes | Online |
EGA | https://www.ebi.ac.uk/ega/ | Reference data collections for human genetics research | Yes | Online |
FIDD | http://www.uwcm.ac.uk/uwcm/mg/fidd/ | Frequency of inherited human disorders of over 200 conditions | No | Offline |
Name | URL | Brief description | Download of Data | Current status |
fitSNPs | http://fitsnps.ucsf.edu/index.php | Functionally interpolating SNPs from differential gene expression | Yes | Offline |
Follicle Online | http://mcg.ustc.edu.cn/sdap1/follicle/index.php | Folliculogenesis-related experimental data from 23 model organisms, including human | No | Offline |
GeneReviews | https://www.uniprot.org/database/DB-0188 | Contains phenotypic information and information on selected variants | Yes | Online |
Genome Trax | Genome Trax Search Tool | Variant analysis of whole genome, exome, and targeted sequences | Yes | Online |
HbVar | http://globin.cse.psu.edu/hbvar/menu.html | Hemoglobin variants, hemoglobinopathies all types of thalassemia | Yes | Online |
HGMD | http://www.hgmd.cf.ac.uk/ac/index.php | Compiles information related to disease-related genetic variation | No | Online |
HGSVP | https://www.internationalgenome.org/human-genome- structural-variation-consortium/ | Map of structural variation with genomic assays | Yes | Online |
HGV&TB | http://genome.igib.res.in/hgvtb/index.html | Human genes and genetic variants associated with Tuberculosis | Yes | Online |
HMDD | http://www.cuilab.cn/hmdd | Experimental evidence for human miRNA and disease associations | Yes | Online |
HPO | https://hpo.jax.org/app/ | Vocabulary of phenotypic abnormalities encountered in human disease | Yes | Online |
Hu.MAP | http://hu.proteincomplexes.org/ | A comprehensive view of protein complexes of disease genes | Yes | Online |
Chr21 SNP DB | http://csnp.unige.ch/ | Genetic variation of human chromosome 21 genes | Yes | Offline |
HUMSAVAR | https://www.uniprot.org/docs/humsavar | An index of human polymorphisms and disease mutations | Yes | Online |
InvFEST | http://invfestdb.uab.cat/ | Catalog of non-redundant human polymorphic inversions | No | Online |
Ion Channels Portal | https://www.nextprot.org/portals/navmut | Present phenotypes caused by genetic variations in voltage-gated sodium channels | Yes | Online |
ITHANET | https://www.ithanet.eu/db/ithagenes | Archive of sequence variations affecting hemoglobin disorders | No | Online |
Kaviar | http://db.systemsbiology.net/kaviar/cgi-pub/Kaviar.pl | Compilation of human SNVs collected from many and diverse sources | Yes | Online |
KMeyeDB | http://mutationview.jp/MutationView/jsp/index.jsp | A database of human gene mutations that cause eye diseases | Yes | Online |
LaforaDB | http://projects.tcag.ca/lafora/ | A human Lafora disease (LD) mutation database | Yes | Online |
LongevityMap | http://genomics.senescence.info/longevity/ | A catalog of human genetic variants associated with longevity | Yes | Online |
LOVD | http://www.lovd.nl/ | Gene-centered collection and display of DNA variations | No | Online |
LSDBs | https://grenada.lumc.nl/LSDB_list/lsdbs | Gene sequence variation associated with human phenotypes | No | Online |
MARRVEL* | http://marrvel.org/ | Model organism aggregated resources for rare variant exploration | Yes | Online |
MelanomaMine | http://melanomamine.bioinfo.cnio.es/ | Data of melanoma-related biomedical knowledge resources | Yes | Online |
MitoVariome | https://www.kobic.re.kr/MitoVariome | Genetic variation in the mitochondrial genome with haplogroups | Yes | Offline |
Mutalyzer | https://mutalyzer.nl/ | Sequence variants according to the standard human sequence variant nomenclature (HGVS) | No | Online |
MutPred | http://mutpred.mutdb.org/ | Classify an amino acid substitution as disease-associated or neutral | No | Online |
NetChop | http://www.cbs.dtu.dk/services/NetChop/ | Neural network predictions for cleavage sites of the proteasome | No | Online |
OCDB | http://alpha.dmi.unict.it/ocdb/ | Data of genes, miRNAs, and drugs for obsessive-compulsive disorder | Yes | Offline |
Name | URL | Brief description | Download of Data | Current status |
OMIM | https://omim.org/ | Online mendelian inheritance in man with genes and genetic disorders | Yes | Online |
PAHKB | https://bioinfo.uth.edu/PAHKB/ | Records core pulmonary hypertension (PH)-related genes | Yes | Online |
PanelApp | https://panelapp.genomicsengland.co.uk/ | Virtual gene panels of disorders to be created, stored and queried | Yes | Online |
PaPI | http://papi.unipv.it/ | Score variants according to the damage their protein-related function | No | Online |
PEDB | http://www.pedb.org | Prostate gene expression database | Yes | Offline |
pfSNP | http://pfs.nus.edu.sg/ | Analysis of SNPs and your possible functionality from sequence motifs | Yes | Offline |
PharmGKB | https://www.pharmgkb.org/ | Pharmacogenomics and impact of genetic variations on drug response | Yes | Online |
PhenCode | http://globin.bx.psu.edu/phencode | Human phenotype and clinical data in various locus-specific databases | No | Offline |
Phenocarta | Expression Experiments | Phenotypes tree of diseases, human and mammalian species | Yes | Online |
PhenoCHF | http://www.nactem.ac.uk/PhenoCHF/ | Phenotypic information related to integrating heterogeneous resources | Yes | Online |
PhenoDB | https://researchphenodb.net/ | Exome/genome sequencing to identify the genes and variants | Yes | Online |
PhenoDigm | https://www.sanger.ac.uk/science/tools/phenodigm | Phenotype comparisons for disease and gene models | Yes | Online |
PhenoHM | https://phenome.cchmc.org/phenoBrowser/Phenome | Human-mouse comparative phenome-genome and orthologous | Yes | Online |
Phenopedia | https://phgkb.cdc.gov/PHGKB/startPagePhenoPedia.action | Genetic association studies in order to facilitate knowledge synthesis | Yes | Online |
PhenoTips | https://phenotips.com/ | Data about phenotypic information for patients with genetic disorders | Yes | Online |
PhosphoPOINT | http://kinase.bioinformatics.tw/ | Comprehensive human kinase interactome and phospho-protein | No | Offline |
PhosphOrtholog | http://www.phosphortholog.com/ | Cross-species mapping of orthologous protein modifications | Yes | Online |
PolyPhen2 | http://genetics.bwh.harvard.edu/pph2/ | Impact of an amino acid substitution on the structure and function | No | Online |
PredictSNP2 | http://loschmidt.chemi.muni.cz/predictsnp2/ | Evaluation of the pathogenic effect of SNPs within the human genome | Yes | Online |
PTM-SNP | http://gcode.kaist.ac.kr/ptmsnp | Collection of non-synonymous SNPs that affect post-translational modification sites | No | Offline |
PubAngioGen | http://www.megabionet.org/aspd/ | The connection between angiogenesis and diseases at multi-levels | Yes | Offline |
RatMine / InterMine | http://ratmine.mcw.edu/ratmine/begin.do | Integrates many types of data for human, mice, rat, and other species | Yes | Online |
RAvariome | http://www.h-invitational.jp/hinv/rav/ | Data about variants of rheumatoid arthritis | No | Online |
SNP2TFBS | https://ccg.epfl.ch/snp2tfbs/ | Approach for identifying regulatory variants | No | Online |
SNPDelScore | https://www.ncbi.nlm.nih.gov/research/snpdelscore/ | Analysis of deleterious effects of noncoding variants | Yes | Online |
SNPedia | https://www.snpedia.com/ | Functional consequences of human genetic variation as published in studies | No | Online |
SNPeffect | https://snpeffect.switchlab.org/ | Information about phenotyping human single nucleotide polymorphisms | Yes | Online |
SNVBox | https://karchinlab.org/apps/appSnvBox.html | Prediction of the impact of either germline or somatic SNVs | Yes | Online |
TMREC | http://210.46.85.180:8080/TMREC/ | Regulatory cascades in specific disease by TF, miRNA or disease name | Yes | Offline |
UGAHash | http://ugahash.uni-frankfurt.de/ | Accession numbers to genomic features with a focus on lncRNAs | No | Online |
UMD-Predictor | http://umd-predictor.eu/index.php | Identify potential pathogenic variations, associates with omics data | Yes | Online |
Name | URL | Brief description | Download of Data | Current status |
VarSome* | https://varsome.com/ | Variant and gene annotation, curated from public repositories | Yes | Online |
Gene expression databases
116 diverse databases and tools are available in the realm of gene expression, providing information on transcript counts and gene expressions in varied tissue conditions. They offer insights into age, apoptosis, RNA-seq data, single-cell studies, chromatin regulators, and histone modifications. The wealth of experimental data available is presented in formats like tables, diagrams, heatmaps, bar plots, and dot plots, aiding in the comprehensive study of genes.
Name | URL | Brief description | Download of Data | Current status |
AgeFactDB | http://agefactdb.jenage.de/ | Integration of ageing phenotype and lifespan data | Yes | Online |
aGEM | http://agem.cnb.csic.es | Anatomic gene expression mapping | Yes | Offline |
Allen Brain Atlas | https://alleninstitute.org/ | Analysis of human brain, the human cell and the immune system | Yes | Online |
AllerGAtlas | http://biokb.ncpsb.org/AlleRGatlas/ | Data of human allergy genes and their related diseases | Yes | Online |
AltExtron | http://bioinformatics.org.au/tools/altExtron/ | Gene expression of human and mouse transcript sequences | Yes | Online |
ANGIOGENES | http://angiogenes.uni-frankfurt.de/ | RNA-seq endothelial data of human, mouse and zebrafish | Yes | Online |
AnnoLnc | http://annolnc.cbi.pku.edu.cn/index.jsp | A web server for systematically annotating novel human lncRNAs | Yes | Offline |
arrayMap | https://arraymap.org/ | Gene expression and copy number profiling data in human cancer | Yes | Online |
AS-ALPS | http://as-alps.nagahama-i-bio.ac.jp/index.php | Alternative splicing-induced alteration of protein structure | Yes | Online |
ASMBrainBlood | https://epigenetics.essex.ac.uk/ASMBrainBlood/ | Expression profile of human brain correlated within whole blood | Yes | Online |
ASpedia | http://combio.snu.ac.kr/aspedia/index.html | Splicing annotation integrating genomic information | Yes | Online |
ASPicDB | https://www.cineca.it/ASPicDB/ | Annotation of predicted isoforms of human genes | Yes | Offline |
Cellosaurus | https://web.expasy.org/cellosaurus/ | Information about immortalized cell lines, naturally immortal cell lines, finite life cell lines of many model organisms and human | Yes | Online |
CHESS | http://ccb.jhu.edu/chess/ | Human RNA sequencing experiments produced by the GTEx project | Yes | Online |
Cistrome DB | http://dc2.cistrome.org/ | ChIP-seq and DNase-seq data in mouse and human | Yes | Online |
Cortecon | http://cortecon.neuralsci.org/ | Captures gene expression in the developing cortex | Yes | Online |
CSPA | https://wlab.ethz.ch/surfaceome/ | Cell surface protein atlas | Yes | Online |
CSTEA | http://comp-sysbio.org/cstea/ | Cell state transition expression and time-course gene expression | Yes | Online |
CYCLONET | http://cyclonet.biouml.org/ | A database on cell cycle regulation in eukaryotes | No | Online |
DAnCER | http://wodaklab.org/dancer/ | Genes with chromatin modification of model organisms, and human | Yes | Online |
DASHR | http://dashr2.lisanwanglab.org/ | Database of small human noncoding RNAs | Yes | Online |
dbCRID | http://c1.accurascience.com/dbCRID/ | Database of chromosomal rearrangements in diseases | Yes | Online |
dbOrg | https://biodbnet-abcc.ncifcrf.gov/ | Provides downloadable files of organism wide conversions | Yes | Online |
Name | URL | Brief description | Download of Data | Current status |
DisGeNET | https://www.disgenet.org/ | Variant-disease associations and gene-disease associations | Yes | Online |
DRG TXome | https://bbs.utdallas.edu/painneurosciencelab/sensoryomics/ drgtxome/ | Gene expression profiles across orthologous human and mouse genes | Yes | Online |
EPConDB | http://www.cbil.upenn.edu/node/90 | Novel pancreatic genes through the sequencing and analysis | Yes | Online |
EPITRANS | http://epitrans.org | Represents relationships between gene expression and epigenetic | No | Offline |
ESCAPE* | http://www.maayanlab.net/ESCAPE/ | A mouse and human embryonic stem cells centered integrating data | Yes | Online |
ESTDAB | https://www.ebi.ac.uk/ipd/estdab/ | Data of HLA type, and immunologically characterised tumour cells | No | Online |
euL1db | http://eul1db.ircan.org/ | Retrotransposon insertion polymorphisms in healthy or pathological human samples and published in journals. | Yes | Online |
EuroDia | http://eurodia.vital-it.ch | Gene expression performed on beta-cells of human, mouse and rat | Yes | Online |
ExpEdit | https://bioinformatics.cineca.it/expedit/ | RNA editing user-specified sites supported by RNA-Seq experiments | Yes | Online |
F-SNP | http://compbio.cs.queensu.ca/F-SNP/ | Identification of disease-causing SNPs in association studies | Yes | Offline |
Fantom/EdgeExpress | https://fantom.gsc.riken.jp/4/edgeexpress/view/#5558263 | Gene expression and miRNA using gene-centric and sub-network | Yes | Online |
FARNA | https://www.cbrc.kaust.edu.sa/farna/?page=home | ncRNA information related to expression, pathways and diseases | No | Online |
FLJ | http://flj.lifesciencedb.jp/top/ | mRNA variations of human genome and cDNA sequences | Yes | Online |
G4LDB | http://www.g4ldb.org/ci2/index.php | G-quadruplexes in human telomeres and gene promoter regions | No | Offline |
GEMiCCL | https://www.kobic.kr/GEMICCL/ | Gene expression and mutations in cancer cell lines | Yes | Online |
GenAge | http://genomics.senescence.info/genes/ | Gene expression in ageing genes | Yes | Online |
Genatlas | http://www.genatlas.org/ | Gene expression with search by phenotype or ontology | Yes | Online |
Gene Microglia | http://shiny.maths.usyd.edu.au/Ellis/MicrogliaPlots | Gene expression in microglia in the aged human brain | Yes | Online |
GeneHub-GEPIS | http://research-public.gene.com/ | Human and mouse gene expression patterns | Yes | Offline |
GeneNote | https://genecards.weizmann.ac.il/cgi- bin/genenote/about_page.pl | Full-genome database of expression in healthy human tissues | No | Online |
GeneTide | http://genecards.weizmann.ac.il/genetide/ | Human transcriptome and annotation | No | Offline |
GENT | http://medicalgenome.kribb.re.kr/GENT/ | Gene expression database of normal and tumor tissues | Yes | Offline |
Globin Gene | http://globin.cse.psu.edu/ | Gene expression and variants in globin related genes | No | Online |
GTEx* | https://gtexportal.org/home/ | Gene expression with quantitative trait locus (eQTLs) | Yes | Online |
H-ANGEL | http://www.jbirc.aist.go.jp/hinv/h-angel/ | Human anatomic gene expression library | No | Offline |
HAGR | http://genomics.senescence.info/index.php | Gene expression of human ageing using animal models and human | Yes | Online |
HCMDB | http://hcmdb.i-sanger.com/index | Human cancer metastasis. Contain gene expression data | Yes | Online |
Healthspan | http://functional.domains/healthspan/ | Pathways and expression of health-associated gene interactions | No | Online |
Hembase | http://hembase.niddk.nih.gov | Erythroblast expressed sequenced tags and erythropoiesis genes | No | Online |
Name | URL | Brief description | Download of Data | Current status |
HGDP | https://www.hagsc.org/hgdp/ | Gene expression in different human populations | Yes | Online |
HipSci | http://www.hipsci.org/ | Omics in human-induced pluripotent stem cells | Yes | Online |
HIVed | http://hivlatency.erc.monash.edu/ | Proteins with differential expression during the human virus infections | No | Online |
hmChIP | http://jilab.biostat.jhsph.edu/database/cgi-bin/hmChIP.pl | ChIP-chip and ChIPseq samples | Yes | Online |
HOMER | http://bio.informatics.iupui.edu/homer | Disease ontology, gene expression, and proteomics of tissues | No | Offline |
HoTResDB | http://hotresdb.bu.edu/ | microarray and NGS data from non-human primates’ models | Yes | Online |
HPMR | http://www.receptome.org/ | Transcriptome and Proteome informations | Yes | Online |
HPRD | http://www.hprd.org/ | Human protein reference database | No | Online |
HSF | http://www.umd.be/HSF3/index.html | Human splice finder | No | Online |
HuGE Navigator | https://phgkb.cdc.gov/PHGKB/hNHome.action | Genotype, phenotype, literature finder and variant mapper | No | Online |
HuGEIndex | https://www.hugeindex.org/ | Human gene expression index | Yes | Offline |
Human Erythroblast Maturation | https://cellline.molbiol.ox.ac.uk/eryth/cgi-bin/HEM.cgi | Maturation expression patterns , comparisons, and gene queries | No | Online |
IGRhCellID | http://igrcid.ibms.sinica.edu.tw/cgi-bin/index.cgi | Integrated genomic resources of human cell lines | Yes | Online |
Inner Ear Transcriptome | https://www.tgen.org/patients/neurological-disorders/ | Coding and non-coding transcripts of the human inner ear | Yes | Online |
Intropolis | Intropolis | RNA-seq samples and exon-exon junctions | Yes | Online |
Islet Regulome Browser | http://www.isletregulome.com/isletregulome/ | Enhancers and transcription factor binding sites in pancreatic progenitors and adult human pancreatic islets | No | Online |
Isobase | http://cb.csail.mit.edu/cb/mna/isobase/ | Orthologous transcripts and functionally related proteins | Yes | Online |
ISOexpresso | http://wiki.tgilab.org/ISOexpresso/main.php?cat=about | Isoform-level expression analysis in human cancer | Yes | Online |
KERIS | http://igenomed.org/immune/ | Expression and gene responses to inflammation among species | No | Offline |
Linc2GO | http://www.bioinfo.tsinghua.edu.cn/~liuke/Linc2GO/index. html | Expression of human lincRNA | Yes | Offline |
Liverbase | http://liverbase.hupo.org.cn/index2.jsp | Proteome and transcriptome of liver samples | Yes | Online |
MetaQuery | http://metaquery.docpollard.org/ | Quantitative analysis of specific genes in the human gut microbiome | Yes | Online |
MGEx-Udb | http://resource.ibab.ac.in/MGEx-Udb/ | Uterus tissues gene expression data in human and animal models | Yes | Online |
MiasDB | http://47.88.84.236/Miasdb/index.php | Gene expression and alternative splicing events | Yes | Online |
microRNA body | https://www.mirnabodymap.org/ | RT-qPCR data and miRNA annotation in normal and diseased tissues | Yes | Online |
MitoAge | http://www.mitoage.info/ | Comparative analysis and gene expression of mtDNA genes | Yes | Online |
MOPED | https://www.moped.proteinspire.org/ | Multi-omics profiling expression in normal and disease tissues | Yes | Offline |
MSGene | http://msgene.bioinfo-minzhao.org/ | Metastasis suppressor gene expression | Yes | Online |
NHGRI Project | https://research.nhgri.nih.gov/microarray/index.shtml | Set cDNA library clones from UniGene clusters | No | Online |
Name | URL | Brief description | Download of Data | Current status |
NHPRTR | http://nhprtr.org/resources.html | Transcriptome data of non-human primates | Yes | Online |
NRED | http://jsm-research.imb.uq.edu.au/NRED | Gene expression of long ncRNAs in human and mouse | Yes | Offline |
OncomiRdbB | http://tdb.ccmb.res.in/OncomiRdbB/index.htm | Gene and miRNA expression of cancer samples | No | Offline |
ORTI | http://orti.sydney.edu.au/index.html | Transcription Factors and Target Genes (TGs) | Yes | Online |
PEpiD | https://wukong.tongji.edu.cn/pepid | Prostate cancer expression and epigenetic data | Yes | Offline |
PhenoScanner | http://www.phenoscanner.medschl.cam.ac.uk/ | Database of human genotype-phenotype associations | Yes | Online |
Primer Z | http://grch37.genepipe.ncgm.sinica.edu.tw/primerz/beginD esign.do | PCR primer design for human, mouse, or rat genes and human SNPs | Yes | Online |
QMEAN | https://swissmodel.expasy.org/qmean/ | Web server for protein model quality estimation | Yes | Online |
REDIportal | http://srv00.recas.ba.infn.it/redidb/index.html | RNA editing and RNA-seq experiments | Yes | Online |
RefEx | https://refex.dbcls.jp/index.php?lang=en | Reference gene expression for the functional analysis of genes | yes | Online |
RenalDB | http://renaldb.uni-frankfurt.de/ | Whole transcriptomes, and lncRNAs of nephrology studies | No | Online |
Retina | http://retina.tigem.it/ | Atlas of gene expression and gene co-regulation in human retina | Yes | Online |
RNALocate | http://www.rna-society.org/rnalocate/ | Curated RNA subcellular localization in multiple biological processes | Yes | Online |
scRNASeqDB | https://bioinfo.uth.edu/scrnaseqdb/ | Tools for visualization of gene expression in single cells | Yes | Online |
SIEGE | http://pulm.bumc.bu.edu/siegeDB | Expression data from epithelial cells of the human intrathoracic airway | Yes | Offline |
SIGNOR | https://signor.uniroma2.it/ | Signalling gene expression based on published scientific literature | Yes | Online |
SpermBase | http://www.spermbase.org/Search.php | Provides large and small RNAseq data, total sperm and sperm heads | Yes | Online |
Symatlas | http://symatlas.gnf.org | Expression patterns for predicted genes (human and mouse) | Yes | Offline |
The Matrisome | http://matrisomeproject.mit.edu/ | Gene expression of extracellular matrix (ECM) proteins | Yes | Online |
The Mito browser | http://mitochondria.matticklab.com/ | Human mitochondrial transcriptome of multiple cell lines and tissues | Yes | Offline |
The RNA Editing | http://srv00.ibbe.cnr.it/editing/ | Inosinome atlas from healthy individuals | No | Offline |
TiGER | http://bioinfo.wilmer.jhu.edu/tiger/ | Tissue-specific gene expression and regulatory elements | Yes | Online |
TiProD | http://tiprod.cbi.pku.edu.cn:8080/index.html | Human promoter sequences for which some functional features | No | Offline |
TiSGeD | http://bioinf.xmu.edu.cn:8080/databases/TiSGeD/index.htm l | Tissue gene expression profiles from human, mouse and rat | No | Offline |
TISSUES | https://tissues.jensenlab.org/Search | Gene-tissue associations in human and mammalian model organisms | Yes | Online |
tRFdb | http://genome.bioch.virginia.edu/trfdb/ | Data of single-stranded RNA derived from mature or precursor tRNA | No | Online |
TRI_tool | https://www.vin.bg.ac.rs/180/tools/tfpred.php | Prediction of protein–protein Interactions in transcriptional regulation | No | Online |
TSEM | https://hood-price.isbscience.org/research/tsem/ | Tissue specific encyclopedia of metabolism | Yes | Online |
UMD TP53 | http://www.umd.be:2072/ | TP53 omics database | Yes | Offline |
Name | URL | Brief description | Download of Data | Current status |
VirusMINT | https://mint.bio.uniroma2.it/virusmint/ | Interactions between human and viral proteins | Yes | Offline |
VMH | https://vmh.life/ | Human metabolism and genetics, microbial metabolism, nutrition, and diseases | Yes | Online |
WeGet | https://coexpression.cmbi.umcn.nl/ | Mammalian genes coexpressed with human gene set of interest | Yes | Online |
Genomic and sequence databases
We found 217 tools (Table S6), related to post-translational (PTM) modification sites and mutations (both germline and somatic) from multiple sources, mitochondrial sequences coming from ancient DNA samples (aDNA), disease-specific genomic data, genomic histone marks, chromatin states and motifs, chromosome annotation, evolutionary relationship of human proteins and animal models, analyses of allelic imbalance in clonal cell populations based on sequence polymorphisms. General information on genes, such as orthologs and paralogs, exon, intron and UTRs, gene classification, transcript sequences, protein sequences, mutations and SNPs, transcript cluster or selected publications can also be found. The general input is a Gene Symbol, Chromosomal position or region. The output is presented in browser visualization, tables with the genomic sequence of the interest, gene report, and heatmaps with pathogenicity of the mutations found in a sequence of the gene or region of interest.
Name | URL | Brief description | Download of Data | Current status |
1000Genomes | http://www.internationalgenome.org/ | A deep catalogue of human genetic variation | Yes | Online |
3DSNP | http://cbportal.org/3dsnp/ | Analysis of human single nucleotide polymorphisms | No | Online |
3Omics | https://3omics.cmdm.tw/ | Transcriptomic, proteomic and metabolomic data | Yes | Online |
A Catalog of Human STR Variation | https://strider.online/ | A catalog of STR variation individuals from 1000Genomes | Yes | Online |
A catalog of enhancers in hESCs | http://www.medical-epigenomics.org/papers/barakat2018/ | Functional enhancers in human embryonic stem cells | No | Online |
ABS | https://www.crg.eu/en/programme/programmes-groups/bioinformatics- and-genomics | Annotated regulatory binding sites | Yes | Online |
AceView | http://www.ncbi.nlm.nih.gov/IEB/Research/Acembly | Quality-filtered cDNA from human transcriptomes | No | Online |
ActiveDriverDB | https://github.com/reimandlab/ActiveDriverDB/issues | Proteogenomics for interpreting human variants | Yes | Online |
Adsn | http://adsn.ddnetbio.com/ | Single cell brain atlas in human Alzheimer’s disease | Yes | Online |
AFND | http://www.allelefrequencies.net/ | Immune gene frequencies in worldwide populations | Yes | Online |
Albumin binding prediction | http://albumin.althotas.com/ | Predicts serum albumin binding site of a ligand | Yes | Offline |
AlloFinder | http://mdl.shsmu.edu.cn/ALF/ | Exogenous allosteric modulators characterization | Yes | Online |
AMAZONIA | http://amazonia.transcriptome.eu/ | Atlas of transcriptome with specific tissues or cells | Yes | Online |
AmtDB | https://amtdb.org/ | Data of ancient human mitochondrial genomes | No | Online |
ANCO-GeneDB | https://bioinfo.uth.edu/ancogenedb/ | Multi Omics and drug-target data with literature mining | Yes | Online |
Aneurysm DB | http://www.cuilab.cn/agd | Human, mouse and rat aneurysm-gene associations | Yes | Online |
AnnoLnc | http://annolnc.cbi.pku.edu.cn/index.jsp | Annotating data of novel human lncRNAs | Yes | Offline |
AVPpred | http://crdd.osdd.net/servers/avppred/ | Antiviral peptide prediction server | Yes | Online |
BDO | http://bioportal.bioontology.org/ontologies/BDO | Bone dysplasia ontology with omics and clinical data | No | Online |
BECon | https://redgar598.shinyapps.io/BECon/ | Relationship between blood and brain methylation | Yes | Online |
BioGPS | http://biogps.org/ | Annotation of gene and protein function | Yes | Online |
BrainScope | https://brainscope.lumc.nl/brainscope | Spatial and temporal human brain transcriptome | No | Online |
Name | URL | Brief description | Download of Data | Current status |
CADD* | https://cadd.gs.washington.edu/ | Predict impact of insertion/deletions genomic variants | Yes | Online |
CAGE Basic Viewer | http://fantom31p.gsc.riken.jp/cage/ | Cap-analysis gene expression for human and mouse | Yes | Offline |
CanGEM | http://www.cangem.org/ | Microarray, CNV and genomic in cancer | No | Offline |
CCB | https://cellcycle.renci.org/ | Timeline of molecular events in cell cycle progression | Yes | Online |
CGMD | http://cgmd.in/ | Cancer annotations and molecular descriptions | No | Offline |
ChIPSummitDB | http://summit.med.unideb.hu/summitdb/index.php | TF binding sites and the topological arrangements | Yes | Online |
Chorogenome | hicexplorer.readthedocs.io | Hi-C data analysis from processing to visualization | No | Online |
Chr7 Annotation | www.chr7.org/ | Sequence, genes, and other annotations from Chr7 | Yes | Online |
Cichlids | http://cichlids.biosci.gatech.edu/ | Evolutionary relationship of each cichlid protein | Yes | Online |
CITGeneDB | http://citgenedb.yubiolab.org | Cold-Induced thermogenesis human and mouse genes | Yes | Online |
CLIMA | http://bioinformatics.hsanmartino.it/clima2/ | Cell line integrated molecular and Identification tool | Yes | Online |
ClinicalTrials | https://clinicaltrials.gov/ | Collects public and private clinical studies | No | Online |
ClinVar | https://www.ncbi.nlm.nih.gov/clinvar/ | Data about germline and somatic variants | Yes | Online |
ComiR | http://www.benoslab.pitt.edu/comir/ | Combinatorial miRNA target prediction | Yes | Online |
CRUNCH | http://crunch.unibas.ch/crunch/ | ChIP-seq data analysis of human and animal models | Yes | Online |
cWords | http://servers.binf.ku.dk/cwords/ | Human miRNA and differential expression tool | Yes | Online |
dbDSM | http://bioinfo.ahu.edu.cn:8080/dbDSM/index.jsp | Database of deleterious synonymous mutation | No | Online |
dbEMT | http://dbemt.bioinfo-minzhao.org/ | Epithelial-mesenchymal transition related genes | Yes | Online |
DBETH | www.hpppi.iicb.res.in/btox/ | Genomic database for bacterial exotoxins | Yes | Online |
DBGC | http://bminfor.tongji.edu.cn/dbgc/index.do | Human gastric cancer-related data resources | Yes | Offline |
dbMAE | https://mae.hms.harvard.edu/ | Monoallelic expression in genome-wide studies | No | Online |
dbNSFP | https://sites.google.com/site/jpopgen/dbNSFP | Predict impact of non-synonymous single-nucleotide and splice- site variants | Yes | Online |
Decryptor | http://decryptor.imtm.cz/ | Proteome analysis for presence of point alterations | Yes | Offline |
DisGeNET* | https://www.disgenet.org/ | Repository of variant-disease associations | Yes | Online |
DO | https://disease-ontology.org/ | Ontologies, phenotypes, and related terms | Yes | Online |
Doc2Hpo | https://impact2.dbmi.columbia.edu/doc2hpo/ | Human Phenotype Ontology concept curation | Yes | Online |
Dr.VIS | http://www.bioinfo.org/drvis | Human disease-related viral integration sites | No | Offline |
DREMECELS | http://www.bioinfoindia.org/dremecels/ | Base excision and mismatch repair mechanisms associated human malignancies | Yes | Offline |
E-RNAi | https://www.dkfz.de/signaling/e-rnai3// | dsRNA constructs suitable for RNAi experiments | No | Online |
Name | URL | Brief description | Download of Data | Current status |
EBI | https://www.ebi.ac.uk/ | Platform of biological sciences | Yes | Online |
eDGAR | http://edgar.biocomp.unibo.it/gene_disease_db/index.html | Disease-gene associations and Relationships among genes | Yes | Online |
EpiACDev | https://cotney.research.uchc.edu/data/ | Epigenomic atlas of craniofacial development | Yes | Online |
EpimiRBase | https://www.epimirbase.eu/ | miRNA-epilepsy association from curated literature | Yes | Online |
Eponine | https://www.sanger.ac.uk/about/who-we-are | Transcription start sites mammalian genome sequence | Yes | Online |
ERGR | http://bioinfo.vipbg.vcu.edu/ERGR/ | Published ethanol-related gene studies | No | Offline |
Exome Variant Server | https://evs.gs.washington.edu/EVS/ | Exome sequencing from human tissues | Yes | Online |
FirstEF | http://rulai.cshl.org/tools/FirstEF/ | 5′ terminal exon and promoter prediction program | Yes | Online |
G2Cdb | http://www.genes2cognition.org | Data of synapse proteins in physiology and disease | Yes | Online |
G2D | http://g2d2.ogic.ca/ | Scans a region for genes related to diseases | Yes | Offline |
GENCODE | https://www.gencodegenes.org/human/ | Annotation for the human and mouse genomes | Yes | Online |
GenePAtlas | http://biocc.hrbmu.edu.cn/GPA/ | Collection of genes, miRNAs and lncRNAs perturbed by knockdown or overexpression | Yes | Online |
Gene Set Builder | http://www.cisreg.ca/gsb/ | Personalized sets of genes | Yes | Online |
Gene Wiki | http://en.wikipedia.org/wiki/Portal:Gene_Wiki | Gathers Wikipedia articles about human genes | No | Online |
GeneCards | genecards.org/ | Biomedical knowledgebase of human biological data | No | Online |
Geneimprint | http://www.geneimprint.com/site/home | Imprinting genes from different species and human | Yes | Online |
GeneLoc | https://genecards.weizmann.ac.il/geneloc/about_new.shtml | The integrated map for human chromosomes | Yes | Online |
GeneMap | www.ncbi.nlm.nih.gov/genemap | Mapping, annotations and associated gene data | Yes | Online |
GeneSeeker | http://www.cmbi.ru.nl/GeneSeeker/ | Candidate genes related to a genetic disorder | No | Offline |
Genome Ref | https://www.ncbi.nlm.nih.gov/grc/report-an-issue | Reference genomes consortium of multiple species | Yes | Online |
GUIDES | http://guides.sanjanalab.org/#/ | CRISPR knockout to target human or mouse genes | Yes | Online |
H-InvDB | http://www.h-invitational.jp/ | Human-transcriptome and alternative splicing | Yes | Online |
HADb | http://autophagy.lu/index.html | Human autophagy database | No | Online |
Harmonizome* | amp.pharm.mssm.edu/Harmonizome/ | Datasets about genes and proteins | Yes | Online |
Harvester | http://harvester.fzk.de/harvester/ | Bioinformatic data and servers for human proteins | No | Offline |
HelmCoP | http://www.nematode.net/helmcop.html | Comparative genomic data from plant, animal and human helminths | Yes | Online |
HEROD | http://bidd2.nus.edu.sg/herod/index.php | Human ethnic and regional specific omics | Yes | Offline |
HERVd | https://herv.img.cas.cz/ | Human endogenous retroviruses data | No | Online |
HExpoChem | http://www.cbs.dtu.dk/services/HExpoChem-1.0/ | Explore human health risk from chemical exposure | No | Online |
Name | URL | Brief description | Download of Data | Current status |
HGMD | http://www.hgmd.cf.ac.uk/ac/index.php | The human gene mutation database | No | Online |
HGNC | https://www.genenames.org | Nomenclature for all genes of the human genome | Yes | Online |
hLGDB | http://lysosome.unipg.it/ | Human lysosome miRNA database | Yes | Online |
HMDAD | http://www.cuilab.cn/hmdad | Human microbe-disease association | Yes | Online |
HMMER3 | https://www.ebi.ac.uk/Tools/hmmer/ | Homologs sequences, and protein alignments | Yes | Online |
HMP | https://portal.hmpdacc.org/ | Human Microbiome Project | Yes | Online |
HmtDB | https://www.hmtdb.uniba.it/ | Mitochondrial genomes application of MtoolBox NGS | Yes | Offline |
HNOCDB | http://gyanxet.com/hno.html | Head neck and oral cancer genomic data | No | Offline |
HOMD | http://www.homd.org | Bacterial species present in the aerodigestive tract | Yes | Online |
HomozygosityMapper | http://www.homozygositymapper.org/ | A web base approach to homozygosity mapping | Yes | Online |
hORFeome Database | http://horfdb.dfci.harvard.edu/ | Genome-scale human ORFeome collections | No | Online |
HPO | https://hpo.jax.org/app/ | The human phenotype ontology disease | Yes | Online |
HUMA | https://huma.rubi.ru.ac.za/ | Analyze variation in protein sequence and structures | Yes | Online |
Human Transporter Database | http://htd.cbi.pku.edu.cn | Molecular and genetic information of transporters for personalized medicine | No | Offline |
HumanMine | http://www.intermine.org | Genes, proteins, pathways, ontology, or literature | Yes | Online |
HumCFS | https://webs.iiitd.edu.in/raghava/humcfs/index.html | Curated human chromosomal fragile sites | No | Online |
HydPred | http://lishuyan.lzu.edu.cn/hydpred/ | Identification of protein hydroxylation sites | No | Online |
HyperCLDB | http://bioinformatics.hsanmartino.it/hypercldb/ | The hypertextual version of the Cell Line Database | No | Online |
IDADE2 | http://bass.uib.es/~jaume/IDADE2/https/index.html | Adult age estimation of human skeletal remains | Yes | Online |
IGSR | https://www.internationalgenome.org/1000-genomes-project-publications | The largest open collection of human variation data | Yes | Online |
iLoc-Cell | http://www.jci-bioinfo.cn/iLoc-Hum | Subcellular locations of proteins with multiple sites | No | Online |
IMGT | http://www.imgt.org/ | ImMunoGeneTics information system | Yes | Online |
Integr8 | https://www.ebi.ac.uk/integr8 | Data of complete genomes and proteomes | Yes | Online |
integrated gene catalog | http://meta.genomics.cn/meta/home | Reference catalog of the human gut microbiome | No | Offline |
IntSplice | https://www.med.nagoya-u.ac.jp/neurogenetics/IntSplice/ | Predict SNV impact in introns of the human genome | No | Online |
InvFEST | http://invfestdb.uab.cat/ | Non-redundant human polymorphic inversions data | No | Online |
ITHANET | https://www.ithanet.eu/db/ithagenes | Variations, epidemiology, and and HbF inducers info | No | Online |
Kaviar | http://db.systemsbiology.net/kaviar/cgi-pub/Kaviar.pl | Compilation of human SNVs data | Yes | Online |
lncRNAtor | http://lncrnator.ewha.ac.kr/ | Multi Omics of animal models and human | No | Offline |
Name | URL | Brief description | Download of Data | Current status |
MAHMI | http://mahmi.org/ | Mechanism of action of the human microbiome | No | Online |
MARome | http://196.1.114.46:8080/MARome/index | Scaffold and Matrix Attachment Regions in Genome | Yes | Online |
MDWeb | http://mmb.irbbarcelona.org/MDWeb2/ | Web-based platform of molecular dynamics | No | Online |
MEME Suite | http://meme-suite.org/ | DNA motifs, transcription factor binding sites or protein domains search tool | Yes | Online |
Mendel,MD | https://mendelmd.org/ | Identify disease causing variants in human exome/genome sequencing data | Yes | Offline |
MetaQuery | http://metaquery.docpollard.org/ | Data of specific genes in the human gut microbiome | Yes | Online |
MetaRanker | http://www.cbs.dtu.dk/services/MetaRanker/ | Prioritize the entire protein-coding part of the human genome based on heterogeneous user-specified data sets | Yes | Online |
MGDB | http://bioinfo.ahu.edu.cn:8080/Melanoma/ | Melanoma genomic and transcriptomic data | Yes | Online |
microDoR | http://reprod.njmu.edu.cn/cgi-bin/microdor/index.py | Predict Human miRNA-mediated gene silencing | Yes | Online |
miR2GO | http://compbio.uthsc.edu/miR2GO/home.php | Comparative analyses of human miRNA functions | Yes | Online |
mLASSO-Hum | http://bioinfo.eie.polyu.edu.hk/mLASSOHumServer/index.html | Human-protein subcellular localization predictor | No | Online |
MSEA | https://www.metaboanalyst.ca/ | Enrichment analyses for metabolomic studies | Yes | Online |
mTCTScan | http://mulinlab.org/mtctscan | Analysis of mutations affecting cancer drug sensitivity based on individual genomic profiles | Yes | Online |
mtDNA-Serve | https://mtdna-server.uibk.ac.at/index.html | mtDNA NGS analysis, heteroplasmy detection, and haplogroup- based contamination deconvolution | Yes | Online |
Mutalyzer | https://mutalyzer.nl/ | Variant effect analysis | No | Online |
MutPred | http://mutpred.mutdb.org/ | Predicts molecular cause of disease | No | Online |
NCBI | https://www.ncbi.nlm.nih.gov/ | Supplies several online resources for biological information | Yes | Online |
NetChop | http://www.cbs.dtu.dk/services/NetChop/ | Cleavage site analysis of the human proteasome | No | Online |
NetGene2 | http://www.cbs.dtu.dk/services/NetGene2/ | Predictions of splice sites | No | Online |
NetNGlyc | http://www.cbs.dtu.dk/services/NetNGlyc/ | Predict N-Glycosylation sites in human proteins | No | Online |
Netview | http://netview.tigem.it/netview_project/netview_tools.html | Human and mouse gene regulatory networks | Yes | Online |
NGD | http://www.nencki-genomics.org | Nencki Genomics Database TFBS motifs | Yes | Online |
NHGRI Project | https://research.nhgri.nih.gov/microarray/index.shtml | Protocols, analysis and resources | No | Online |
NIF | https://neuinfo.org/ | Multi omics and neuroscience portal of Wikipedia | No | Online |
OKdb | http://okdb.appliedbioinfo.net/ | Function, expression pattern and regulation of genes expressed in the ovary | Yes | Online |
Name | URL | Brief description | Download of Data | Current status |
OMIM | https://omim.org/ | Catalog of mendelian diseases | Yes | Online |
OncoDB.HCC | http://oncodb.hcc.ibms.sinica.edu.tw/index.htm | Oncogenomic database for Hepatocellular Carcinoma | Yes | Online |
ONTOAD | http://bioportal.bioontology.org/ontologies/ONTOAD | Text mining disease ontology | No | Online |
Open Targets Platform | https://www.targetvalidation.org/ | Systematic drug target identification and prioritisation | Yes | Online |
OrthoDisease | http://orthodisease.sbc.su.se/cgi-bin/index.cgi | Gene ortholog between human and other species | Yes | Online |
OsteoporosAtlas | http://biokb.ncpsb.org/osteoporosis/index.php | Osteoporosis-related gene database | Yes | Online |
OverGeneDB | http://overgenedb.amu.edu.pl | Protein overlapping genes in Human and Mouse | Yes | Online |
p53FamTaG | http://www2.ba.itb.cnr.it/p53FamTaG/ | p53 family target genes | No | Offline |
PanelApp | https://panelapp.genomicsengland.co.uk/ | Virtual gene panels related to human disorders | Yes | Online |
PaPI | http://papi.unipv.it/ | Classification of variants | No | Online |
PathogenFinder | https://cge.cbs.dtu.dk/services/PathogenFinder/ | Prediction of a bacteria’s pathogenicity in human hosts | No | Online |
PDID | http://biomine.cs.vcu.edu/servers/PDID/index.php | Protein-drug interactions in the structural human proteome | Yes | Online |
PDZPepInt | http://modpepint.informatik.uni-freiburg.de/PDZPepInt/Input.jsp | Predict binding peptides of PDZ domains in human, mouse, fly and worm | Yes | Online |
Pedican | http://pedican.bioinfo-minzhao.org/ | Pediatric cancer gene database | Yes | Online |
PepPSy | http://peppsy.genouest.org/query | A gene expression-based prioritization system | Yes | Online |
PGP | https://www.personalgenomes.org/ | Interpretation of genomic traits in human tissues | Yes | Online |
PharmGKB | https://www.pharmgkb.org/ | Pharmacogenomic information database | Yes | Online |
PhenoHM | https://phenome.cchmc.org/phenoBrowser/Phenome | Phenome-genome cross species identification of genes associated with orthologous phenotypes | Yes | Online |
Phenolyzer | http://phenolyzer.wglab.org/ | Discovering genes based on user-specific disease/phenotype terms | Yes | Online |
PhenomicDB | https://en.wikipedia.org/wiki/PhenomicDB | A multi-organism phenotype-genotype database | Yes | Online |
Phenomizer | http://compbio.charite.de/phenomizer/ | Differential diagnosis in the field of human genetics | Yes | Online |
PhenoScanner | http://www.phenoscanner.medschl.cam.ac.uk/ | Database of human genotype-phenotype associations | Yes | Online |
PhenoTips | https://phenotips.com/ | Phenotype information of genetic disorders | Yes | Online |
PhosphOrtholog | http://www.phosphortholog.com/ | Orthologous protein post-translational modifications | Yes | Online |
PICKLE | http://www.pickle.gr/ | Direct human protein-protein interactions network | Yes | Offline |
PINTA | https://securehomes.esat.kuleuven.be/~bioiuser/pinta/input.php | Genome-wide protein-protein interaction network | Yes | Offline |
Piphillin | http://piphillin.secondgenome.com/ | Metagenomic by Inference from Human Microbiomes | Yes | Online |
PolyPhen2 | http://genetics.bwh.harvard.edu/pph2/ | Variant effect prediction tool | No | Online |
Name | URL | Brief description | Download of Data | Current status |
PolySearch2 | http://polysearch.cs.ualberta.ca/index | Discovering associations between human diseases, genes, drugs, metabolites, toxins and more | Yes | Online |
POMO | https://ruoho.uta.fi/wp/pomo/ | Plotting Omics-associations for Multiple Organisms | No | Offline |
PredictSNP2 | http://loschmidt.chemi.muni.cz/predictsnp2/ | Variant effect prediction tool | Yes | Online |
Primer Z | http://grch37.genepipe.ncgm.sinica.edu.tw/primerz/beginDesign.do | Interface for PCR primer design | Yes | Online |
PrimerStation | https://ps.cb.k.u-tokyo.ac.jp/ | Multiplex genomic PCR primer design tool | Yes | Online |
Progenetix | https://www.progenetix.org/ | Curated oncogenomic database | No | Online |
ProteomicsDB | https://www.proteomicsdb.org/proteomicsdb/#overview | Enables navigation of proteomes | No | Online |
ProteoRE | http://www.proteore.org/ | Proteomics and Transcriptomic Research Environment | Yes | Online |
PRS | http://mrcieu.mrsoftware.org/PRS_atlas/ | Polygenic burden associations in the human phenome | No | Online |
pseudoMap | http://pseudomap.mbc.nctu.edu.tw/php/index.php | Information of pseudogenes | No | Offline |
PubGene | https://www.pubgene.com/ | Identification of siRNA mechanisms in pseudogenes | Yes | Online |
QMEAN | https://swissmodel.expasy.org/qmean/ | Qualitative model energy analysis | Yes | Online |
QTRG | https://geneticmedicine.weill.cornell.edu/genome | Reference genome research in the Qatari population | No | Online |
Quokka | http://quokka.erc.monash.edu/ | Prediction of kinase family-specific phosphorylation | No | Online |
R spider | http://www.bioprofiling.de/gene_list.html | KEGG and Reactome pathway analysis | No | Online |
RAAR | http://www.lerner.ccf.org/cancerbio/heemers/RAAR/ | Regulators of Androgen Action Resource | No | Online |
RasMol | http://www.bernstein-plus-sons.com/software/rasmol/ | 3D structure viewer, web browser helper application | No | Online |
RatMine | https://omictools.com/ratmine-tool | Omics data of human, mouse, rat and other organisms | Yes | Online |
RefGene | https://omictools.com/refgene-tool | Reference genomes and annotation | Yes | Online |
REGene | http://regene.bioinfo-minzhao.org/ | Regeneration Gene database | Yes | Online |
Repositive | https://discover.repositive.io/help/searching-for-data | Multiple repositories for the human genomic data | No | Offline |
RIDDLE | http://www.functionalnet.org/riddle/ | Functional network and gene set analysis | No | Online |
RSSsite | https://www.itb.cnr.it/rss/ | Recombination signal sequences in human and mouse | Yes | Online |
Saqqaq project | http://genomebrowser.binf.ku.dk/cgi- bin/hgTracks?db=hg18&position=chrX%3A151073054- 151383976&hgsid=80767_Yr7Y1ao0Y92AKta3Whb9lqcaEfLg | Provides data about the genome sequence of ancestor human | Yes | Offline |
ScaPD | http://bioinfo.wilmer.jhu.edu/ScaPD/ | Database for human scaffold proteins | No | Online |
sciAI | https://sci.ai/ | Biomedical papers, trials, and projects and interlinks research findings in a semantic graph | Yes | Online |
SEGEL | http://www.chengfeng.info/smoking_database.html | Smoking Effects on Gene Expression of Lung | No | Online |
Name | URL | Brief description | Download of Data | Current status |
Semantic Body Browser | http://sbb.cellfinder.org/ | Visualising expression profiles by means of semantically annotated illustrations | Yes | Online |
SNP2TFBS | https://ccg.epfl.ch/snp2tfbs/ | Variant effect prediction tool | No | Online |
SNPDelScore | https://www.ncbi.nlm.nih.gov/research/snpdelscore/ | Deleterious effects of noncoding variants | Yes | Online |
SNPs GO | https://snps-and-go.biocomp.unibo.it/snps-and-go/index.html | Variant effect prediction tool | Yes | Online |
SPEED | https://speed2.sys-bio.net/ | A signaling pathway annotation enrichment analysis | Yes | Online |
SpindleP | http://www.cbs.dtu.dk/services/SpindleP/ | Neural networks prediction of whether a human gene is located at the meiotic spindle | Yes | Online |
StemCellNet | http://stemcellnet.sysbiolab.eu/ | Molecular networks in the context of stem cell biology | Yes | Online |
StSNP | http://ilyinlab.org/StSNP/ | Structure SNP variant effect prediction tool | No | Online |
SubPhosPred | http://bioinfo.ncu.edu.cn/SubPhosPred.aspx | Phosphorylation sites in subcellular compartments | No | Online |
SugarBindDB | https://sugarbind.expasy.org/ | Glycan binding of human pathogen lectins and adhesins data | No | Online |
SURFY | http://wlab.ethz.ch/surfaceome/ | Visualize the human surface proteome (surfaceome) and load your own expression data | Yes | Online |
T1Dbase | http://www.t1dbase.org | Resources for study of susceptibility of T1 Diabetes | No | Online |
T2D-Db | http://t2ddb.ibab.ac.in | Pathogenesis of T2 diabetes in human, mouse and rat | Yes | Online |
TCGA Portal | https://www.cancer.gov/ | Multi omic cancer and clinical data | Yes | Online |
UCSCBrowser | https://genome.ucsc.edu/cgi-bin/hgGateway | Multi omic web resources across species | Yes | Online |
UK10K | https://www.uk10k.org/ | Whole genomes in the British population | Yes | Online |
UMD-Predictor | http://umd-predictor.eu/index.php | Identify potential pathogenic variations | Yes | Online |
UniReD | http://bioinformatics.med.uoc.gr/unired/ | Annotation and non-redundant Human or Mouse proteins from UniProtKB/Swiss-Prot | No | Online |
VarSome | https://varsome.com/ | Compiles human genomic variants | No | Online |
VDJsolver | http://www.cbs.dtu.dk/services/VDJsolver/ | Human immunoglobulin VDJ recombination analysis | No | Online |
VectorBase | https://www.vectorbase.org/genomes | Vectors and other organisms related with diseases | Yes | Offline |
Vega | http://vega.sanger.ac.uk | Vertebrate Genome Annotation | Yes | Online |
Vega Browser | http://vega.archive.ensembl.org/index.html | Major histocompatibility complex (MHC) annotation and LCR across species | No | Online |
VeryGene | http://www.verygene.com | Annotation of tissue-specific/enriched genes | No | Online |
VHLdb | http://vhldb.bio.unipd.it/ | Interactors and mutations of the human von Hippel-Lindau tumor suppressor protein | No | Online |
XenoSite | https://swami.wustl.edu/xenosite/ | Predictions about the human in vivo metabolism of small molecules | No | Offline |
Name | URL | Brief description | Download of Data | Current status |
Zikv-CDB | http://zikadb.cpqrr.fiocruz.br | Data of genes associated with ZIKV, their expression and interaction with miRNAs and snoRNAs | Yes | Online |
LncRNA and miRNA databases
We found 73 tools related to miRNA and long non-conding RNAs (lncRNAs) in different organisms and pathogenic conditions. Of special interest may be data on putative antagomirs-miRNA heterodimers, protein-protein interactions (PPI) and functionally synergistic miRNA pairs (including transcription factors). The input of the search can be a Gene symbol, miRNA or LncRNA ID or target (hsa-let-7a, for example), Fasta file of the region of interest, or chromosomal location (any position in hg38 version, for example). In the case of LncRNA, the output is a table with the basic information of sequence, strand, class (antisense, for example), and conservation across species, with or without prediction scores. For miRNA, the output show information about the seed region, conservation score, accessibility, and secondary structures, minimum free energy estimation, correlations about expression, and start/end of the miRNA sequences. In disease-specific databases, the table may present the disease name, information about causality, and related literature.
Name | URL | Brief description | Download of Data | Current status |
Antagomirbase | http://bioinfopresidencycollegekolkata.edu.in/antagomirs.html | Design antagomirs using GC content and secondary structures | No | Offline |
CancerNet | http://bis.zju.edu.cn/CancerNet/ | Cancer-specific miRNA and protein-protein interactions | Yes | Online |
CircuitsDB | http://penelope.unito.it/circuitsdb2 | miRNA/TF regulatory circuits in the human and mouse genomes | Yes | Offline |
ComiR | http://www.benoslab.pitt.edu/comir/ | Combinatorial miRNA target prediction | Yes | Online |
CSmiRTar | http://cosbi.ee.ncku.edu.tw/CSmiRTar/ | Predicted targets of human and mouse miRNAs | No | Offline |
cWords | http://servers.binf.ku.dk/cwords/ | Gene expression analysis and prioritization of miRNA | Yes | Online |
DASHR | http://dashr2.lisanwanglab.org/ | sncRNA and miRNA prediction | Yes | Online |
dbDEMC | https://www.picb.ac.cn/dbDEMC/ | Differentially expressed miRNAs in human cancers | Yes | Online |
dbSMR | http://miracle.igib.res.in/dbSMR | Predicted and validated miRNA sites and SNPs in human genome | Yes | Offline |
DES-ncRNA | https://www.cbrc.kaust.edu.sa/des_ncrna/ | miRNA and lncRNAs based on literature-mining | Yes | Online |
DMD | http://sbbi.unl.edu/dmd/ | Published and novel miRNAs discovered in dietary resources | Yes | Offline |
dPORE | http://cbrc.kaust.edu.sa/dpore | miRNA genes, SNPs, and predicted TFBSs in the promoter regions | Na | Offline |
E-RNAi | https://www.dkfz.de/signaling/e-rnai3// | Designing and evaluating dsRNA constructs for RNAi experiments | No | Online |
exoRBase* | http://www.exoRBase.org | circRNA, IncRNA and mRNA in human blood exosomes | Yes | Online |
ExprTargetDB | http://www.scandb.org/apps/microrna/ | miRNA-mediated gene regulation in the HapMap LCLs | Yes | Online |
fat_deposition | http://www.integratomics-time.com/fat_deposition | Human, cattle, rat, and mice miRNA related to obesity | No | Offline |
GED | http://gametsepi.nwsuaflmz.com/ | DNA methylation, histone modification and miRNA regulation in gametogenesis | Yes | Online |
Gene Perturbation Atlas | http://biocc.hrbmu.edu.cn/GPA/ | Collection of transcriptome profiles genes, miRNAs and lncRNAs | Yes | Online |
hLGDB | http://lysosome.unipg.it/ | miRNA and Transcription Factors in Lysosomal Storage Diseases | Yes | Online |
HLungDB | http://www.megabionet.org/bio/hlung | miRNAs and clinical information in Lung cancer | Yes | Offline |
HMDD | http://www.cuilab.cn/hmdd | Experiment-supported evidence for miRNA and disease associations | Yes | Online |
HumanViCe | http://gyanxet-beta.com/humanvice/ | ceRNA and miRNA networks in virus infected human cells | Yes | Online |
IntmiR | https://www.rgcb.res.in/intmir/ | Intronic miRNAs of human and mouse genome | Yes | Online |
IRBase/IRFinder | http://mimirna.centenary.org.au/irfinder/database/ | Online database of intron retention and intronic miRNAs | No | Online |
Name | URL | Brief description | Download of Data | Current status |
Lnc2Meth | http://bio-bigdata.hrbmu.edu.cn/Lnc2Meth/ | lncRNAs and associated DNA methylation in diseases and cancer | Yes | Online |
LncATLAS | http://lncatlas.crg.eu/ | lncRNA in human cells based on RNA-sequencing datasets | Yes | Online |
lnCeDB | http://gyanxet-beta.com/lncedb/ | List lncRNAs that can potentially act as ceRNAs | Yes | Online |
LNCediting | http://bioinfo.life.hust.edu.cn/LNCediting/ | Adenosine-to-Inosine editing sites in lncRNAs across human, rhesus, mouse, and fly | Yes | Online |
LNCipedia | https://lncipedia.org/ | Function of RNA editing in lncRNA and miRNA | Yes | Online |
LncRBase | http://bicresources.jcbose.ac.in/zhumur/lncrbase/ | Overlapping small noncoding RNAs, associated Repeat Elements, methylation, and lncRNA promoter information | Yes | Online |
LncRNA2Function | http://mlg.hit.edu.cn/lncrna2function | Annotate functionally a set of human lncRNAs of interest | Yes | Offline |
lncRNAMap | http://lncrnamap.mbc.nctu.edu.tw/php/ | lncRNAs, miRNA, and siRNAs annotations and analysis | Yes | Offline |
lncRNASNP | http://bioinfo.life.hust.edu.cn/lncRNASNP#!/ | Data of SNP effects on lncRNA structure and lncRNA:miRNA binding | Yes | Online |
lncRNAtor | http://lncrnator.ewha.ac.kr/ | Expression profile, (binding) proteins, integrated sequence curation, evolutionary scores, and coding potential of lncRNAs | No | Online |
LncRNAWiki | http://lncrna.big.ac.cn/index.php/Main_Page | Community-based curation and collection of information on lncRNAs | No | Online |
lncRNome | http://genome.igib.res.in/lncRNome | Biologically oriented knowledgebase for lncRNAs in humans | No | Online |
MethmiRbase | https://madlab.cpe.ku.ac.th/TR2/?itemID=108747 | Experimentally verified cancer-associated miRNA target genes | Yes | Online |
microDoR | http://reprod.njmu.edu.cn/cgi-bin/microdor/index.py | miRNA-mediated gene silencing: mRNA degradation or translational repression | Yes | Online |
microPIR | http://www4a.biotec.or.th/micropir2 | Predicted miRNA target sites within human promoter sequences | Yes | Offline |
microRNA.org | http://www.microrna.org/ | microRNA target predictions and expression profiles in mammals | Yes | Online |
microTranspoGene | http://transpogene.tau.ac.il/ | Human, mouse, zebrafish and nematode miRNAs derived from Transposable elements | Yes | Offline |
miR-EdiTar | http://microrna.osumc.edu/mireditar/ | Prediction of miRNA binding sites | No | Online |
miR-host | http://www.integratomics-time.com/miR-host/catalog | Information of intragenic miRNAs in human, mouse, and chicken | Yes | Offline |
miR2Disease | http://www.miR2Disease.org | Repository for miRNA deregulation in various human diseases | Yes | Online |
miR2GO | http://compbio.uthsc.edu/miR2GO/home.php | Comparative analyses of human miRNA functions | Yes | Online |
miRCancer | http://mircancer.ecu.edu/ | Collection of miRNA expression profiles in various human cancers | Yes | Online |
miRDB* | http://mirdb.org/ | Resource for miRNA target prediction and functional annotations | Yes | Online |
mirDIP | http://ophid.utoronto.ca/mirDIP/ | Integrative score assigned to each unique miRNA–target interaction | Yes | Online |
miREnvironment | http://cmbi.hsc.pku.edu.cn/miren | Data of miRNA characteristics have roles in miRNA–EFs interactions | Yes | Offline |
miRGate | http://mirgate.bioinfo.cnio.es/miRGate/ | miRNA and gene isoforms lists of human, mouse and rat | Yes | Online |
Name | URL | Brief description | Download of Data | Current status |
miRGen | http://carolina.imis.athena- innovation.gr/diana_tools/web/index.php?r=mirgenv3 | Map of transcription factor-microRNA interactions for multiple tissues and cell-lines in human and mouse | Yes | Online |
MirGeneDB | https://mirgenedb.org/ | Annotation of vertebrate miRNA Genes and evolutionary analysis | Yes | Online |
miRNA TF loop | https://rth.dk/resources/tfmirloop/ | Regulatory network containing loop motifs for human and mouse using predicted miRNA and transcription factor binding sites | Yes | Online |
miRNAMap | http://mirnamap.mbc.nctu.edu.tw/ | Information of miRNAs and target sites in metazoan genomes | Yes | Online |
miRPathDB | https://mpd.bioinf.uni-sb.de/ | miRNA pathway regulation, gene ontologies and other categories | Yes | Online |
MirSNP | http://cmbi.bjmu.edu.cn/mirsnp | Polymorphisms altering miRNA target sites, miRNA-related SNPs in GWAS and eQTLs | Yes | Online |
miRStart | http://mirstart.mbc.nctu.edu.tw/ | Data source of human microRNA transcription start sites | No | Offline |
miRvar | http://genome.igib.res.in/mirlovd | A Comprehensive database for genomic variations in miRNAs | Yes | Online |
miRWalk | http://mirwalk.umm.uni-heidelberg.de/ | Predict miRNA interactions from existing miRNA-target resources | Yes | Online |
PITA | https://genie.weizmann.ac.il/pubs/mir07/mir07_prediction.html | Lists of predicted microRNA targets in worm, mouse, fly and human | Yes | Online |
Polymirts | http://compbio.uthsc.edu/miRSNP/ | Functional impact of genetic polymorphisms in miRNA seed regions and miRNA target sites | Yes | Online |
PuTmiR | https://www.isical.ac.in/~bioinfo_miu/TF-miRNA/TF-miRNA.html | Direct and indirect regulation of human miRNAs | Yes | Online |
RenalDB | http://renaldb.uni-frankfurt.de/ | Human, mice, zebrafish lncRNAs in nephrotic tissues and cells | No | Online |
S-MED | https://www.oncomir.umn.edu/SMED/basic_search.php | miRNA expression in various human sarcoma types | Yes | Online |
SlideBase | http://slidebase.binf.ku.dk/ | microRNAs expressed/used in a specified set of cells/tissues | Yes | Online |
The Functional lncRNA Database | http://www.valadkhanlab.org/database | A repository of mammalian lncRNA that have been experimentally shown to be both non-coding and functional | No | Online |
TissueAtlas | https://ccb-web.cs.uni-saarland.de/tissueatlas/ | An atlas of miRNA expression in multiple human tissues | Yes | Online |
TriplexRNA | https://triplexrna.org/ | Human genes or miRNAs in RNA triplexes | Yes | Online |
TUMIR | http://www.ncrnalab.com/TUMIR/ | Validated resource of microRNA deregulation in various cancers | Yes | Online |
UCbase & miRfunc | http://microrna.osu.edu/.UCbase4 | Correlation between miRNAs, ultraconserved sequences and the disorders related to their aberrant expression | Yes | Offline |
UGAHash | http://ugahash.uni-frankfurt.de/ | lncRNAs resources | No | Online |
Vir-Mir db* | http://alk.ibms.sinica.edu.tw/cgi-bin/miRNA/miRNA.cgi | predicted viral miRNA candidate hairpins | Yes | Online |
Name | URL | Brief description | Download of data | Current status |
2D-PAGE | http://web.mpiib-berlin.mpg.de/cgi-bin/pdbs/2d- page/extern/index.cgi | 2-DPAGE maps, representing proteomes of various species | Yes | Online |
AMPAD Knowledge Portal | https://www.synapse.org/#!Synapse:syn2580853/wiki/409840 | Aging’s Alzheimer’s disease translational research | No | Online |
BioCarta | http://www.biocarta.com/ | Diagram library displaying gene interactions in pathways | No | Online |
BRD | https://brd.nci.nih.gov/brd/ | Review articles of human Biospecimen Science | No | Online |
Calcium Gene Database | http://cagedb.uhlenlab.org/ | Mapping genes for calcium signaling and their associated human genetic disorders | Yes | Online |
CaspDB | http://caspdb.sanfordburnham.org | Potential cleavage sites in a set of all human proteins | No | Offline |
CaspNeuroD | http://caspdb.sanfordburnham.org/caspneurod.php | Predicted caspase cleavage sites in human proteins associated with Neurological Diseases | No | Offline |
CCSB Interactome | http://interactome.dfci.harvard.edu/ | Interactomes and phenotypes in human disease | Yes | Online |
ChemProt | http://potentia.cbs.dtu.dk/ChemProt/ | Compilation of chemical-protein-disease annotation resources | Yes | Offline |
CIDeR | http://mips.helmholtz-muenchen.de/cider/ | Information from neurological and metabolic diseases | Yes | Online |
ComPPI | https://comppi.linkgroup.hu/ | Protein-Protein Interaction Database | Yes | Online |
dbDEPC | https://www.scbit.org/dbdepc3/index.php | Curated cancer proteomics data | Yes | Online |
DegraBase | http://wellslab.ucsf.edu/degrabase/ | Mass spectrometry experiments in healthy and apoptotic cell lines | Yes | Offline |
Degradome database | http://degradome.uniovi.es/ | Protease alterations in hereditary diseases | No | Online |
DenHunt | http://proline.biochem.iisc.ernet.in/DenHunt/about_database.p hp | Experimentally verified dengue-human interactions | Yes | Online |
DEPhOsphorylation database | http://depod.bioss.uni-freiburg.de/ | Data of phosphatases, their substrates, and the pathways in which they function | Yes | Online |
DIIP | http://bioinfo.lab.mcgill.ca/resources/diip/ | Isoform interactome prediction from experiments | Yes | Online |
Dynamic Proteomics | http://www.dynamicproteomics.net/ | Endogenously tagged proteins and their time-lapse microscopy movies | Yes | Offline |
fat_deposition | http://www.integratomics-time.com/fat_deposition | Protein interactions in human, cattle, rat, and mice obesity | No | Offline |
FixPred | http://www.fixpred.com | Protein sequences corrected by the FixPred pipeline | Yes | Offline |
Name | URL | Brief description | Download of data | Current status |
GutCyc | http://www.gutcyc.org/ | Pathway/genome databases from the human gut | Yes | Offline |
HADb | http://autophagy.lu/index.html | Autophagy related genes and proteins | No | Online |
HAPPI | http://discovery.informatics.uab.edu/HAPPI/ | Human annotated and predicted protein interaction | Yes | Online |
Harvester | http://harvester.fzk.de/harvester/ | Databases and servers for human proteins | No | Offline |
HCPIN | http://nmr.cabm.rutgers.edu/hcpin | Human cancer pathway protein interaction network | No | Offline |
HERVd | https://herv.img.cas.cz/ | Human endogenous retroviruses database | No | Online |
HGPD | https://hgpd.lifesciencedb.jp/cgi/ | Human Gene and Protein Database | Yes | Online |
hiPathDB | https://www.kobic.re.kr/ | Curated human protein and pathway data | No | Offline |
HKUPP | http://www.hkupp.org/ | Human kidney and urine proteome information | No | Online |
HMMER3 | https://www.ebi.ac.uk/Tools/hmmer/ | Homologs of protein sequences, and protein alignments | Yes | Online |
HmtDB | https://www.hmtdb.uniba.it/ | Database of human mitochondrial genomes | Yes | Offline |
HPID | http://wilab.inha.ac.kr/hpid/webforms/intro.aspx | Protein interaction information from structural and experimental data | Yes | Online |
Human Interactome Map | http://www.actrec.gov.in/ | Exploring the human protein interaction network | Yes | Online |
Human PPI network | https://gene.sfari.org/ | Functional and network organization of proteome of Autism datasets | Yes | Online |
Human Proteinpedia | http://www.humanproteinpedia.org | A community portal for sharing and integration of human protein data | Yes | Online |
HumanNet | http://www.functionalnet.org/humannet/about.html | Human gene functional interaction Network | Yes | Online |
HuPho | http://hupho.uniroma2.it/index.php | Information about human protein phosphatases | No | Online |
HuPI | https://hupi.ircm.qc.ca/ | Human Proteotheque Initiative | Yes | Online |
HuRI | http://www.interactome-atlas.org/ | Human reference protein interactome mapping project | Yes | Online |
HydPred | http://lishuyan.lzu.edu.cn/hydpred/ | protein hydroxylation sites in human inherited disease | No | Online |
HypoxiaDB | http://www.hypoxiadb.com/hypoxiadb.html | Catalog of human hypoxia-regulated proteins | No | Online |
iLoc-Cell | http://www.jci-bioinfo.cn/iLoc-Hum | Subcellular locations of human proteins | No | Online |
Instruct | http://instruct.yulab.org/ | Protein interactome networks in human and six model organisms | Yes | Online |
Integr8 | https://www.ebi.ac.uk/integr8 | An integrated views of complete genomes and proteomes | Yes | Offline |
Integrated Interactions Database | http://dcv.uhnres.utoronto.ca/iid/ | Tissue-specific protein-protein interactions | Yes | Online |
InterMitoBase | https://mcube.nju.edu.cn/cgi-bin/intermitobase/home.pl | High quality protein-protein interaction (PPI) data in human mitochondria | No | Offline |
InWeb_IM | https://www.intomics.com/inbio/map.html#search | Provides an integrated human PPI network | Yes | Online |
KEGG PATHWAY | https://www.kegg.jp/ | Collection of manually drawn pathway maps | Yes | Online |
KinMap | http://www.kinhub.org/kinmap/ | Interactive navigation through human kinome data | Yes | Online |
Kinome NetworkX | http://www.kinasenet.ca/ | A systems biology-based framework to catalogue the human kinome | Yes | Online |
KLIFS | https://klifs.vu-compmedchem.nl/ | Kinase-Ligand Interaction Fingerprints and Structures | No | Online |
Proteome and protein-protein interaction databases
We found 24 tools involving databases with information about potential cleavage sites in datasets of all human proteins collected in Uniprot and their orthologs, allowing for tracing of cleavage motif conservation, bioactive molecules, human metabolites, natural products, patented agents and other molecules. Databases are organized as disease-specific, tissue-specific, organelle-related or by protein families. Epigenetic enzymes and chemical modulators focused on epigenetic therapeutics, as well as functional databases including information from cells and tissues at a variety of physiological conditions, are also available. The input of the analyses is either a GO term, gene symbol or name, chromosomal location, metabolite or molecule name, or enzyme family name. Compartment and subsystem 2D maps, tables with literature related, enzyme domains, Uniprot ID, plots of classic or multivariate ROC curves, and images illustrating predicted small molecules are present in the output.
Name | URL | Brief description | Download of data | Current status |
Labeledln | https://ftp.ncbi.nlm.nih.gov/pub/lu/LabeledIn/ | Drug indications via text-mining | No | Online |
Ligandbook | https://ligandbook.org | Force-field parameters of small and drug-like molecules | Yes | Online |
Membranome | https://membranome.org/ | 3D transmembrane domains and classification | Yes | Online |
MiasDB | http://47.88.84.236/Miasdb/index.php | Interactions between human splicing factors, RNA elements, transcription factors, kinases and modified histones | Yes | Online |
MitoP2 | http://www.mitop2.de/ | Evaluated yeast, mouse, and human mitochondrial proteins | No | Online |
mLASSO-Hum | http://bioinfo.eie.polyu.edu.hk/mLASSOHumServer/index.htm l | Interpretable human-protein subcellular localization | No | Online |
Molecular INTeraction Database | http://mint.bio.uniroma2.it/mint/ | Molecular interactions by extracting experimental details from work published | Yes | Offline |
NetNGlyc | http://www.cbs.dtu.dk/services/NetNGlyc/ | Predict N-Glycosylation sites in human proteins | No | Online |
neXtProt | https://www.nextprot.org/about/nextprot | Proteomics data for over 85% of human proteins | Yes | Online |
PaPI | http://papi.unipv.it/ | Predict impact of variants estimating the probability to damage their protein- related function | No | Online |
PCDq | http://h-invitational.jp/hinv/pcdq/ | Human protein complex database | No | Online |
PDID* | http://biomine.cs.vcu.edu/servers/PDID/index.php | Molecular-level putative protein-drug interactions in the structural human proteome | Yes | Online |
PepSweetener | https://glycoproteome.expasy.org/pepsweetener/app/ | Manual annotation of MS data for intact glycopeptides | Yes | Online |
PhenoPPIOrth | http://jjwanglab.org/PhenoPPIOrth/ | Orthology and protein-protein interaction information to infer gene-phenotype associations for multiple species | Yes | Offline |
PhosphoPICK | http://bioinf.scmb.uq.edu.au/phosphopick/phosphopick | Method for predicting kinase substrates using cellular context information | Yes | Online |
PhosphoPredict | http://phosphopredict.erc.monash.edu/ | Predict kinase-specific phosphorylation substrates and sites in the human proteome | Yes | Online |
PhosphOrtholog | http://www.phosphortholog.com/ | Cross-species mapping of orthologous protein post-translational modifications | Yes | Online |
PICKLE | http://www.pickle.gr/Search | Predicts human protein-protein interactions network | Yes | Offline |
PINdb | http://pin.mskcc.org/ | Multiprotein nuclear complexes of human or yeast cells | Yes | |
PINTA | https://securehomes.esat.kuleuven.be/~bioiuser/pinta/input.php | Genome-wide protein-protein interaction network for the prioritization of candidate genes | Yes | Offline |
PIPs | http://www.compbio.dundee.ac.uk/www-pips/index.jsp | Protein interaction bayesian method that combines information from expression, orthology, domain co-occurrence, post-translational modifications and sub-cellular location | No | Online |
PolyQ | http://lightning.med.monash.edu/polyq2/ | Information of human polyQ repeat-containing proteins | Yes | Offline |
PrePPI | https://bhapp.c2b2.columbia.edu/PrePPI/index.html | Predicted and experimentally determined (PPIs) for yeast and human | Yes | Online |
Primate Orthologous Exon Database | https://giladlab.uchicago.edu/orthoExon/ | Unique, non-overlapping, orthologous exon regions of human, chimpanzee, and rhesus macaque. | No | Offline |
Name | URL | Brief description | Download of data | Current status |
ProKinO | http://vulcan.cs.uga.edu/prokino/about/browser | Kinase activation and regulatory mechanisms | No | Online |
Protein kinase resource | http://www.kinasenet.org/ | Human kinome tree via an interactive display | No | Offline |
ProteomicsDB | https://www.proteomicsdb.org/ | Predicted and experimental human proteomes | Yes | Online |
Quokka* | http://quokka.erc.monash.edu/ | Kinase phosphorylation sites in the human proteome | No | Online |
RasMol | http://www.bernstein-plus-sons.com/software/rasmol/ | Protein 3D structure viewer | No | Online |
ScaPD | http://bioinfo.wilmer.jhu.edu/ScaPD/ | Database for human scaffold proteins | No | Online |
SMPDB | https://smpdb.ca/view/SMP0000179 | Small molecule pathway dataBase | No | Online |
SpindleP | http://www.cbs.dtu.dk/services/SpindleP/ | Location of proteins or genes in the meiotic spindle | No | Online |
StSNP | http://ilyinlab.org/StSNP/ | Compare protein structures, protein complexes, protein-protein interfaces and metabolic networks | No | Online |
SubPhosPred | http://bioinfo.ncu.edu.cn/SubPhosPred.aspx | Phosphorylation sites in subcellular compartments | No | Online |
SURFY | http://wlab.ethz.ch/surfaceome/ | Visualize the human surface proteome (surfaceome) | Yes | Online |
Sys-BodyFluid | http://www.biosino.org/bodyfluid/ | Contains eleven kinds of body fluid proteomes info | Yes | Offline |
The Proteome Browser* | http://proteomebrowser.org/tpb/home.jspx | Tissue localization, post-translational modifications, or interactions in human proteome | No | Online |
TissueNet | http://netbio.bgu.ac.il/tissuenet/ | Experimentally-identified PPIs with human tissues | Yes | Online |
TOPPR | https://iomics.ugent.be/toppr/ | The online protein processing resource | Yes | Offline |
TRI_tool | https://www.vin.bg.ac.rs/180/tools/tfpred.php | Prediction of PPIs in human Transcriptional Regulation | No | Online |
UniHI | http://www.unihi.org/ | Analysis and visualization of human molecular interaction networks | Yes | Online |
VDJsolver | http://www.cbs.dtu.dk/services/VDJsolver/ | Data of human immunoglobulin VDJ recombination | No | Online |
VHLdb | http://vhldb.bio.unipd.it/ | Interactors and mutations of the human von Hippel-Lindau tumor suppressor protein | No | Online |
Other databases
A total of 64 databases are available, focusing on various aspects of immunogenetics. These databases offer a comprehensive understanding of cytokine receptors, their ligands, involvement in diseases, and their applications in clinical treatments. They house intricate details about human Major Histocompatibility Complex (MHC) genes, peptides, predictions, and proteins related to human leukocyte antigen (HLA) I and HLA II-restricted peptides. Additionally, they provide extensive literature about immunoproteins, tumor T cell antigens, and in silico predictions of epitopes.
Name | URL | Brief description | Download of data | Current status |
AAgAtlas | http://biokb.ncpsb.org/aagatlas/ | Autoantigen or autoantibody curated information | Yes | Online |
CHOP CNV | http://cnv.chop.edu | Genomic Copy Number Variation (CNVs) that were derived from 2026 healthy individuals | Yes | Offline |
CLIMA | http://bioinformatics.hsanmartino.it/clima2/ | Molecular authentication of human cell lines | Yes | Offline |
CytReD | http://www.cro-m.eu/CytReD/ | Cytokine receptors, ligands, involvement in diseases | No | Online |
dbMHC | https://ftp.ncbi.nlm.nih.gov/pub/mhc/mhc/Final%20Archive/ | DNA and clinical data related to MHC | Yes | Online |
Epipox | http://imed.med.ucm.es/epipox/ | Peptides (HLA-I and HLA-II), predictions, and proteins | No | Online |
G2D | http://g2d2.ogic.ca/ | Precomputed candidate genes for diseases | Yes | Offline |
GADGET | http://gadget.biosci.gatech.edu | Genetic traits of human phenotypic diversity | No | Online |
Gene Set Builder | http://www.cisreg.ca/gsb/ | Compile, store, export, and share sets of genes | Yes | Online |
Genetic Association Database | https://geneticassociationdb.nih.gov/ | Genetic association studies information | Yes | Online |
GIANT | https://portals.broadinstitute.org/collaboration/giant/index.php/GIANT_ consortium | Genetic investigation of anthropometric traits meta-analysis of genome- wide association data | Yes | Online |
Global Biobank Engine | https://biobankengine.stanford.edu/ | Visualize phenotypes, variants, genes, genetic correlation and human leukocyte antigens (HLA) alleles | No | Online |
GuavaH | http://www.guavah.org/ | Genome-wide association (GWAS) of HIV phenotypes | No | Online |
GUIDES | http://guides.sanjanalab.org/#/ | CRISPR knockout libraries in human or mouse genome | Yes | Online |
H2P2 | http://h2p2.oit.duke.edu/H2P2Home/ | Cellular and infections agents in GWAS studies data | No | Online |
HLA-ADR | http://www.allelefrequencies.net/hla-adr/ | Exploring immunogenetic disease associations | No | Online |
HLAsupE | http://www.immunoinformatics.net/HLAsupE/index.html | Human leucocyte antigens supertype-specific epitopes | Yes | Online |
HomozygosityMapper | http://www.homozygositymapper.org/ | Homozygous detection in SNP genotype or sequencing | Yes | Online |
HPtaa database | http://www.bioinfo.org.cn/hptaa/ | Human potential tumor associated antigens | No | Online |
HyperCLDB | http://bioinformatics.hsanmartino.it/hypercldb/ | Collection of information on human and animal cell lines | No | Online |
Name | URL | Brief description | Download of data | Current status |
IEDB | https://www.iedb.org/ | Antibody and T-cell epitopes studied in various species | No | Online |
iLoc-Cell | http://www.jci-bioinfo.cn/iLoc-Hum | Predictor for subcellular locations in proteins sites | No | Online |
IMGT | http://www.imgt.org/ | International immunogenetics information system | Yes | Online |
IPD-IMGT/HLA | https://www.ebi.ac.uk/ipd/imgt/hla/ | Provides a specialist database for sequences of HLA | No | Online |
IPD-MHC | https://www.ebi.ac.uk/ipd/mhc/ | Sequence repository of MHC from different species | Yes | Online |
LD Hub | http://ldsc.broadinstitute.org/ | Summary of GWAS studies | No | Online |
MARome | http://196.1.114.46:8080/MARome/index | Annotation of scaffold and matrix attachment regions | Yes | Online |
Metabolomics GWAS Server | http://metabolomics.helmholtz-muenchen.de/gwas/index.php | GWAS studies on the human metabolome | No | Online |
MitoAge | http://www.mitoage.info/ | Analysis of mtDNA, focus on animal longevity | Yes | Online |
MNDR | http://www.rna-society.org/mndr/ | Disease association and mapping disease ncRNA | Yes | Online |
mtDNA-Server | https://mtdna-server.uibk.ac.at/index.html | Heteroplasmy detection and haplogroup-based mtDNA | Yes | Online |
NetMHC-3.0 | http://www.cbs.dtu.dk/services/NetMHC/ | Human, mouse or monkey MHC Class I-peptide binding | No | Online |
NetMHCIIpan | http://www.cbs.dtu.dk/services/NetMHCIIpan/ | HLA-DR, HLA-DP, HLA-DQ human and mouse data | No | Online |
PathogenFinder | https://cge.cbs.dtu.dk/services/PathogenFinder/ | Bacterial pathogenicity estimation | No | Online |
PEPVAC | http://imed.med.ucm.es/PEPVAC/ | Tool of development of multi-epitope vaccines | Yes | Online |
PhosphoPICK | http://bioinf.scmb.uq.edu.au/phosphopick/phosphopick | Predicting kinase substrates using cellular context info | Yes | Online |
PolyDoms | https://polydoms.cchmc.org/polydoms/ | Impact of variations in human genes to facilitate sequence-based association studies | No | Online |
PolySearch2 | http://polysearch.cs.ualberta.ca/index | Associations between human diseases, genes, drugs, metabolites, toxins and more | Yes | Online |
Primer Z | http://grch37.genepipe.ncgm.sinica.edu.tw/primerz/beginDesign.do | Interface for PCR primer design | Yes | Online |
PrimerStation | https://ps.cb.k.u-tokyo.ac.jp/ | Multiplex genomic PCR primer design tool | Yes | Online |
PRS | http://mrcieu.mrsoftware.org/PRS_atlas/ | An atlas of polygenic burden associations across the human phenome | No | Online |
pseudoMap | http://pseudomap.mbc.nctu.edu.tw/ | Explores the relationships between TPG and its cognate gene with miRNA decoyed mechanisms | Yes | Offline |
Psmir | http://bio-bigdata.hrbmu.edu.cn/Psmir/ | Gene expression profiles under miRNA perturbation and drug treatment | Yes | Online |
ReCGiP | http://klab.sjtu.edu.cn/ReCGiP/ | Candidate genes in pigs based on bibliomics | Yes | Online |
RepTar | http://bioinformatics.ekmd.huji.ac.il/reptar | Genome-wide predictions of human and mouse viral miRNAs | Yes | Offline |
Semantic Body Browser* | http://sbb.cellfinder.org/ | Graphically exploring an organism by means of ontologically annotated anatomical illustrations | Yes | Online |
SHOGoiN | https://stemcellinformatics.org/ | Human omics of ips and normal cells | No | Online |
Name | URL | Brief description | Download of data | Current status |
SNPDelScore | https://www.ncbi.nlm.nih.gov/research/snpdelscore/ | Deleterious effects of noncoding variants using a large panel of currently available methods | Yes | Online |
SNPxGE(2) | http://lambchop.ads.uga.edu/snpxge2/index.php | Human population gene expression and variation | Yes | Offline |
SPIKE | https://www.cs.tau.ac.il/~spike/ | Curated human signaling pathways | Yes | Online |
StemCellNet | http://stemcellnet.sysbiolab.eu/ | Molecular networks in the context of stem cell biology | Yes | Online |
SWATHAtlas | http://www.swathatlas.org/ | Immunogenetics systems biology information | Yes | Online |
SysteMHC Atlas | https://systemhcatlas.org/ | Atlas of immune peptidomics MS-related | No | Online |
TCLP | http://celllines.tron-mainz.de/ | HLA data, neo-epitopes, virus, and gene expression | Yes | Online |
TCRex | https://tcrex.biodatamining.be/instructions/ | Recognition of pathogenic & cancer epitopes by human T cell receptors (TCR) | Yes | Online |
TFcheckpoint | http://www.tfcheckpoint.org/ | Genome-scale regulatory network studies | Yes | Offline |
The SBT | https://ftp.ncbi.nlm.nih.gov/pub/mhc/mhc/Final%20Archive/ | MHC human data sequences | Yes | Online |
VaDE | http://bmi-tokai.jp/VaDE/ | Genomic polymorphisms associated to diseases, traits, and pharmacogenomics | Yes | Online |
VDJdb* | https://vdjdb.cdr3.net/ | Antigen-specific TCR sequences acquired by manual processing | Yes | Online |
Reference
Villalba, G. C., & Matte, U. (2021). Fantastic databases and where to find them: Web applications for researchers in a rush. Genetics and Molecular Biology, 44, e20200203.