Bioinformatics

How to Use Bioinformatics Databases and Tools to Accelerate Your Research

September 23, 2023 Off By admin
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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

NameURLBrief descriptionDownload of DataCurrent status
1-CMDbhttp://slsdb.manipal.edu/ocm/Multi omics associated with one carbon metabolismYesOnline
CaspDBhttp://caspdb.sanfordburnham.orgCleavage sites in proteins collected in Uniprot and their orthologsNoOffline
CFamhttp://bidd2.nus.edu.sg/cfamCluster drugs, bioactive molecules, human metabolites, natural products, patented agents and other moleculesNoOffline
CIDeR*http://mips.helmholtz-muenchen.de/cider/Information from neurological and metabolic diseasesYesOnline
DESTAFhttps://www.cbrc.kaust.edu.sa/destaf/Metabolism and toxins in diseases and tissuesYesOnline
dkNEThttps://dknet.org//Integrated data of Diabetes and Digestive and Kidney DiseasesYesOnline
HEMDhttp://mdl.shsmu.edu.cn/HEMD/Human epigenetic enzymes and chemical modulatorsYesOnline
HEPATONET1http://www.ebi.ac.uk/biomodels-main/MODEL1009150000Genome-scale metabolic network of human hepatocytesNoOnline
HMAhttps://metabolicatlas.org/Comprehensive human metabolic information as modelsYesOnline
HumanCychttps://humancyc.org/Human nutrition that associates with a set of metabolic pathwaysNoOnline
HMDB*https://hmdb.ca/Human Metabolome DatabaseYesOnline
KinMaphttp://www.kinhub.org/kinmap/Interactive navigation through human kinome dataYesOnline
KinMutRFhttp://kinmut2.bioinfo.cnio.es/KinMut2Prediction of variants in the human protein kinase superfamilyNoOffline
metabolicMinehttps://www.humanmine.org/humanmine/begin.doMetabolome profiling and model organismsYesOnline
MetSigDishttp://www.bio-annotation.cn/MetSigDis/Metabolite alterations in various diseasesYesOffline
MSEAhttps://www.metaboanalyst.ca/Enrichment analyses for (primarily human) metabolomic studiesYesOnline
NOPdbhttp://www.lamondlab.com/NOPdbNucleolar proteins identified by mass spectrometry analysesNoOffline
PeroxisomeDBhttp://www.peroxisomedb.org/Peroxisomal proteins, molecular function, metabolic pathway and disordersYesOnline
PhosphoPredicthttp://phosphopredict.erc.monash.edu/Predict kinase-specific phosphorylation substrates and sites in the human proteomeYesOnline
Piphillinhttp://piphillin.secondgenome.com/Metagenomic data by Direct Inference from Human MicrobiomesYesOnline
R spiderhttp://www.bioprofiling.de/gene_list.htmlPathway analysis from KEGG and ReactomeNoOnline
RegenBasehttp://regenbase.org/Effect of compounds on enzyme activity and cell growthYesOnline
TSEMhttps://hood-price.isbscience.org/research/tsem/Tissue specific encyclopedia of metabolism and metabolic modelsYesOnline
VMHhttps://vmh.life/Human metabolism and genetics, microbial metabolism, nutrition, and diseasesYes

Methylation databases

NameURLBrief descriptionDownload of DataCurrent status
ANCOGeneDBhttps://bioinfo.uth.edu/ancogenedb/Epigenomic, enhancers, and expression quantitative trait lociYesOnline
BECon*https://redgar598.shinyapps.io/BECon/Interpreting methylation findings from blood in the context of brainYesOnline
CMShttp://cbbiweb.uthscsa.edu/KMethylomes/Analytic functions for cancer methylome datasetsNoOffline
DBCAThttp://dbcat.cgm.ntu.edu.tw/Methylation profiles of DNA alteration in human cancerYesOnline
DiseaseMeth*http://bio-bigdata.hrbmu.edu.cn/diseasemeth/Aberrant methylomes of human diseasesNoOnline
GEDhttp://gametsepi.nwsuaflmz.com/Epigenetic modification of gametogenesis in mammalsYesOnline
Geneimprinthttp://www.geneimprint.com/site/homeGene imprinting and which allele is expressedYesOnline
Lnc2Methhttp://bio-bigdata.hrbmu.edu.cn/Lnc2Meth/Informs about RNAs and DNA methylation of transcriptsYesOnline
MeInfoTexthttp://bws.iis.sinica.edu.tw:8081/MeInfoText2/Gene methylation and cancers, protein-protein interactions, and biological pathwaysYesOffline
MethHChttp://methhc.mbc.nctu.edu.tw/Focuses on aberrant methylomes of human diseasesNoOffline
MethylomeDBhttp://epigenomics.columbia.edu/methylomedb/index.htmlDNA methylation profiles for human and mouse brainsYesOffline
mPodwww.genome.orgGenome-wide tissue-specific DNA methylation profilesNoOnline
PhenoScannerhttp://www.phenoscanner.medschl.cam.ac.uk/Methylation and human genotype-phenotype associationsYesOnline
ROADMAPhttps://egg2.wustl.edu/roadmap/web_portal/index.htmlEpigenetic modifications and mRNA expression of human cell types and tissuesYesOnline
TCGAhttps://www.cancer.gov/Cancer methylation and expressionYesOnline
TSGenehttp://bioinfo.mc.vanderbilt.edu/TSGene/Methylation status of tumor suppressor genesNoOffline

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.

NameURLBrief descriptionDownload of DataCurrent status
ChIPSummitDBhttp://summit.med.unideb.hu/summitdb/index.phpChIP-seq-based data of transcription factor binding sites and the topological arrangements of the proteinsYesOnline
CREMEhttps://creme.dcode.org/Cis-regulatory module explorer for the human genomeYesOnline
CRUNCHhttp://crunch.unibas.ch/crunch/ChIP-seq data analysisYesOnline
FirstEFhttp://rulai.cshl.org/tools/FirstEF/First Exon Finder (FirstEF) is a 5’ terminal exon and promoter prediction programYesOnline
GlycoViewerhttp://www.glycoviewer.babs.unsw.edu.au/Visualisation tool for representing a set of glycan structuresYesOnline
HERVdhttps://herv.img.cas.cz/Human endogenous retroviruses databaseNoOnline
HumCFShttps://webs.iiitd.edu.in/raghava/humcfs/index.htmlHuman chromosomal fragile sites dataNoOnline
Interferome*http://interferome.its.monash.edu.au/interferome/home.jspxContains type I, II and III interferon (IFN) regulated genesNoOnline
JASPARhttp://jaspar.genereg.net/The high-quality transcription factor binding profile databaseYesOnline
MANTAhttp://manta.cmmt.ubc.ca/manta2/uploadMaps of transcription factor binding sitesYesOnline
MAPPERhttp://genome.ufl.edu/mapperdbMulti-genome analysis of positions and patterns of elements of regulationNoOffline
MEME Suitehttp://meme-suite.org/DNA motifs, transcription factor binding sites or protein domainYesOnline
METhttp://veda.cs.uiuc.edu/MET/The motif enrichment tool identifies significantly associated sets of genes that share a regulatory motifYesOnline
microDoRhttp://reprod.njmu.edu.cn/cgi-bin/microdor/index.pyPredict Human miRNA-mediated gene silencingYesOnline
OsteoporosAtlashttp://biokb.ncpsb.org/osteoporosis/index.phpRegulatory sequences in osteoporosis-related genesYesOnline
PReModhttp://genomequebec.mcgill.ca/PReModPredict transcriptional regulatory modules of human genomeYesOnline
pseudoMaphttp://pseudomap.mbc.nctu.edu.tw/php/index.phpGathers information about transcribed pseudogenesNoOffline
SM-TFhttp://zoulab.dalton.missouri.edu/SM-TF/Database of small molecule-transcription factor complexesYesOnline
SNP@lincTFBShttp://210.46.85.180:8080/SNP_linc_tfbs/SNPs in potential TFBSs of human Large intergenic non-coding RNAs (lincRNAs)YesOffline
TcoF-DBhttps://tools.sschmeier.com/tcof/home/Human transcription co-factors and transcription factor interacting proteinsNoOnline
TFBSbankhttp://tfbsbank.co.uk/Chip-seq data of 585 transcription factors in 5 speciesYesOnline
TFCathttp://www.tfcat.ca/Curated catalog of mouse and human transcription factorsNoOffline
TFClasshttp://tfclass.bioinf.med.uni-goettingen.de/Eukaryotic TFs according to their DNA-binding domainsNoOnline
TFCONEShttp://tfcones.fugu-sg.org/Transcription factor genes and conserved noncoding elementsYesOnline
TFM-Explorerhttps://bioinfo.lifl.fr/TFM/Putative TFBS within a set of upstream regulatory sequences for a given set of genesYesOnline
TMREChttp://www.jianglab.cn/TMREC/TF and miRNA regulatorY cascades in human diseasesYesOnline
TRANSFAChttp://genexplain.com/transfac/Eukaryotic TF, their experimentally-proven binding sites, consensus binding sequences and regulated genesNoOnline
TTSMI database*http://ttsmi.bii.a-star.edu.sg/Triplex target DNA site mapping and integration databaseNoOnline

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.

NameURLBrief descriptionDownload of DataCurrent status
AltExtronhttp://bioinformatics.org.au/tools/altExtron/Constitutively and alternatively spliced introns and exons, for conservation in mouse.YesOnline
AS-ALPShttp://as-alps.nagahama-i-bio.ac.jp/index.phpAlternative splicing-induced alteration of protein structureYesOnline
ASpediahttp://combio.snu.ac.kr/aspedia/index.htmlAlternative splicing encyclopedia with genomic annotationYesOnline
ASPicDB*http://srv00.recas.ba.infn.it/ASPicDB/Alternative splicing pattern of human genes, and functional annotation of predicted isoformsYesOnline
BrainRNA-seqhttps://www.brainrnaseq.org/Alternative splicing events in cell typesYesOnline
DBASShttp://www.dbass.org.uk/Splice-site prediction, and definition of auxiliary splicing signalsYesOnline
EDAShttp://www.gene-bee.msu.ru/edas/EST-derived alternative splicing databaseNoOffline
FAST DBhttp://www.genosplice.com/alternative-splicingAlternative splicing and alteration of splicing regulationNoOnline
FLJ DBhttp://flj.lifesciencedb.jp/top/Variations of transcription start site (TSS) and splicingYesOnline
H-DBAShttp://www.h-invitational.jp/h-dbas/Human-transcriptome data of alternative splicingYesOnline
HEXEventhttp://hexevent.mmg.uci.edu/cgi-bin/HEXEvent/HEXEventWEB.cgiSplice events based on EST informationNoOnline
HOLLYWOODhttp://hollywood.mit.edu/hollywood/Login.phpSplicing patterns derived from spliced alignment of cDNAsYesOnline
HSFhttp://www.umd.be/HSF3/index.htmlPrediction of mutations in splice sitesNoOnline
HYBRIDdbhttp://www.primate.or.kr/hybriddb/Identify intergenic splicing-mediated gene fusionNoOffline
IntSplicehttps://www.med.nagoya-u.ac.jp/neurogenetics/IntSplice/Predict a splicing consequence of SNVYesOnline
IsoFunchttps://guanlab.ccmb.med.umich.edu/isofuncA tool for assigning function to protein-coding splice variantsNoOffline
MiasDBhttp://47.88.84.236/Miasdb/index.phpMolecular interactions associated with human splicingYesOnline
NetGene2http://www.cbs.dtu.dk/services/NetGene2/Splice sites in human, C. elegans and A. thalianaNoOnline
NetUTRhttp://www.cbs.dtu.dk/services/NetUTR/Prediction of splice sites in 5′ UTR regionsNoOnline
PALS DBhttp://palsdb.ym.edu.tw/Collection of Putative Alternative SplicingNoOffline
SpliceInfohttp://SpliceInfo.mbc.NCTU.edu.tw/Info of exon skipping, 5’ or 3’-alternative splicing and intron retentionYesOffline
SplicePorthttp://spliceport.cbcb.umd.edu/Splice-site predictions for submitted sequencesNoOnline
SpliceProthttp://bioinfoteam.fiocruz.br/spliceprot/index.phpAlternative spliced variants based on experimental human transcriptomic dataYesOnline
TassDB*http://tassdb2.leibniz-fli.de/Search for specific genes or for genes containing tandem splice sitesYesOnline

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.

NameURLBrief descriptionDownload of DataCurrent status
MGDBMGDBMultiomics catalog of genes involved in melanomaYesOnline
MiRCancerMiRCancerExpression profiles in human cancers and curated literatureYesOnline
MiTranscriptomeMiTranscriptomePrimary tumor, metastases, and normal or benign adjacent tissuesYesOnline
MSGeneMSGeneComprehensive gene resource for metastasis suppressorYesOnline
MTCTScanMTCTScanMutations affecting cancer drug sensitivity based on genomic profilesYesOnline
NCI ALMANACNCI ALMANACInformation about greater antitumor activity than either agent aloneYesOnline
NeXtProtNeXtProtGene expression of genes in hereditary cancers and channelopathiesYesOnline
OncoDB.HCCOncoDB.HCCQuantitative trait loci of rodent models and human Hepatocellular cancerYesOnline
OncomiRdbBOncomiRdbBData of microRNAs which are known to be deregulated in various cancersNoOnline
OncotatorOncotatorCancer-specific annotations from public resourcesYesOffline
OncoyeastiOncoyeastiHuman homologs of yeast genes in samples of TCGA and CCLENoOnline
PedicanPedicanGene expression in pediatric/childhood cancerYesOnline
PepiDPepiDEpigenetic data in prostate cancer of human, mouse, and ratYesOffline
ProgenetixProgenetixOncogenomic database that provides copy number aberration dataNoOnline
S-MEDS-MEDmiRNA expression in various human sarcoma typesYesOnline
SelTarbaseSelTarbaseCollection of human microsatellite instability tumor and cell lineYesOnline
TANTIGENTANTIGENTumor T cell antigens and validated epitopes for discovered peptidesNoOnline
TCGA Portal*TCGA Portal*The cancer genome atlas with multi-omic and clinical dataYesOnline
TCRexTCRexPredict the recognition of pathogenic & cancer epitopes by human TCRYesOnline
TICdbTICdbGene expression and translocation breakpoints in human tumorsYesOffline
TUMIRTUMIRValidated resource of microRNA deregulation in various cancersYesOffline
UMDTP53dbUMDTP53dbA reference for all scientists working on p53YesOnline

     
arrayMaphttps://arraymap.org/Resource targeting copy number profiling dataYesOnline
CGAProjecthttps://mitelmandatabase.isb-cgc.org/Gene expression profiles of normal, precancer, and cancer cellsYesOnline
CancerNethttp://bis.zju.edu.cn/CancerNet/Contains cancer-specific miRNA and protein-protein interactionsYesOnline
CanGEMhttp://www.cangem.org/Clinical information, transcriptome, genome, and aCGH dataNoOffline
CanProVarhttp://canprovar.zhang-lab.org/index.phpConservation, protein expression, and domains in cancer dataYesOnline
CARGOhttp://cargo2.bioinfo.cnio.es/Visualize 3D SNPs, and view summarized gene annotationYesOnline
CaSNPhttp://cistrome.dfci.harvard.edu/CaSNP/Identifying CNAs in cancers and in the human genomeNoOffline
CCLE*https://portals.broadinstitute.org/ccleCancer cell line encyclopedia with 36 tumor types.YesOnline
CGMDhttp://cgmd.in/A database of tumor genes and markers with experimental evidenceNoOffline
ChiTaRShttp://chitars.md.biu.ac.il/Data of chimeric RNAs from eight organismsYesOnline
CMShttp://cbbiweb.uthscsa.edu/KMethylomes/Gene expression and cancer methylome datasetsNoOffline
COSMIChttps://cancer.sanger.ac.uk/cosmicGene expression and somatic mutations in human cancerYesOnline
CPDBhttps://www.library.ucdavis.edu/database/carcinogenic-potencydatabase-cpdb/Human exposures to chemicals that cause cancer in rodent testsNoOnline
DBCAThttp://dbcat.cgm.ntu.edu.tw/DataBase of CpG islands with a genome browserYesOnline
DbDEMChttps://www.picb.ac.cn/dbDEMC/A database of differentially expressed miRNAs in human cancersYesOnline
dbDEPChttps://www.scbit.org/dbdepc3/index.phpA database with curated cancer proteomics dataYesOnline
DBGChttp://bminfor.tongji.edu.cn/dbgc/index.doHuman gastric cancer-related gene expression dataNoOffline
DiseaseMethhttp://bio-bigdata.hrbmu.edu.cn/diseasemeth/Associations between diseases and methylation of specific DNA regionsNoOnline
DriverDBhttp://120.110.158.132:8787/driverdbv2/cancer.phpGene expression and driver gene/mutation identificationYesOnline
DSTHOhttp://203.199.182.73/gnsmmg/databases/dstho.htmlDatabase of siRNAs Targeted at Human OncogenesNoOffline
GCODhttp://compbio.dfci.harvard.edu/gcodMicroarray data on GeneChip arrays related to human cancersYesOffline
GEMiCCLhttps://www.kobic.kr/GEMICCL/Repository of cancer cell lines genotype and expression information.YesOnline
GeneHub-GEPIShttp://www.cgl.ucsf.edu/Research/genentech/genehub-gepis/Human and mouse gene expression of normal and cancer tissuesYesOnline
GSRhttps://popmodels.cancercontrol.cancer.gov/gsr/Genetic simulation resources provided by the National Cancer InstituteNoOnline
HCMDBhttp://hcmdb.i-sanger.com/indexHuman cancer metastasis database with gene expression dataYesOnline
HCPINhttp://nmr.cabm.rutgers.edu/hcpinGene expression of human cancer with protein interaction networkNoOffline
HNOCDBHNOCDBMethylation and gene expression in Head Neck and Oral CancerNoOnline
ISOexpressoISOexpressoIsoform-level gene expression analysis in human cancerYesOnline
MCF10AMCF10AVisualizing data from normal and mammary tumorsNoOnline
MeInfoTextMeInfoTextManual curation of gene methylation-cancer relationsYesOffline
MERAVMERAVGene expression in normal tissues, cancer cell lines, and primary tumorsYesOnline
MethHCMethHCExpression profiles and methylation of cancers and other diseasesNoOffline
MethmiRbaseMethmiRbaseEpigenetic regulated miRNA in human cancersYesOnline

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.

NameURLBrief descriptionDownload of DataCurrent status
EVOGEVOGPhylogenetic evolution analysis for genes among speciesNoOnline
GALAGALAHuman-mouse whole-genome alignments and annotationsYesOnline
GMOGMOAnalysis of the gametogenesis genes in human and mouseYesOnline
Gene Set BuilderGene Set BuilderGene sets and Homology annotations among speciesYesOnline
HelmCoPHelmCoPComparative genomic data from plant, animal and human helminthsYesOnline
HomophilaHomophilaLinks between human diseases and the Drosophila genomeYesOnline
IdiographicaIdiographicaCreate idiograms of human, mouse, rat, and fruit flyYesOnline
IRViewIRViewInteracting regions in human and mouse proteinsYesOnline
LMPDLMPDLipidomics and genomics from several speciesYesOnline
MANTEIAMANTEIAComparative genomics of human and model organismsYesOnline
MDWebMDWebStandard molecular dynamics simulationsNoOnline
Metab2MeSHMetab2MeSHAnnotations of PubChem and Human Metabolome DatabaseYesOnline
MGCMGCCollection of cDNA clones for human, mouse, and rat genesNoOnline
NetviewNetviewExplore the human and mouse gene regulatory networksYesOnline
NHPRTRNHPRTRNon-human primate transcriptomes and tissue poolsYesOnline
NREDNREDGene expression of long ncRNAs in human and mouseYesOffline
OpenDOAROpenDOARDirectory of open access repositories, outputs, and resourcesNoOnline
PhenoHMPhenoHMIdentification of genes associated with phenotypesYesOnline
POMOPOMOOmics relationships and annotations across organismsNoOffline
POEDBPOEDBOrthologous exon regions in human, chimpanzee, and rhesusNoOffline
RasMolRasMolMolecular graphics visualization toolNoOnline
ReCGiPReCGiPProviding candidate genes for reproductive researchesYesOnline
SQUATSQUATAnalysis tools for human, mouse, and chicken dataNoOffline
StemMapperStemMapperInfo of stem cell/progenitor cell types of mouse and humanYesOnline
TiSGeDTiSGeDTissue-specific genes of human, mouse, and ratNoOffline
TISSUES*TISSUES*Gene-tissue associations in human and mammalian modelsYesOnline
ToppCluster*ToppCluster*Comparative enrichment and network analysis of multiple gene lists of human/mammalian organismsYesOnline
TBrowserTBrowserHuman and mouse molecular interactionsYesOffline
tRFdbtRFdbTransfer RNA Fragments of human and model organismsNoOnline
Vega BrowserVega BrowserVertebrate genome annotationNoOnline
VISTA BrowserVISTA BrowserExperimentally validated human and mouse enhancersYesOnline

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.

NameURLBrief descriptionDownload of DataCurrent status
Globin Serverhttp://globin.cse.psu.eduExperimental data and tools of human hemoglobin mutationsNoOnline
AutDBhttp://autism.mindspec.org/autdb/Welcome.doGenetic variations related to autism spectrum disordersYesOnline
BioAfricahttps://www.krisp.org.za/tools.phpData of Human Immunodeficiency Virus proteins and other virusesYesOnline
C/VDhttp://www.padb.org/cvd/index.htmlCompiles multi-omics data of cardiovascular-related traitsNoOnline
ClinVarhttps://www.ncbi.nlm.nih.gov/clinvar/Interpretations of clinical significance of variants for reported conditionsYesOnline
DbAARDhttp://genomeinformatics.dce.edu/dbAARD/Database of Aging and age-related disordersYesOffline
DbDNVhttp://goods.ibms.sinica.edu.tw/DNVs/Data of variants of duplicated gene loci in the human reference genomeYesOnline
DbGaPhttps://www.ncbi.nlm.nih.gov/gap/Archives and distributes the results of genotype-phenotype studiesYesOnline
dbPEChttp://ptbdb.cs.brown.edu/dbpec/Resource of preeclampsia phenotypes and associated genesYesOffline
dbSNPhttp://www.ncbi.nlm.nih.gov/SNPDisease-causing clinical mutations as well as neutral polymorphismsYesOnline
dbWGFPhttp://bioinfo.au.tsinghua.edu.cn/dbwgfpData about whole-genome SNVs and their functional predictionsYesOffline
DECIPHERhttps://decipher.sanger.ac.uk/Genomic variants and phenotype using Ensembl resourcesNoOnline
Denovo-dbhttp://denovo-db.gs.washington.edu/denovo-db/Contains data about human de novo variantsYesOnline
DES-Mutationhttps://www.cbrc.kaust.edu.sa/des-mutation/mykbase/Mutation-focused knowledge-base of Pubmed articlesNoOffline
DGPhttp://maine.ebi.ac.uk:8000/services/dgpProbability scores for genes being involved in hereditary diseaseYesOffline
DGVhttp://dgv.tcag.ca/Collection of structural variation in the human genomeNoOnline
Digital Ageing Atlashttp://ageing-map.org/Integrated data about human ageing changes and pathologiesYesOnline
  Diseasome  http://www.kobic.kr/diseasome/  Genetic variation in disease focus on polymorphisms  No  Online
DisGeNEThttps://www.disgenet.org/Variant and gene-disease associations in more than 20000 diseasesYesOnline
DMDMhttp://bioinf.umbc.edu/dmdm/Visualization of human coding disease-related mutations and SNPs for each protein domainYesOnline
EGAhttps://www.ebi.ac.uk/ega/Reference data collections for human genetics researchYesOnline
FIDDhttp://www.uwcm.ac.uk/uwcm/mg/fidd/Frequency of inherited human disorders of over 200 conditionsNoOffline
NameURLBrief descriptionDownload of DataCurrent status
fitSNPshttp://fitsnps.ucsf.edu/index.phpFunctionally interpolating SNPs from differential gene expressionYesOffline
Follicle Onlinehttp://mcg.ustc.edu.cn/sdap1/follicle/index.phpFolliculogenesis-related experimental data from 23 model organisms, including humanNoOffline
GeneReviewshttps://www.uniprot.org/database/DB-0188Contains phenotypic information and information on selected variantsYesOnline
Genome TraxGenome Trax Search ToolVariant analysis of whole genome, exome, and targeted sequencesYesOnline
HbVarhttp://globin.cse.psu.edu/hbvar/menu.htmlHemoglobin variants, hemoglobinopathies all types of thalassemiaYesOnline
HGMDhttp://www.hgmd.cf.ac.uk/ac/index.phpCompiles information related to disease-related genetic variationNoOnline
HGSVPhttps://www.internationalgenome.org/human-genome- structural-variation-consortium/Map of structural variation with genomic assaysYesOnline
HGV&TBhttp://genome.igib.res.in/hgvtb/index.htmlHuman genes and genetic variants associated with TuberculosisYesOnline
HMDDhttp://www.cuilab.cn/hmddExperimental evidence for human miRNA and disease associationsYesOnline
HPOhttps://hpo.jax.org/app/Vocabulary of phenotypic abnormalities encountered in human diseaseYesOnline
Hu.MAPhttp://hu.proteincomplexes.org/A comprehensive view of protein complexes of disease genesYesOnline
Chr21 SNP DBhttp://csnp.unige.ch/Genetic variation of human chromosome 21 genesYesOffline
HUMSAVARhttps://www.uniprot.org/docs/humsavarAn index of human polymorphisms and disease mutationsYesOnline
InvFESThttp://invfestdb.uab.cat/Catalog of non-redundant human polymorphic inversionsNoOnline
Ion Channels Portalhttps://www.nextprot.org/portals/navmutPresent phenotypes caused by genetic variations in voltage-gated sodium channelsYesOnline
ITHANEThttps://www.ithanet.eu/db/ithagenesArchive of sequence variations affecting hemoglobin disordersNoOnline
Kaviarhttp://db.systemsbiology.net/kaviar/cgi-pub/Kaviar.plCompilation of human SNVs collected from many and diverse sourcesYesOnline
KMeyeDBhttp://mutationview.jp/MutationView/jsp/index.jspA database of human gene mutations that cause eye diseasesYesOnline
LaforaDBhttp://projects.tcag.ca/lafora/A human Lafora disease (LD) mutation databaseYesOnline
LongevityMaphttp://genomics.senescence.info/longevity/A catalog of human genetic variants associated with longevityYesOnline
LOVDhttp://www.lovd.nl/Gene-centered collection and display of DNA variationsNoOnline
LSDBshttps://grenada.lumc.nl/LSDB_list/lsdbsGene sequence variation associated with human phenotypesNoOnline
MARRVEL*http://marrvel.org/Model organism aggregated resources for rare variant explorationYesOnline
MelanomaMinehttp://melanomamine.bioinfo.cnio.es/Data of melanoma-related biomedical knowledge resourcesYesOnline
MitoVariomehttps://www.kobic.re.kr/MitoVariomeGenetic variation in the mitochondrial genome with haplogroupsYesOffline
Mutalyzerhttps://mutalyzer.nl/Sequence variants according to the standard human sequence variant nomenclature (HGVS)NoOnline
MutPredhttp://mutpred.mutdb.org/Classify an amino acid substitution as disease-associated or neutralNoOnline
NetChophttp://www.cbs.dtu.dk/services/NetChop/Neural network predictions for cleavage sites of the proteasomeNoOnline
OCDBhttp://alpha.dmi.unict.it/ocdb/Data of genes, miRNAs, and drugs for obsessive-compulsive disorderYesOffline
NameURLBrief descriptionDownload of DataCurrent status
OMIMhttps://omim.org/Online mendelian inheritance in man with genes and genetic disordersYesOnline
PAHKBhttps://bioinfo.uth.edu/PAHKB/Records core pulmonary hypertension (PH)-related genesYesOnline
PanelApphttps://panelapp.genomicsengland.co.uk/Virtual gene panels of disorders to be created, stored and queriedYesOnline
PaPIhttp://papi.unipv.it/Score variants according to the damage their protein-related functionNoOnline
PEDBhttp://www.pedb.orgProstate gene expression databaseYesOffline
pfSNPhttp://pfs.nus.edu.sg/Analysis of SNPs and your possible functionality from sequence motifsYesOffline
PharmGKBhttps://www.pharmgkb.org/Pharmacogenomics and impact of genetic variations on drug responseYesOnline
PhenCodehttp://globin.bx.psu.edu/phencodeHuman phenotype and clinical data in various locus-specific databasesNoOffline
PhenocartaExpression ExperimentsPhenotypes tree of diseases, human and mammalian speciesYesOnline
PhenoCHFhttp://www.nactem.ac.uk/PhenoCHF/Phenotypic information related to integrating heterogeneous resourcesYesOnline
PhenoDBhttps://researchphenodb.net/Exome/genome sequencing to identify the genes and variantsYesOnline
PhenoDigmhttps://www.sanger.ac.uk/science/tools/phenodigmPhenotype comparisons for disease and gene modelsYesOnline
PhenoHMhttps://phenome.cchmc.org/phenoBrowser/PhenomeHuman-mouse comparative phenome-genome and orthologousYesOnline
Phenopediahttps://phgkb.cdc.gov/PHGKB/startPagePhenoPedia.actionGenetic association studies in order to facilitate knowledge synthesisYesOnline
PhenoTipshttps://phenotips.com/Data about phenotypic information for patients with genetic disordersYesOnline
PhosphoPOINThttp://kinase.bioinformatics.tw/Comprehensive human kinase interactome and phospho-proteinNoOffline
PhosphOrthologhttp://www.phosphortholog.com/Cross-species mapping of orthologous protein modificationsYesOnline
PolyPhen2http://genetics.bwh.harvard.edu/pph2/Impact of an amino acid substitution on the structure and functionNoOnline
PredictSNP2http://loschmidt.chemi.muni.cz/predictsnp2/Evaluation of the pathogenic effect of SNPs within the human genomeYesOnline
PTM-SNPhttp://gcode.kaist.ac.kr/ptmsnpCollection of non-synonymous SNPs that affect post-translational modification sitesNoOffline
PubAngioGenhttp://www.megabionet.org/aspd/The connection between angiogenesis and diseases at multi-levelsYesOffline
RatMine / InterMinehttp://ratmine.mcw.edu/ratmine/begin.doIntegrates many types of data for human, mice, rat, and other speciesYesOnline
RAvariomehttp://www.h-invitational.jp/hinv/rav/Data about variants of rheumatoid arthritisNoOnline
SNP2TFBShttps://ccg.epfl.ch/snp2tfbs/Approach for identifying regulatory variantsNoOnline
SNPDelScorehttps://www.ncbi.nlm.nih.gov/research/snpdelscore/Analysis of deleterious effects of noncoding variantsYesOnline
SNPediahttps://www.snpedia.com/Functional consequences of human genetic variation as published in studiesNoOnline
SNPeffecthttps://snpeffect.switchlab.org/Information about phenotyping human single nucleotide polymorphismsYesOnline
SNVBoxhttps://karchinlab.org/apps/appSnvBox.htmlPrediction of the impact of either germline or somatic SNVsYesOnline
TMREChttp://210.46.85.180:8080/TMREC/Regulatory cascades in specific disease by TF, miRNA or disease nameYesOffline
UGAHashhttp://ugahash.uni-frankfurt.de/Accession numbers to genomic features with a focus on lncRNAsNoOnline
UMD-Predictorhttp://umd-predictor.eu/index.phpIdentify potential pathogenic variations, associates with omics dataYesOnline
NameURLBrief descriptionDownload of DataCurrent status
VarSome*https://varsome.com/Variant and gene annotation, curated from public repositoriesYesOnline

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.

NameURLBrief descriptionDownload of DataCurrent status
AgeFactDBhttp://agefactdb.jenage.de/Integration of ageing phenotype and lifespan dataYesOnline
aGEMhttp://agem.cnb.csic.esAnatomic gene expression mappingYesOffline
Allen Brain Atlashttps://alleninstitute.org/Analysis of human brain, the human cell and the immune systemYesOnline
AllerGAtlashttp://biokb.ncpsb.org/AlleRGatlas/Data of human allergy genes and their related diseasesYesOnline
AltExtronhttp://bioinformatics.org.au/tools/altExtron/Gene expression of human and mouse transcript sequencesYesOnline
ANGIOGENEShttp://angiogenes.uni-frankfurt.de/RNA-seq endothelial data of human, mouse and zebrafishYesOnline
AnnoLnchttp://annolnc.cbi.pku.edu.cn/index.jspA web server for systematically annotating novel human lncRNAsYesOffline
arrayMaphttps://arraymap.org/Gene expression and copy number profiling data in human cancerYesOnline
AS-ALPShttp://as-alps.nagahama-i-bio.ac.jp/index.phpAlternative splicing-induced alteration of protein structureYesOnline
ASMBrainBloodhttps://epigenetics.essex.ac.uk/ASMBrainBlood/Expression profile of human brain correlated within whole bloodYesOnline
ASpediahttp://combio.snu.ac.kr/aspedia/index.htmlSplicing annotation integrating genomic informationYesOnline
ASPicDBhttps://www.cineca.it/ASPicDB/Annotation of predicted isoforms of human genesYesOffline
Cellosaurushttps://web.expasy.org/cellosaurus/Information about immortalized cell lines, naturally immortal cell lines, finite life cell lines of many model organisms and humanYesOnline
CHESShttp://ccb.jhu.edu/chess/Human RNA sequencing experiments produced by the GTEx projectYesOnline
Cistrome DBhttp://dc2.cistrome.org/ChIP-seq and DNase-seq data in mouse and humanYesOnline
Corteconhttp://cortecon.neuralsci.org/Captures gene expression in the developing cortexYesOnline
CSPAhttps://wlab.ethz.ch/surfaceome/Cell surface protein atlasYesOnline
CSTEAhttp://comp-sysbio.org/cstea/Cell state transition expression and time-course gene expressionYesOnline
CYCLONEThttp://cyclonet.biouml.org/A database on cell cycle regulation in eukaryotesNoOnline
DAnCERhttp://wodaklab.org/dancer/Genes with chromatin modification of model organisms, and humanYesOnline
DASHRhttp://dashr2.lisanwanglab.org/Database of small human noncoding RNAsYesOnline
dbCRIDhttp://c1.accurascience.com/dbCRID/Database of chromosomal rearrangements in diseasesYesOnline
dbOrghttps://biodbnet-abcc.ncifcrf.gov/Provides downloadable files of organism wide conversionsYesOnline
NameURLBrief descriptionDownload of DataCurrent status
DisGeNEThttps://www.disgenet.org/Variant-disease associations and gene-disease associationsYesOnline
DRG TXomehttps://bbs.utdallas.edu/painneurosciencelab/sensoryomics/ drgtxome/Gene expression profiles across orthologous human and mouse genesYesOnline
EPConDBhttp://www.cbil.upenn.edu/node/90Novel pancreatic genes through the sequencing and analysisYesOnline
EPITRANShttp://epitrans.orgRepresents relationships between gene expression and epigeneticNoOffline
ESCAPE*http://www.maayanlab.net/ESCAPE/A mouse and human embryonic stem cells centered integrating dataYesOnline
ESTDABhttps://www.ebi.ac.uk/ipd/estdab/Data of HLA type, and immunologically characterised tumour cellsNoOnline
euL1dbhttp://eul1db.ircan.org/Retrotransposon insertion polymorphisms in healthy or pathological human samples and published in journals.YesOnline
EuroDiahttp://eurodia.vital-it.chGene expression performed on beta-cells of human, mouse and ratYesOnline
ExpEdithttps://bioinformatics.cineca.it/expedit/RNA editing user-specified sites supported by RNA-Seq experimentsYesOnline
F-SNPhttp://compbio.cs.queensu.ca/F-SNP/Identification of disease-causing SNPs in association studiesYesOffline
Fantom/EdgeExpresshttps://fantom.gsc.riken.jp/4/edgeexpress/view/#5558263Gene expression and miRNA using gene-centric and sub-networkYesOnline
FARNAhttps://www.cbrc.kaust.edu.sa/farna/?page=homencRNA information related to expression, pathways and diseasesNoOnline
FLJhttp://flj.lifesciencedb.jp/top/mRNA variations of human genome and cDNA sequencesYesOnline
G4LDBhttp://www.g4ldb.org/ci2/index.phpG-quadruplexes in human telomeres and gene promoter regionsNoOffline
GEMiCCLhttps://www.kobic.kr/GEMICCL/Gene expression and mutations in cancer cell linesYesOnline
GenAgehttp://genomics.senescence.info/genes/Gene expression in ageing genesYesOnline
Genatlashttp://www.genatlas.org/Gene expression with search by phenotype or ontologyYesOnline
Gene Microgliahttp://shiny.maths.usyd.edu.au/Ellis/MicrogliaPlotsGene expression in microglia in the aged human brainYesOnline
GeneHub-GEPIShttp://research-public.gene.com/Human and mouse gene expression patternsYesOffline
GeneNotehttps://genecards.weizmann.ac.il/cgi- bin/genenote/about_page.plFull-genome database of expression in healthy human tissuesNoOnline
GeneTidehttp://genecards.weizmann.ac.il/genetide/Human transcriptome and annotationNoOffline
GENThttp://medicalgenome.kribb.re.kr/GENT/Gene expression database of normal and tumor tissuesYesOffline
Globin Genehttp://globin.cse.psu.edu/Gene expression and variants in globin related genesNoOnline
GTEx*https://gtexportal.org/home/Gene expression with quantitative trait locus (eQTLs)YesOnline
H-ANGELhttp://www.jbirc.aist.go.jp/hinv/h-angel/Human anatomic gene expression libraryNoOffline
HAGRhttp://genomics.senescence.info/index.phpGene expression of human ageing using animal models and humanYesOnline
HCMDBhttp://hcmdb.i-sanger.com/indexHuman cancer metastasis. Contain gene expression dataYesOnline
Healthspanhttp://functional.domains/healthspan/Pathways and expression of health-associated gene interactionsNoOnline
Hembasehttp://hembase.niddk.nih.govErythroblast expressed sequenced tags and erythropoiesis genesNoOnline
NameURLBrief descriptionDownload of DataCurrent status
HGDPhttps://www.hagsc.org/hgdp/Gene expression in different human populationsYesOnline
HipScihttp://www.hipsci.org/Omics in human-induced pluripotent stem cellsYesOnline
HIVedhttp://hivlatency.erc.monash.edu/Proteins with differential expression during the human virus infectionsNoOnline
hmChIPhttp://jilab.biostat.jhsph.edu/database/cgi-bin/hmChIP.plChIP-chip and ChIPseq samplesYesOnline
HOMERhttp://bio.informatics.iupui.edu/homerDisease ontology, gene expression, and proteomics of tissuesNoOffline
HoTResDBhttp://hotresdb.bu.edu/microarray and NGS data from non-human primates’ modelsYesOnline
HPMRhttp://www.receptome.org/Transcriptome and Proteome informationsYesOnline
HPRDhttp://www.hprd.org/Human protein reference databaseNoOnline
HSFhttp://www.umd.be/HSF3/index.htmlHuman splice finderNoOnline
HuGE Navigatorhttps://phgkb.cdc.gov/PHGKB/hNHome.actionGenotype, phenotype, literature finder and variant mapperNoOnline
HuGEIndexhttps://www.hugeindex.org/Human gene expression indexYesOffline
Human Erythroblast Maturationhttps://cellline.molbiol.ox.ac.uk/eryth/cgi-bin/HEM.cgiMaturation expression patterns , comparisons, and gene queriesNoOnline
IGRhCellIDhttp://igrcid.ibms.sinica.edu.tw/cgi-bin/index.cgiIntegrated genomic resources of human cell linesYesOnline
Inner Ear Transcriptomehttps://www.tgen.org/patients/neurological-disorders/Coding and non-coding transcripts of the human inner earYesOnline
IntropolisIntropolisRNA-seq samples and exon-exon junctionsYesOnline
Islet Regulome Browserhttp://www.isletregulome.com/isletregulome/Enhancers and transcription factor binding sites in pancreatic progenitors and adult human pancreatic isletsNoOnline
Isobasehttp://cb.csail.mit.edu/cb/mna/isobase/Orthologous transcripts and functionally related proteinsYesOnline
ISOexpressohttp://wiki.tgilab.org/ISOexpresso/main.php?cat=aboutIsoform-level expression analysis in human cancerYesOnline
KERIShttp://igenomed.org/immune/Expression and gene responses to inflammation among speciesNoOffline
Linc2GOhttp://www.bioinfo.tsinghua.edu.cn/~liuke/Linc2GO/index. htmlExpression of human lincRNAYesOffline
Liverbasehttp://liverbase.hupo.org.cn/index2.jspProteome and transcriptome of liver samplesYesOnline
MetaQueryhttp://metaquery.docpollard.org/Quantitative analysis of specific genes in the human gut microbiomeYesOnline
MGEx-Udbhttp://resource.ibab.ac.in/MGEx-Udb/Uterus tissues gene expression data in human and animal modelsYesOnline
MiasDBhttp://47.88.84.236/Miasdb/index.phpGene expression and alternative splicing eventsYesOnline
microRNA bodyhttps://www.mirnabodymap.org/RT-qPCR data and miRNA annotation in normal and diseased tissuesYesOnline
MitoAgehttp://www.mitoage.info/Comparative analysis and gene expression of mtDNA genesYesOnline
MOPEDhttps://www.moped.proteinspire.org/Multi-omics profiling expression in normal and disease tissuesYesOffline
MSGenehttp://msgene.bioinfo-minzhao.org/Metastasis suppressor gene expressionYesOnline
NHGRI Projecthttps://research.nhgri.nih.gov/microarray/index.shtmlSet cDNA library clones from UniGene clustersNoOnline
NameURLBrief descriptionDownload of DataCurrent status
NHPRTRhttp://nhprtr.org/resources.htmlTranscriptome data of non-human primatesYesOnline
NREDhttp://jsm-research.imb.uq.edu.au/NREDGene expression of long ncRNAs in human and mouseYesOffline
OncomiRdbBhttp://tdb.ccmb.res.in/OncomiRdbB/index.htmGene and miRNA expression of cancer samplesNoOffline
ORTIhttp://orti.sydney.edu.au/index.htmlTranscription Factors and Target Genes (TGs)YesOnline
PEpiDhttps://wukong.tongji.edu.cn/pepidProstate cancer expression and epigenetic dataYesOffline
PhenoScannerhttp://www.phenoscanner.medschl.cam.ac.uk/Database of human genotype-phenotype associationsYesOnline
Primer Zhttp://grch37.genepipe.ncgm.sinica.edu.tw/primerz/beginD esign.doPCR primer design for human, mouse, or rat genes and human SNPsYesOnline
QMEANhttps://swissmodel.expasy.org/qmean/Web server for protein model quality estimationYesOnline
REDIportalhttp://srv00.recas.ba.infn.it/redidb/index.htmlRNA editing and RNA-seq experimentsYesOnline
RefExhttps://refex.dbcls.jp/index.php?lang=enReference gene expression for the functional analysis of genesyesOnline
RenalDBhttp://renaldb.uni-frankfurt.de/Whole transcriptomes, and lncRNAs of nephrology studiesNoOnline
Retinahttp://retina.tigem.it/Atlas of gene expression and gene co-regulation in human retinaYesOnline
RNALocatehttp://www.rna-society.org/rnalocate/Curated RNA subcellular localization in multiple biological processesYesOnline
scRNASeqDBhttps://bioinfo.uth.edu/scrnaseqdb/Tools for visualization of gene expression in single cellsYesOnline
SIEGEhttp://pulm.bumc.bu.edu/siegeDBExpression data from epithelial cells of the human intrathoracic airwayYesOffline
SIGNORhttps://signor.uniroma2.it/Signalling gene expression based on published scientific literatureYesOnline
SpermBasehttp://www.spermbase.org/Search.phpProvides large and small RNAseq data, total sperm and sperm headsYesOnline
Symatlashttp://symatlas.gnf.orgExpression patterns for predicted genes (human and mouse)YesOffline
The Matrisomehttp://matrisomeproject.mit.edu/Gene expression of extracellular matrix (ECM) proteinsYesOnline
The Mito browserhttp://mitochondria.matticklab.com/Human mitochondrial transcriptome of multiple cell lines and tissuesYesOffline
The RNA Editinghttp://srv00.ibbe.cnr.it/editing/Inosinome atlas from healthy individualsNoOffline
TiGERhttp://bioinfo.wilmer.jhu.edu/tiger/Tissue-specific gene expression and regulatory elementsYesOnline
TiProDhttp://tiprod.cbi.pku.edu.cn:8080/index.htmlHuman promoter sequences for which some functional featuresNoOffline
TiSGeDhttp://bioinf.xmu.edu.cn:8080/databases/TiSGeD/index.htm lTissue gene expression profiles from human, mouse and ratNoOffline
TISSUEShttps://tissues.jensenlab.org/SearchGene-tissue associations in human and mammalian model organismsYesOnline
tRFdbhttp://genome.bioch.virginia.edu/trfdb/Data of single-stranded RNA derived from mature or precursor tRNANoOnline
TRI_toolhttps://www.vin.bg.ac.rs/180/tools/tfpred.phpPrediction of protein–protein Interactions in transcriptional regulationNoOnline
TSEMhttps://hood-price.isbscience.org/research/tsem/Tissue specific encyclopedia of metabolismYesOnline
UMD TP53http://www.umd.be:2072/TP53 omics databaseYesOffline
NameURLBrief descriptionDownload of DataCurrent status
VirusMINThttps://mint.bio.uniroma2.it/virusmint/Interactions between human and viral proteinsYesOffline
VMHhttps://vmh.life/Human metabolism and genetics, microbial metabolism, nutrition, and diseasesYesOnline
WeGethttps://coexpression.cmbi.umcn.nl/Mammalian genes coexpressed with human gene set of interestYesOnline

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.

NameURLBrief descriptionDownload of DataCurrent status
1000Genomeshttp://www.internationalgenome.org/A deep catalogue of human genetic variationYesOnline
3DSNPhttp://cbportal.org/3dsnp/Analysis of human single nucleotide polymorphismsNoOnline
3Omicshttps://3omics.cmdm.tw/Transcriptomic, proteomic and metabolomic dataYesOnline
A Catalog of Human STR Variationhttps://strider.online/A catalog of STR variation individuals from 1000GenomesYesOnline
A catalog of enhancers in hESCshttp://www.medical-epigenomics.org/papers/barakat2018/Functional enhancers in human embryonic stem cellsNoOnline
ABShttps://www.crg.eu/en/programme/programmes-groups/bioinformatics- and-genomicsAnnotated regulatory binding sitesYesOnline
AceViewhttp://www.ncbi.nlm.nih.gov/IEB/Research/AcemblyQuality-filtered cDNA from human transcriptomesNoOnline
ActiveDriverDBhttps://github.com/reimandlab/ActiveDriverDB/issuesProteogenomics for interpreting human variantsYesOnline
Adsnhttp://adsn.ddnetbio.com/Single cell brain atlas in human Alzheimer’s diseaseYesOnline
AFNDhttp://www.allelefrequencies.net/Immune gene frequencies in worldwide populationsYesOnline
Albumin binding predictionhttp://albumin.althotas.com/Predicts serum albumin binding site of a ligandYesOffline
AlloFinderhttp://mdl.shsmu.edu.cn/ALF/Exogenous allosteric modulators characterizationYesOnline
AMAZONIAhttp://amazonia.transcriptome.eu/Atlas of transcriptome with specific tissues or cellsYesOnline
AmtDBhttps://amtdb.org/Data of ancient human mitochondrial genomesNoOnline
ANCO-GeneDBhttps://bioinfo.uth.edu/ancogenedb/Multi Omics and drug-target data with literature miningYesOnline
Aneurysm DBhttp://www.cuilab.cn/agdHuman, mouse and rat aneurysm-gene associationsYesOnline
AnnoLnchttp://annolnc.cbi.pku.edu.cn/index.jspAnnotating data of novel human lncRNAsYesOffline
AVPpredhttp://crdd.osdd.net/servers/avppred/Antiviral peptide prediction serverYesOnline
BDOhttp://bioportal.bioontology.org/ontologies/BDOBone dysplasia ontology with omics and clinical dataNoOnline
BEConhttps://redgar598.shinyapps.io/BECon/Relationship between blood and brain methylationYesOnline
BioGPShttp://biogps.org/Annotation of gene and protein functionYesOnline
BrainScopehttps://brainscope.lumc.nl/brainscopeSpatial and temporal human brain transcriptomeNoOnline
NameURLBrief descriptionDownload of DataCurrent status
CADD*https://cadd.gs.washington.edu/Predict impact of insertion/deletions genomic variantsYesOnline
CAGE Basic Viewerhttp://fantom31p.gsc.riken.jp/cage/Cap-analysis gene expression for human and mouseYesOffline
CanGEMhttp://www.cangem.org/Microarray, CNV and genomic in cancerNoOffline
CCBhttps://cellcycle.renci.org/Timeline of molecular events in cell cycle progressionYesOnline
CGMDhttp://cgmd.in/Cancer annotations and molecular descriptionsNoOffline
ChIPSummitDBhttp://summit.med.unideb.hu/summitdb/index.phpTF binding sites and the topological arrangementsYesOnline
Chorogenomehicexplorer.readthedocs.ioHi-C data analysis from processing to visualizationNoOnline
Chr7 Annotationwww.chr7.org/Sequence, genes, and other annotations from Chr7YesOnline
Cichlidshttp://cichlids.biosci.gatech.edu/Evolutionary relationship of each cichlid proteinYesOnline
CITGeneDBhttp://citgenedb.yubiolab.orgCold-Induced thermogenesis human and mouse genesYesOnline
CLIMAhttp://bioinformatics.hsanmartino.it/clima2/Cell line integrated molecular and Identification toolYesOnline
ClinicalTrialshttps://clinicaltrials.gov/Collects public and private clinical studiesNoOnline
ClinVarhttps://www.ncbi.nlm.nih.gov/clinvar/Data about germline and somatic variantsYesOnline
ComiRhttp://www.benoslab.pitt.edu/comir/Combinatorial miRNA target predictionYesOnline
CRUNCHhttp://crunch.unibas.ch/crunch/ChIP-seq data analysis of human and animal modelsYesOnline
cWordshttp://servers.binf.ku.dk/cwords/Human miRNA and differential expression toolYesOnline
dbDSMhttp://bioinfo.ahu.edu.cn:8080/dbDSM/index.jspDatabase of deleterious synonymous mutationNoOnline
dbEMThttp://dbemt.bioinfo-minzhao.org/Epithelial-mesenchymal transition related genesYesOnline
DBETHwww.hpppi.iicb.res.in/btox/Genomic database for bacterial exotoxinsYesOnline
DBGChttp://bminfor.tongji.edu.cn/dbgc/index.doHuman gastric cancer-related data resourcesYesOffline
dbMAEhttps://mae.hms.harvard.edu/Monoallelic expression in genome-wide studiesNoOnline
dbNSFPhttps://sites.google.com/site/jpopgen/dbNSFPPredict impact of non-synonymous single-nucleotide and splice- site variantsYesOnline
Decryptorhttp://decryptor.imtm.cz/Proteome analysis for presence of point alterationsYesOffline
DisGeNET*https://www.disgenet.org/Repository of variant-disease associationsYesOnline
DOhttps://disease-ontology.org/Ontologies, phenotypes, and related termsYesOnline
Doc2Hpohttps://impact2.dbmi.columbia.edu/doc2hpo/Human Phenotype Ontology concept curationYesOnline
Dr.VIShttp://www.bioinfo.org/drvisHuman disease-related viral integration sitesNoOffline
DREMECELShttp://www.bioinfoindia.org/dremecels/Base excision and mismatch repair mechanisms associated human malignanciesYesOffline
E-RNAihttps://www.dkfz.de/signaling/e-rnai3//dsRNA constructs suitable for RNAi experimentsNoOnline
NameURLBrief descriptionDownload of DataCurrent status
EBIhttps://www.ebi.ac.uk/Platform of biological sciencesYesOnline
eDGARhttp://edgar.biocomp.unibo.it/gene_disease_db/index.htmlDisease-gene associations and Relationships among genesYesOnline
EpiACDevhttps://cotney.research.uchc.edu/data/Epigenomic atlas of craniofacial developmentYesOnline
EpimiRBasehttps://www.epimirbase.eu/miRNA-epilepsy association from curated literatureYesOnline
Eponinehttps://www.sanger.ac.uk/about/who-we-areTranscription start sites mammalian genome sequenceYesOnline
ERGRhttp://bioinfo.vipbg.vcu.edu/ERGR/Published ethanol-related gene studiesNoOffline
Exome Variant Serverhttps://evs.gs.washington.edu/EVS/Exome sequencing from human tissuesYesOnline
FirstEFhttp://rulai.cshl.org/tools/FirstEF/5′ terminal exon and promoter prediction programYesOnline
G2Cdbhttp://www.genes2cognition.orgData of synapse proteins in physiology and diseaseYesOnline
G2Dhttp://g2d2.ogic.ca/Scans a region for genes related to diseasesYesOffline
GENCODEhttps://www.gencodegenes.org/human/Annotation for the human and mouse genomesYesOnline
GenePAtlashttp://biocc.hrbmu.edu.cn/GPA/Collection of genes, miRNAs and lncRNAs perturbed by knockdown or overexpressionYesOnline
Gene Set Builderhttp://www.cisreg.ca/gsb/Personalized sets of genesYesOnline
Gene Wikihttp://en.wikipedia.org/wiki/Portal:Gene_WikiGathers Wikipedia articles about human genesNoOnline
GeneCardsgenecards.org/Biomedical knowledgebase of human biological dataNoOnline
Geneimprinthttp://www.geneimprint.com/site/homeImprinting genes from different species and humanYesOnline
GeneLochttps://genecards.weizmann.ac.il/geneloc/about_new.shtmlThe integrated map for human chromosomesYesOnline
GeneMapwww.ncbi.nlm.nih.gov/genemapMapping, annotations and associated gene dataYesOnline
GeneSeekerhttp://www.cmbi.ru.nl/GeneSeeker/Candidate genes related to a genetic disorderNoOffline
Genome Refhttps://www.ncbi.nlm.nih.gov/grc/report-an-issueReference genomes consortium of multiple speciesYesOnline
GUIDEShttp://guides.sanjanalab.org/#/CRISPR knockout to target human or mouse genesYesOnline
H-InvDBhttp://www.h-invitational.jp/Human-transcriptome and alternative splicingYesOnline
HADbhttp://autophagy.lu/index.htmlHuman autophagy databaseNoOnline
Harmonizome*amp.pharm.mssm.edu/Harmonizome/Datasets about genes and proteinsYesOnline
Harvesterhttp://harvester.fzk.de/harvester/Bioinformatic data and servers for human proteinsNoOffline
HelmCoPhttp://www.nematode.net/helmcop.htmlComparative genomic data from plant, animal and human helminthsYesOnline
HERODhttp://bidd2.nus.edu.sg/herod/index.phpHuman ethnic and regional specific omicsYesOffline
HERVdhttps://herv.img.cas.cz/Human endogenous retroviruses dataNoOnline
HExpoChemhttp://www.cbs.dtu.dk/services/HExpoChem-1.0/Explore human health risk from chemical exposureNoOnline
NameURLBrief descriptionDownload of DataCurrent status
HGMDhttp://www.hgmd.cf.ac.uk/ac/index.phpThe human gene mutation databaseNoOnline
HGNChttps://www.genenames.orgNomenclature for all genes of the human genomeYesOnline
hLGDBhttp://lysosome.unipg.it/Human lysosome miRNA databaseYesOnline
HMDADhttp://www.cuilab.cn/hmdadHuman microbe-disease associationYesOnline
HMMER3https://www.ebi.ac.uk/Tools/hmmer/Homologs sequences, and protein alignmentsYesOnline
HMPhttps://portal.hmpdacc.org/Human Microbiome ProjectYesOnline
HmtDBhttps://www.hmtdb.uniba.it/Mitochondrial genomes application of MtoolBox NGSYesOffline
HNOCDBhttp://gyanxet.com/hno.htmlHead neck and oral cancer genomic dataNoOffline
HOMDhttp://www.homd.orgBacterial species present in the aerodigestive tractYesOnline
HomozygosityMapperhttp://www.homozygositymapper.org/A web base approach to homozygosity mappingYesOnline
hORFeome Databasehttp://horfdb.dfci.harvard.edu/Genome-scale human ORFeome collectionsNoOnline
HPOhttps://hpo.jax.org/app/The human phenotype ontology diseaseYesOnline
HUMAhttps://huma.rubi.ru.ac.za/Analyze variation in protein sequence and structuresYesOnline
Human Transporter Databasehttp://htd.cbi.pku.edu.cnMolecular and genetic information of transporters for personalized medicineNoOffline
HumanMinehttp://www.intermine.orgGenes, proteins, pathways, ontology, or literatureYesOnline
HumCFShttps://webs.iiitd.edu.in/raghava/humcfs/index.htmlCurated human chromosomal fragile sitesNoOnline
HydPredhttp://lishuyan.lzu.edu.cn/hydpred/Identification of protein hydroxylation sitesNoOnline
HyperCLDBhttp://bioinformatics.hsanmartino.it/hypercldb/The hypertextual version of the Cell Line DatabaseNoOnline
IDADE2http://bass.uib.es/~jaume/IDADE2/https/index.htmlAdult age estimation of human skeletal remainsYesOnline
IGSRhttps://www.internationalgenome.org/1000-genomes-project-publicationsThe largest open collection of human variation dataYesOnline
iLoc-Cellhttp://www.jci-bioinfo.cn/iLoc-HumSubcellular locations of proteins with multiple sitesNoOnline
IMGThttp://www.imgt.org/ImMunoGeneTics information systemYesOnline
Integr8https://www.ebi.ac.uk/integr8Data of complete genomes and proteomesYesOnline
integrated gene cataloghttp://meta.genomics.cn/meta/homeReference catalog of the human gut microbiomeNoOffline
IntSplicehttps://www.med.nagoya-u.ac.jp/neurogenetics/IntSplice/Predict SNV impact in introns of the human genomeNoOnline
InvFESThttp://invfestdb.uab.cat/Non-redundant human polymorphic inversions dataNoOnline
ITHANEThttps://www.ithanet.eu/db/ithagenesVariations, epidemiology, and and HbF inducers infoNoOnline
Kaviarhttp://db.systemsbiology.net/kaviar/cgi-pub/Kaviar.plCompilation of human SNVs dataYesOnline
lncRNAtorhttp://lncrnator.ewha.ac.kr/Multi Omics of animal models and humanNoOffline
NameURLBrief descriptionDownload of DataCurrent status
MAHMIhttp://mahmi.org/Mechanism of action of the human microbiomeNoOnline
MARomehttp://196.1.114.46:8080/MARome/indexScaffold and Matrix Attachment Regions in GenomeYesOnline
MDWebhttp://mmb.irbbarcelona.org/MDWeb2/Web-based platform of molecular dynamicsNoOnline
MEME Suitehttp://meme-suite.org/DNA motifs, transcription factor binding sites or protein domains search toolYesOnline
Mendel,MDhttps://mendelmd.org/Identify disease causing variants in human exome/genome sequencing dataYesOffline
MetaQueryhttp://metaquery.docpollard.org/Data of specific genes in the human gut microbiomeYesOnline
MetaRankerhttp://www.cbs.dtu.dk/services/MetaRanker/Prioritize the entire protein-coding part of the human genome based on heterogeneous user-specified data setsYesOnline
MGDBhttp://bioinfo.ahu.edu.cn:8080/Melanoma/Melanoma genomic and transcriptomic dataYesOnline
microDoRhttp://reprod.njmu.edu.cn/cgi-bin/microdor/index.pyPredict Human miRNA-mediated gene silencingYesOnline
miR2GOhttp://compbio.uthsc.edu/miR2GO/home.phpComparative analyses of human miRNA functionsYesOnline
mLASSO-Humhttp://bioinfo.eie.polyu.edu.hk/mLASSOHumServer/index.htmlHuman-protein subcellular localization predictorNoOnline
MSEAhttps://www.metaboanalyst.ca/Enrichment analyses for metabolomic studiesYesOnline
mTCTScanhttp://mulinlab.org/mtctscanAnalysis of mutations affecting cancer drug sensitivity based on individual genomic profilesYesOnline
mtDNA-Servehttps://mtdna-server.uibk.ac.at/index.htmlmtDNA NGS analysis, heteroplasmy detection, and haplogroup- based contamination deconvolutionYesOnline
Mutalyzerhttps://mutalyzer.nl/Variant effect analysisNoOnline
MutPredhttp://mutpred.mutdb.org/Predicts molecular cause of diseaseNoOnline
NCBIhttps://www.ncbi.nlm.nih.gov/Supplies several online resources for biological informationYesOnline
NetChophttp://www.cbs.dtu.dk/services/NetChop/Cleavage site analysis of the human proteasomeNoOnline
NetGene2http://www.cbs.dtu.dk/services/NetGene2/Predictions of splice sitesNoOnline
NetNGlychttp://www.cbs.dtu.dk/services/NetNGlyc/Predict N-Glycosylation sites in human proteinsNoOnline
Netviewhttp://netview.tigem.it/netview_project/netview_tools.htmlHuman and mouse gene regulatory networksYesOnline
NGDhttp://www.nencki-genomics.orgNencki Genomics Database TFBS motifsYesOnline
NHGRI Projecthttps://research.nhgri.nih.gov/microarray/index.shtmlProtocols, analysis and resourcesNoOnline
NIFhttps://neuinfo.org/Multi omics and neuroscience portal of WikipediaNoOnline
OKdbhttp://okdb.appliedbioinfo.net/Function, expression pattern and regulation of genes expressed in the ovaryYesOnline
NameURLBrief descriptionDownload of DataCurrent status
OMIMhttps://omim.org/Catalog of mendelian diseasesYesOnline
OncoDB.HCChttp://oncodb.hcc.ibms.sinica.edu.tw/index.htmOncogenomic database for Hepatocellular CarcinomaYesOnline
ONTOADhttp://bioportal.bioontology.org/ontologies/ONTOADText mining disease ontologyNoOnline
Open Targets Platformhttps://www.targetvalidation.org/Systematic drug target identification and prioritisationYesOnline
OrthoDiseasehttp://orthodisease.sbc.su.se/cgi-bin/index.cgiGene ortholog between human and other speciesYesOnline
OsteoporosAtlashttp://biokb.ncpsb.org/osteoporosis/index.phpOsteoporosis-related gene databaseYesOnline
OverGeneDBhttp://overgenedb.amu.edu.plProtein overlapping genes in Human and MouseYesOnline
p53FamTaGhttp://www2.ba.itb.cnr.it/p53FamTaG/p53 family target genesNoOffline
PanelApphttps://panelapp.genomicsengland.co.uk/Virtual gene panels related to human disordersYesOnline
PaPIhttp://papi.unipv.it/Classification of variantsNoOnline
PathogenFinderhttps://cge.cbs.dtu.dk/services/PathogenFinder/Prediction of a bacteria’s pathogenicity in human hostsNoOnline
PDIDhttp://biomine.cs.vcu.edu/servers/PDID/index.phpProtein-drug interactions in the structural human proteomeYesOnline
PDZPepInthttp://modpepint.informatik.uni-freiburg.de/PDZPepInt/Input.jspPredict binding peptides of PDZ domains in human, mouse, fly and wormYesOnline
Pedicanhttp://pedican.bioinfo-minzhao.org/Pediatric cancer gene databaseYesOnline
PepPSyhttp://peppsy.genouest.org/queryA gene expression-based prioritization systemYesOnline
PGPhttps://www.personalgenomes.org/Interpretation of genomic traits in human tissuesYesOnline
PharmGKBhttps://www.pharmgkb.org/Pharmacogenomic information databaseYesOnline
PhenoHMhttps://phenome.cchmc.org/phenoBrowser/PhenomePhenome-genome cross species identification of genes associated with orthologous phenotypesYesOnline
Phenolyzerhttp://phenolyzer.wglab.org/Discovering genes based on user-specific disease/phenotype termsYesOnline
PhenomicDBhttps://en.wikipedia.org/wiki/PhenomicDBA multi-organism phenotype-genotype databaseYesOnline
Phenomizerhttp://compbio.charite.de/phenomizer/Differential diagnosis in the field of human geneticsYesOnline
PhenoScannerhttp://www.phenoscanner.medschl.cam.ac.uk/Database of human genotype-phenotype associationsYesOnline
PhenoTipshttps://phenotips.com/Phenotype information of genetic disordersYesOnline
PhosphOrthologhttp://www.phosphortholog.com/Orthologous protein post-translational modificationsYesOnline
PICKLEhttp://www.pickle.gr/Direct human protein-protein interactions networkYesOffline
PINTAhttps://securehomes.esat.kuleuven.be/~bioiuser/pinta/input.phpGenome-wide protein-protein interaction networkYesOffline
Piphillinhttp://piphillin.secondgenome.com/Metagenomic by Inference from Human MicrobiomesYesOnline
PolyPhen2http://genetics.bwh.harvard.edu/pph2/Variant effect prediction toolNoOnline
NameURLBrief descriptionDownload of DataCurrent status
PolySearch2http://polysearch.cs.ualberta.ca/indexDiscovering associations between human diseases, genes, drugs, metabolites, toxins and moreYesOnline
POMOhttps://ruoho.uta.fi/wp/pomo/Plotting Omics-associations for Multiple OrganismsNoOffline
PredictSNP2http://loschmidt.chemi.muni.cz/predictsnp2/Variant effect prediction toolYesOnline
Primer Zhttp://grch37.genepipe.ncgm.sinica.edu.tw/primerz/beginDesign.doInterface for PCR primer designYesOnline
PrimerStationhttps://ps.cb.k.u-tokyo.ac.jp/Multiplex genomic PCR primer design toolYesOnline
Progenetixhttps://www.progenetix.org/Curated oncogenomic databaseNoOnline
ProteomicsDBhttps://www.proteomicsdb.org/proteomicsdb/#overviewEnables navigation of proteomesNoOnline
ProteoREhttp://www.proteore.org/Proteomics and Transcriptomic Research EnvironmentYesOnline
PRShttp://mrcieu.mrsoftware.org/PRS_atlas/Polygenic burden associations in the human phenomeNoOnline
pseudoMaphttp://pseudomap.mbc.nctu.edu.tw/php/index.phpInformation of pseudogenesNoOffline
PubGenehttps://www.pubgene.com/Identification of siRNA mechanisms in pseudogenesYesOnline
QMEANhttps://swissmodel.expasy.org/qmean/Qualitative model energy analysisYesOnline
QTRGhttps://geneticmedicine.weill.cornell.edu/genomeReference genome research in the Qatari populationNoOnline
Quokkahttp://quokka.erc.monash.edu/Prediction of kinase family-specific phosphorylationNoOnline
R spiderhttp://www.bioprofiling.de/gene_list.htmlKEGG and Reactome pathway analysisNoOnline
RAARhttp://www.lerner.ccf.org/cancerbio/heemers/RAAR/Regulators of Androgen Action ResourceNoOnline
RasMolhttp://www.bernstein-plus-sons.com/software/rasmol/3D structure viewer, web browser helper applicationNoOnline
RatMinehttps://omictools.com/ratmine-toolOmics data of human, mouse, rat and other organismsYesOnline
RefGenehttps://omictools.com/refgene-toolReference genomes and annotationYesOnline
REGenehttp://regene.bioinfo-minzhao.org/Regeneration Gene databaseYesOnline
Repositivehttps://discover.repositive.io/help/searching-for-dataMultiple repositories for the human genomic dataNoOffline
RIDDLEhttp://www.functionalnet.org/riddle/Functional network and gene set analysisNoOnline
RSSsitehttps://www.itb.cnr.it/rss/Recombination signal sequences in human and mouseYesOnline
Saqqaq projecthttp://genomebrowser.binf.ku.dk/cgi- bin/hgTracks?db=hg18&position=chrX%3A151073054- 151383976&hgsid=80767_Yr7Y1ao0Y92AKta3Whb9lqcaEfLgProvides data about the genome sequence of ancestor humanYesOffline
ScaPDhttp://bioinfo.wilmer.jhu.edu/ScaPD/Database for human scaffold proteinsNoOnline
sciAIhttps://sci.ai/Biomedical papers, trials, and projects and interlinks research findings in a semantic graphYesOnline
SEGELhttp://www.chengfeng.info/smoking_database.htmlSmoking Effects on Gene Expression of LungNoOnline
NameURLBrief descriptionDownload of DataCurrent status
Semantic Body Browserhttp://sbb.cellfinder.org/Visualising expression profiles by means of semantically annotated illustrationsYesOnline
SNP2TFBShttps://ccg.epfl.ch/snp2tfbs/Variant effect prediction toolNoOnline
SNPDelScorehttps://www.ncbi.nlm.nih.gov/research/snpdelscore/Deleterious effects of noncoding variantsYesOnline
SNPs GOhttps://snps-and-go.biocomp.unibo.it/snps-and-go/index.htmlVariant effect prediction toolYesOnline
SPEEDhttps://speed2.sys-bio.net/A signaling pathway annotation enrichment analysisYesOnline
SpindlePhttp://www.cbs.dtu.dk/services/SpindleP/Neural networks prediction of whether a human gene is located at the meiotic spindleYesOnline
StemCellNethttp://stemcellnet.sysbiolab.eu/Molecular networks in the context of stem cell biologyYesOnline
StSNPhttp://ilyinlab.org/StSNP/Structure SNP variant effect prediction toolNoOnline
SubPhosPredhttp://bioinfo.ncu.edu.cn/SubPhosPred.aspxPhosphorylation sites in subcellular compartmentsNoOnline
SugarBindDBhttps://sugarbind.expasy.org/Glycan binding of human pathogen lectins and adhesins dataNoOnline
SURFYhttp://wlab.ethz.ch/surfaceome/Visualize the human surface proteome (surfaceome) and load your own expression dataYesOnline
T1Dbasehttp://www.t1dbase.orgResources for study of susceptibility of T1 DiabetesNoOnline
T2D-Dbhttp://t2ddb.ibab.ac.inPathogenesis of T2 diabetes in human, mouse and ratYesOnline
TCGA Portalhttps://www.cancer.gov/Multi omic cancer and clinical dataYesOnline
UCSCBrowserhttps://genome.ucsc.edu/cgi-bin/hgGatewayMulti omic web resources across speciesYesOnline
UK10Khttps://www.uk10k.org/Whole genomes in the British populationYesOnline
UMD-Predictorhttp://umd-predictor.eu/index.phpIdentify potential pathogenic variationsYesOnline
UniReDhttp://bioinformatics.med.uoc.gr/unired/Annotation and non-redundant Human or Mouse proteins from UniProtKB/Swiss-ProtNoOnline
VarSomehttps://varsome.com/Compiles human genomic variantsNoOnline
VDJsolverhttp://www.cbs.dtu.dk/services/VDJsolver/Human immunoglobulin VDJ recombination analysisNoOnline
VectorBasehttps://www.vectorbase.org/genomesVectors and other organisms related with diseasesYesOffline
Vegahttp://vega.sanger.ac.ukVertebrate Genome AnnotationYesOnline
Vega Browserhttp://vega.archive.ensembl.org/index.htmlMajor histocompatibility complex (MHC) annotation and LCR across speciesNoOnline
VeryGenehttp://www.verygene.comAnnotation of tissue-specific/enriched genesNoOnline
VHLdbhttp://vhldb.bio.unipd.it/Interactors and mutations of the human von Hippel-Lindau tumor suppressor proteinNoOnline
XenoSitehttps://swami.wustl.edu/xenosite/Predictions about the human in vivo metabolism of small moleculesNoOffline
NameURLBrief descriptionDownload of DataCurrent status
Zikv-CDBhttp://zikadb.cpqrr.fiocruz.brData of genes associated with ZIKV, their expression and interaction with miRNAs and snoRNAsYesOnline

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.

NameURLBrief descriptionDownload of DataCurrent status
Antagomirbasehttp://bioinfopresidencycollegekolkata.edu.in/antagomirs.htmlDesign antagomirs using GC content and secondary structuresNoOffline
CancerNethttp://bis.zju.edu.cn/CancerNet/Cancer-specific miRNA and protein-protein interactionsYesOnline
CircuitsDBhttp://penelope.unito.it/circuitsdb2miRNA/TF regulatory circuits in the human and mouse genomesYesOffline
ComiRhttp://www.benoslab.pitt.edu/comir/Combinatorial miRNA target predictionYesOnline
CSmiRTarhttp://cosbi.ee.ncku.edu.tw/CSmiRTar/Predicted targets of human and mouse miRNAsNoOffline
cWordshttp://servers.binf.ku.dk/cwords/Gene expression analysis and prioritization of miRNAYesOnline
DASHRhttp://dashr2.lisanwanglab.org/sncRNA and miRNA predictionYesOnline
dbDEMChttps://www.picb.ac.cn/dbDEMC/Differentially expressed miRNAs in human cancersYesOnline
dbSMRhttp://miracle.igib.res.in/dbSMRPredicted and validated miRNA sites and SNPs in human genomeYesOffline
DES-ncRNAhttps://www.cbrc.kaust.edu.sa/des_ncrna/miRNA and lncRNAs based on literature-miningYesOnline
DMDhttp://sbbi.unl.edu/dmd/Published and novel miRNAs discovered in dietary resourcesYesOffline
dPOREhttp://cbrc.kaust.edu.sa/dporemiRNA genes, SNPs, and predicted TFBSs in the promoter regionsNaOffline
E-RNAihttps://www.dkfz.de/signaling/e-rnai3//Designing and evaluating dsRNA constructs for RNAi experimentsNoOnline
exoRBase*http://www.exoRBase.orgcircRNA, IncRNA and mRNA in human blood exosomesYesOnline
ExprTargetDBhttp://www.scandb.org/apps/microrna/miRNA-mediated gene regulation in the HapMap LCLsYesOnline
fat_depositionhttp://www.integratomics-time.com/fat_depositionHuman, cattle, rat, and mice miRNA related to obesityNoOffline
GEDhttp://gametsepi.nwsuaflmz.com/DNA methylation, histone modification and miRNA regulation in gametogenesisYesOnline
Gene Perturbation Atlashttp://biocc.hrbmu.edu.cn/GPA/Collection of transcriptome profiles genes, miRNAs and lncRNAsYesOnline
hLGDBhttp://lysosome.unipg.it/miRNA and Transcription Factors in Lysosomal Storage DiseasesYesOnline
HLungDBhttp://www.megabionet.org/bio/hlungmiRNAs and clinical information in Lung cancerYesOffline
HMDDhttp://www.cuilab.cn/hmddExperiment-supported evidence for miRNA and disease associationsYesOnline
HumanViCehttp://gyanxet-beta.com/humanvice/ceRNA and miRNA networks in virus infected human cellsYesOnline
IntmiRhttps://www.rgcb.res.in/intmir/Intronic miRNAs of human and mouse genomeYesOnline
IRBase/IRFinderhttp://mimirna.centenary.org.au/irfinder/database/Online database of intron retention and intronic miRNAsNoOnline
NameURLBrief descriptionDownload of DataCurrent status
Lnc2Methhttp://bio-bigdata.hrbmu.edu.cn/Lnc2Meth/lncRNAs and associated DNA methylation in diseases and cancerYesOnline
LncATLAShttp://lncatlas.crg.eu/lncRNA in human cells based on RNA-sequencing datasetsYesOnline
lnCeDBhttp://gyanxet-beta.com/lncedb/List lncRNAs that can potentially act as ceRNAsYesOnline
LNCeditinghttp://bioinfo.life.hust.edu.cn/LNCediting/Adenosine-to-Inosine editing sites in lncRNAs across human, rhesus, mouse, and flyYesOnline
LNCipediahttps://lncipedia.org/Function of RNA editing in lncRNA and miRNAYesOnline
LncRBasehttp://bicresources.jcbose.ac.in/zhumur/lncrbase/Overlapping small noncoding RNAs, associated Repeat Elements, methylation, and lncRNA promoter informationYesOnline
LncRNA2Functionhttp://mlg.hit.edu.cn/lncrna2functionAnnotate functionally a set of human lncRNAs of interestYesOffline
lncRNAMaphttp://lncrnamap.mbc.nctu.edu.tw/php/lncRNAs, miRNA, and siRNAs annotations and analysisYesOffline
lncRNASNPhttp://bioinfo.life.hust.edu.cn/lncRNASNP#!/Data of SNP effects on lncRNA structure and lncRNA:miRNA bindingYesOnline
lncRNAtorhttp://lncrnator.ewha.ac.kr/Expression profile, (binding) proteins, integrated sequence curation, evolutionary scores, and coding potential of lncRNAsNoOnline
LncRNAWikihttp://lncrna.big.ac.cn/index.php/Main_PageCommunity-based curation and collection of information on lncRNAsNoOnline
lncRNomehttp://genome.igib.res.in/lncRNomeBiologically oriented knowledgebase for lncRNAs in humansNoOnline
MethmiRbasehttps://madlab.cpe.ku.ac.th/TR2/?itemID=108747Experimentally verified cancer-associated miRNA target genesYesOnline
microDoRhttp://reprod.njmu.edu.cn/cgi-bin/microdor/index.pymiRNA-mediated gene silencing: mRNA degradation or translational repressionYesOnline
microPIRhttp://www4a.biotec.or.th/micropir2Predicted miRNA target sites within human promoter sequencesYesOffline
microRNA.orghttp://www.microrna.org/microRNA target predictions and expression profiles in mammalsYesOnline
microTranspoGenehttp://transpogene.tau.ac.il/Human, mouse, zebrafish and nematode miRNAs derived from Transposable elementsYesOffline
miR-EdiTarhttp://microrna.osumc.edu/mireditar/Prediction of miRNA binding sitesNoOnline
miR-hosthttp://www.integratomics-time.com/miR-host/catalogInformation of intragenic miRNAs in human, mouse, and chickenYesOffline
miR2Diseasehttp://www.miR2Disease.orgRepository for miRNA deregulation in various human diseasesYesOnline
miR2GOhttp://compbio.uthsc.edu/miR2GO/home.phpComparative analyses of human miRNA functionsYesOnline
miRCancerhttp://mircancer.ecu.edu/Collection of miRNA expression profiles in various human cancersYesOnline
miRDB*http://mirdb.org/Resource for miRNA target prediction and functional annotationsYesOnline
mirDIPhttp://ophid.utoronto.ca/mirDIP/Integrative score assigned to each unique miRNA–target interactionYesOnline
miREnvironmenthttp://cmbi.hsc.pku.edu.cn/mirenData of miRNA characteristics have roles in miRNA–EFs interactionsYesOffline
miRGatehttp://mirgate.bioinfo.cnio.es/miRGate/miRNA and gene isoforms lists of human, mouse and ratYesOnline
NameURLBrief descriptionDownload of DataCurrent status
miRGenhttp://carolina.imis.athena- innovation.gr/diana_tools/web/index.php?r=mirgenv3Map of transcription factor-microRNA interactions for multiple tissues and cell-lines in human and mouseYesOnline
MirGeneDBhttps://mirgenedb.org/Annotation of vertebrate miRNA Genes and evolutionary analysisYesOnline
miRNA TF loophttps://rth.dk/resources/tfmirloop/Regulatory network containing loop motifs for human and mouse using predicted miRNA and transcription factor binding sitesYesOnline
miRNAMaphttp://mirnamap.mbc.nctu.edu.tw/Information of miRNAs and target sites in metazoan genomesYesOnline
miRPathDBhttps://mpd.bioinf.uni-sb.de/miRNA pathway regulation, gene ontologies and other categoriesYesOnline
MirSNPhttp://cmbi.bjmu.edu.cn/mirsnpPolymorphisms altering miRNA target sites, miRNA-related SNPs in GWAS and eQTLsYesOnline
miRStarthttp://mirstart.mbc.nctu.edu.tw/Data source of human microRNA transcription start sitesNoOffline
miRvarhttp://genome.igib.res.in/mirlovdA Comprehensive database for genomic variations in miRNAsYesOnline
miRWalkhttp://mirwalk.umm.uni-heidelberg.de/Predict miRNA interactions from existing miRNA-target resourcesYesOnline
PITAhttps://genie.weizmann.ac.il/pubs/mir07/mir07_prediction.htmlLists of predicted microRNA targets in worm, mouse, fly and humanYesOnline
Polymirtshttp://compbio.uthsc.edu/miRSNP/Functional impact of genetic polymorphisms in miRNA seed regions and miRNA target sitesYesOnline
PuTmiRhttps://www.isical.ac.in/~bioinfo_miu/TF-miRNA/TF-miRNA.htmlDirect and indirect regulation of human miRNAsYesOnline
RenalDBhttp://renaldb.uni-frankfurt.de/Human, mice, zebrafish lncRNAs in nephrotic tissues and cellsNoOnline
S-MEDhttps://www.oncomir.umn.edu/SMED/basic_search.phpmiRNA expression in various human sarcoma typesYesOnline
SlideBasehttp://slidebase.binf.ku.dk/microRNAs expressed/used in a specified set of cells/tissuesYesOnline
The Functional lncRNA Databasehttp://www.valadkhanlab.org/databaseA repository of mammalian lncRNA that have been experimentally shown to be both non-coding and functionalNoOnline
TissueAtlashttps://ccb-web.cs.uni-saarland.de/tissueatlas/An atlas of miRNA expression in multiple human tissuesYesOnline
TriplexRNAhttps://triplexrna.org/Human genes or miRNAs in RNA triplexesYesOnline
TUMIRhttp://www.ncrnalab.com/TUMIR/Validated resource of microRNA deregulation in various cancersYesOnline
UCbase & miRfunchttp://microrna.osu.edu/.UCbase4Correlation between miRNAs, ultraconserved sequences and the disorders related to their aberrant expressionYesOffline
UGAHashhttp://ugahash.uni-frankfurt.de/lncRNAs resourcesNoOnline
Vir-Mir db*http://alk.ibms.sinica.edu.tw/cgi-bin/miRNA/miRNA.cgipredicted viral miRNA candidate hairpinsYesOnline
NameURLBrief descriptionDownload of dataCurrent status
2D-PAGEhttp://web.mpiib-berlin.mpg.de/cgi-bin/pdbs/2d- page/extern/index.cgi2-DPAGE maps, representing proteomes of various speciesYesOnline
AMPAD Knowledge Portalhttps://www.synapse.org/#!Synapse:syn2580853/wiki/409840Aging’s Alzheimer’s disease translational researchNoOnline
BioCartahttp://www.biocarta.com/Diagram library displaying gene interactions in pathwaysNoOnline
BRDhttps://brd.nci.nih.gov/brd/Review articles of human Biospecimen ScienceNoOnline
Calcium Gene Databasehttp://cagedb.uhlenlab.org/Mapping genes for calcium signaling and their associated human genetic disordersYesOnline
CaspDBhttp://caspdb.sanfordburnham.orgPotential cleavage sites in a set of all human proteinsNoOffline
CaspNeuroDhttp://caspdb.sanfordburnham.org/caspneurod.phpPredicted caspase cleavage sites in human proteins associated with Neurological DiseasesNoOffline
CCSB Interactomehttp://interactome.dfci.harvard.edu/Interactomes and phenotypes in human diseaseYesOnline
ChemProthttp://potentia.cbs.dtu.dk/ChemProt/Compilation of chemical-protein-disease annotation resourcesYesOffline
CIDeRhttp://mips.helmholtz-muenchen.de/cider/Information from neurological and metabolic diseasesYesOnline
ComPPIhttps://comppi.linkgroup.hu/Protein-Protein Interaction DatabaseYesOnline
dbDEPChttps://www.scbit.org/dbdepc3/index.phpCurated cancer proteomics dataYesOnline
DegraBasehttp://wellslab.ucsf.edu/degrabase/Mass spectrometry experiments in healthy and apoptotic cell linesYesOffline
Degradome databasehttp://degradome.uniovi.es/Protease alterations in hereditary diseasesNoOnline
DenHunthttp://proline.biochem.iisc.ernet.in/DenHunt/about_database.p hpExperimentally verified dengue-human interactionsYesOnline
DEPhOsphorylation databasehttp://depod.bioss.uni-freiburg.de/Data of phosphatases, their substrates, and the pathways in which they functionYesOnline
DIIPhttp://bioinfo.lab.mcgill.ca/resources/diip/Isoform interactome prediction from experimentsYesOnline
Dynamic Proteomicshttp://www.dynamicproteomics.net/Endogenously tagged proteins and their time-lapse microscopy moviesYesOffline
fat_depositionhttp://www.integratomics-time.com/fat_depositionProtein interactions in human, cattle, rat, and mice obesityNoOffline
FixPredhttp://www.fixpred.comProtein sequences corrected by the FixPred pipelineYesOffline
NameURLBrief descriptionDownload of dataCurrent status
GutCychttp://www.gutcyc.org/Pathway/genome databases from the human gutYesOffline
HADbhttp://autophagy.lu/index.htmlAutophagy related genes and proteinsNoOnline
HAPPIhttp://discovery.informatics.uab.edu/HAPPI/Human annotated and predicted protein interactionYesOnline
Harvesterhttp://harvester.fzk.de/harvester/Databases and servers for human proteinsNoOffline
HCPINhttp://nmr.cabm.rutgers.edu/hcpinHuman cancer pathway protein interaction networkNoOffline
HERVdhttps://herv.img.cas.cz/Human endogenous retroviruses databaseNoOnline
HGPDhttps://hgpd.lifesciencedb.jp/cgi/Human Gene and Protein DatabaseYesOnline
hiPathDBhttps://www.kobic.re.kr/Curated human protein and pathway dataNoOffline
HKUPPhttp://www.hkupp.org/Human kidney and urine proteome informationNoOnline
HMMER3https://www.ebi.ac.uk/Tools/hmmer/Homologs of protein sequences, and protein alignmentsYesOnline
HmtDBhttps://www.hmtdb.uniba.it/Database of human mitochondrial genomesYesOffline
HPIDhttp://wilab.inha.ac.kr/hpid/webforms/intro.aspxProtein interaction information from structural and experimental dataYesOnline
Human Interactome Maphttp://www.actrec.gov.in/Exploring the human protein interaction networkYesOnline
Human PPI networkhttps://gene.sfari.org/Functional and network organization of proteome of Autism datasetsYesOnline
Human Proteinpediahttp://www.humanproteinpedia.orgA community portal for sharing and integration of human protein dataYesOnline
HumanNethttp://www.functionalnet.org/humannet/about.htmlHuman gene functional interaction NetworkYesOnline
HuPhohttp://hupho.uniroma2.it/index.phpInformation about human protein phosphatasesNoOnline
HuPIhttps://hupi.ircm.qc.ca/Human Proteotheque InitiativeYesOnline
HuRIhttp://www.interactome-atlas.org/Human reference protein interactome mapping projectYesOnline
HydPredhttp://lishuyan.lzu.edu.cn/hydpred/protein hydroxylation sites in human inherited diseaseNoOnline
HypoxiaDBhttp://www.hypoxiadb.com/hypoxiadb.htmlCatalog of human hypoxia-regulated proteinsNoOnline
iLoc-Cellhttp://www.jci-bioinfo.cn/iLoc-HumSubcellular locations of human proteinsNoOnline
Instructhttp://instruct.yulab.org/Protein interactome networks in human and six model organismsYesOnline
Integr8https://www.ebi.ac.uk/integr8An integrated views of complete genomes and proteomesYesOffline
Integrated Interactions Databasehttp://dcv.uhnres.utoronto.ca/iid/Tissue-specific protein-protein interactionsYesOnline
InterMitoBasehttps://mcube.nju.edu.cn/cgi-bin/intermitobase/home.plHigh quality protein-protein interaction (PPI) data in human mitochondriaNoOffline
InWeb_IMhttps://www.intomics.com/inbio/map.html#searchProvides an integrated human PPI networkYesOnline
KEGG PATHWAYhttps://www.kegg.jp/Collection of manually drawn pathway mapsYesOnline
KinMaphttp://www.kinhub.org/kinmap/Interactive navigation through human kinome dataYesOnline
Kinome NetworkXhttp://www.kinasenet.ca/A systems biology-based framework to catalogue the human kinomeYesOnline
KLIFShttps://klifs.vu-compmedchem.nl/Kinase-Ligand Interaction Fingerprints and StructuresNoOnline

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.

NameURLBrief descriptionDownload of dataCurrent status
Labeledlnhttps://ftp.ncbi.nlm.nih.gov/pub/lu/LabeledIn/Drug indications via text-miningNoOnline
Ligandbookhttps://ligandbook.orgForce-field parameters of small and drug-like moleculesYesOnline
Membranomehttps://membranome.org/3D transmembrane domains and classificationYesOnline
MiasDBhttp://47.88.84.236/Miasdb/index.phpInteractions between human splicing factors, RNA elements, transcription factors, kinases and modified histonesYesOnline
MitoP2http://www.mitop2.de/Evaluated yeast, mouse, and human mitochondrial proteinsNoOnline
mLASSO-Humhttp://bioinfo.eie.polyu.edu.hk/mLASSOHumServer/index.htm lInterpretable human-protein subcellular localizationNoOnline
Molecular INTeraction Databasehttp://mint.bio.uniroma2.it/mint/Molecular interactions by extracting experimental details from work publishedYesOffline
NetNGlychttp://www.cbs.dtu.dk/services/NetNGlyc/Predict N-Glycosylation sites in human proteinsNoOnline
neXtProthttps://www.nextprot.org/about/nextprotProteomics data for over 85% of human proteinsYesOnline
PaPIhttp://papi.unipv.it/Predict impact of variants estimating the probability to damage their protein- related functionNoOnline
PCDqhttp://h-invitational.jp/hinv/pcdq/Human protein complex databaseNoOnline
PDID*http://biomine.cs.vcu.edu/servers/PDID/index.phpMolecular-level putative protein-drug interactions in the structural human proteomeYesOnline
PepSweetenerhttps://glycoproteome.expasy.org/pepsweetener/app/Manual annotation of MS data for intact glycopeptidesYesOnline
PhenoPPIOrthhttp://jjwanglab.org/PhenoPPIOrth/Orthology and protein-protein interaction information to infer gene-phenotype associations for multiple speciesYesOffline
PhosphoPICKhttp://bioinf.scmb.uq.edu.au/phosphopick/phosphopickMethod for predicting kinase substrates using cellular context informationYesOnline
PhosphoPredicthttp://phosphopredict.erc.monash.edu/Predict kinase-specific phosphorylation substrates and sites in the human proteomeYesOnline
PhosphOrthologhttp://www.phosphortholog.com/Cross-species mapping of orthologous protein post-translational modificationsYesOnline
PICKLEhttp://www.pickle.gr/SearchPredicts human protein-protein interactions networkYesOffline
PINdbhttp://pin.mskcc.org/Multiprotein nuclear complexes of human or yeast cellsYes 
PINTAhttps://securehomes.esat.kuleuven.be/~bioiuser/pinta/input.phpGenome-wide protein-protein interaction network for the prioritization of candidate genesYesOffline
PIPshttp://www.compbio.dundee.ac.uk/www-pips/index.jspProtein interaction bayesian method that combines information from expression, orthology, domain co-occurrence, post-translational modifications and sub-cellular locationNoOnline
PolyQhttp://lightning.med.monash.edu/polyq2/Information of human polyQ repeat-containing proteinsYesOffline
PrePPIhttps://bhapp.c2b2.columbia.edu/PrePPI/index.htmlPredicted and experimentally determined (PPIs) for yeast and humanYesOnline
Primate Orthologous Exon Databasehttps://giladlab.uchicago.edu/orthoExon/Unique, non-overlapping, orthologous exon regions of human, chimpanzee, and rhesus macaque.NoOffline
NameURLBrief descriptionDownload of dataCurrent status
ProKinOhttp://vulcan.cs.uga.edu/prokino/about/browserKinase activation and regulatory mechanismsNoOnline
Protein kinase resourcehttp://www.kinasenet.org/Human kinome tree via an interactive displayNoOffline
ProteomicsDBhttps://www.proteomicsdb.org/Predicted and experimental human proteomesYesOnline
Quokka*http://quokka.erc.monash.edu/Kinase phosphorylation sites in the human proteomeNoOnline
RasMolhttp://www.bernstein-plus-sons.com/software/rasmol/Protein 3D structure viewerNoOnline
ScaPDhttp://bioinfo.wilmer.jhu.edu/ScaPD/Database for human scaffold proteinsNoOnline
SMPDBhttps://smpdb.ca/view/SMP0000179Small molecule pathway dataBaseNoOnline
SpindlePhttp://www.cbs.dtu.dk/services/SpindleP/Location of proteins or genes in the meiotic spindleNoOnline
StSNPhttp://ilyinlab.org/StSNP/Compare protein structures, protein complexes, protein-protein interfaces and metabolic networksNoOnline
SubPhosPredhttp://bioinfo.ncu.edu.cn/SubPhosPred.aspxPhosphorylation sites in subcellular compartmentsNoOnline
SURFYhttp://wlab.ethz.ch/surfaceome/Visualize the human surface proteome (surfaceome)YesOnline
Sys-BodyFluidhttp://www.biosino.org/bodyfluid/Contains eleven kinds of body fluid proteomes infoYesOffline
The Proteome Browser*http://proteomebrowser.org/tpb/home.jspxTissue localization, post-translational modifications, or interactions in human proteomeNoOnline
TissueNethttp://netbio.bgu.ac.il/tissuenet/Experimentally-identified PPIs with human tissuesYesOnline
TOPPRhttps://iomics.ugent.be/toppr/The online protein processing resourceYesOffline
TRI_toolhttps://www.vin.bg.ac.rs/180/tools/tfpred.phpPrediction of PPIs in human Transcriptional RegulationNoOnline
UniHIhttp://www.unihi.org/Analysis and visualization of human molecular interaction networksYesOnline
VDJsolverhttp://www.cbs.dtu.dk/services/VDJsolver/Data of human immunoglobulin VDJ recombinationNoOnline
VHLdbhttp://vhldb.bio.unipd.it/Interactors and mutations of the human von Hippel-Lindau tumor suppressor proteinNoOnline

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.

NameURLBrief descriptionDownload of dataCurrent status
AAgAtlashttp://biokb.ncpsb.org/aagatlas/Autoantigen or autoantibody curated informationYesOnline
CHOP CNVhttp://cnv.chop.eduGenomic Copy Number Variation (CNVs) that were derived from 2026 healthy individualsYesOffline
CLIMAhttp://bioinformatics.hsanmartino.it/clima2/Molecular authentication of human cell linesYesOffline
CytReDhttp://www.cro-m.eu/CytReD/Cytokine receptors, ligands, involvement in diseasesNoOnline
dbMHChttps://ftp.ncbi.nlm.nih.gov/pub/mhc/mhc/Final%20Archive/DNA and clinical data related to MHCYesOnline
Epipoxhttp://imed.med.ucm.es/epipox/Peptides (HLA-I and HLA-II), predictions, and proteinsNoOnline
G2Dhttp://g2d2.ogic.ca/Precomputed candidate genes for diseasesYesOffline
GADGEThttp://gadget.biosci.gatech.eduGenetic traits of human phenotypic diversityNoOnline
Gene Set Builderhttp://www.cisreg.ca/gsb/Compile, store, export, and share sets of genesYesOnline
Genetic Association Databasehttps://geneticassociationdb.nih.gov/Genetic association studies informationYesOnline
GIANThttps://portals.broadinstitute.org/collaboration/giant/index.php/GIANT_ consortiumGenetic investigation of anthropometric traits meta-analysis of genome- wide association dataYesOnline
Global Biobank Enginehttps://biobankengine.stanford.edu/Visualize phenotypes, variants, genes, genetic correlation and human leukocyte antigens (HLA) allelesNoOnline
GuavaHhttp://www.guavah.org/Genome-wide association (GWAS) of HIV phenotypesNoOnline
GUIDEShttp://guides.sanjanalab.org/#/CRISPR knockout libraries in human or mouse genomeYesOnline
H2P2http://h2p2.oit.duke.edu/H2P2Home/Cellular and infections agents in GWAS studies dataNoOnline
HLA-ADRhttp://www.allelefrequencies.net/hla-adr/Exploring immunogenetic disease associationsNoOnline
HLAsupEhttp://www.immunoinformatics.net/HLAsupE/index.htmlHuman leucocyte antigens supertype-specific epitopesYesOnline
HomozygosityMapperhttp://www.homozygositymapper.org/Homozygous detection in SNP genotype or sequencingYesOnline
HPtaa databasehttp://www.bioinfo.org.cn/hptaa/Human potential tumor associated antigensNoOnline
HyperCLDBhttp://bioinformatics.hsanmartino.it/hypercldb/Collection of information on human and animal cell linesNoOnline
NameURLBrief descriptionDownload of dataCurrent status
IEDBhttps://www.iedb.org/Antibody and T-cell epitopes studied in various speciesNoOnline
iLoc-Cellhttp://www.jci-bioinfo.cn/iLoc-HumPredictor for subcellular locations in proteins sitesNoOnline
IMGThttp://www.imgt.org/International immunogenetics information systemYesOnline
IPD-IMGT/HLAhttps://www.ebi.ac.uk/ipd/imgt/hla/Provides a specialist database for sequences of HLANoOnline
IPD-MHChttps://www.ebi.ac.uk/ipd/mhc/Sequence repository of MHC from different speciesYesOnline
LD Hubhttp://ldsc.broadinstitute.org/Summary of GWAS studiesNoOnline
MARomehttp://196.1.114.46:8080/MARome/indexAnnotation of scaffold and matrix attachment regionsYesOnline
Metabolomics GWAS Serverhttp://metabolomics.helmholtz-muenchen.de/gwas/index.phpGWAS studies on the human metabolomeNoOnline
MitoAgehttp://www.mitoage.info/Analysis of mtDNA, focus on animal longevityYesOnline
MNDRhttp://www.rna-society.org/mndr/Disease association and mapping disease ncRNAYesOnline
mtDNA-Serverhttps://mtdna-server.uibk.ac.at/index.htmlHeteroplasmy detection and haplogroup-based mtDNAYesOnline
NetMHC-3.0http://www.cbs.dtu.dk/services/NetMHC/Human, mouse or monkey MHC Class I-peptide bindingNoOnline
NetMHCIIpanhttp://www.cbs.dtu.dk/services/NetMHCIIpan/HLA-DR, HLA-DP, HLA-DQ human and mouse dataNoOnline
PathogenFinderhttps://cge.cbs.dtu.dk/services/PathogenFinder/Bacterial pathogenicity estimationNoOnline
PEPVAChttp://imed.med.ucm.es/PEPVAC/Tool of development of multi-epitope vaccinesYesOnline
PhosphoPICKhttp://bioinf.scmb.uq.edu.au/phosphopick/phosphopickPredicting kinase substrates using cellular context infoYesOnline
PolyDomshttps://polydoms.cchmc.org/polydoms/Impact of variations in human genes to facilitate sequence-based association studiesNoOnline
PolySearch2http://polysearch.cs.ualberta.ca/indexAssociations between human diseases, genes, drugs, metabolites, toxins and moreYesOnline
Primer Zhttp://grch37.genepipe.ncgm.sinica.edu.tw/primerz/beginDesign.doInterface for PCR primer designYesOnline
PrimerStationhttps://ps.cb.k.u-tokyo.ac.jp/Multiplex genomic PCR primer design toolYesOnline
PRShttp://mrcieu.mrsoftware.org/PRS_atlas/An atlas of polygenic burden associations across the human phenomeNoOnline
pseudoMaphttp://pseudomap.mbc.nctu.edu.tw/Explores the relationships between TPG and its cognate gene with miRNA decoyed mechanismsYesOffline
Psmirhttp://bio-bigdata.hrbmu.edu.cn/Psmir/Gene expression profiles under miRNA perturbation and drug treatmentYesOnline
ReCGiPhttp://klab.sjtu.edu.cn/ReCGiP/Candidate genes in pigs based on bibliomicsYesOnline
RepTarhttp://bioinformatics.ekmd.huji.ac.il/reptarGenome-wide predictions of human and mouse viral miRNAsYesOffline
Semantic Body Browser*http://sbb.cellfinder.org/Graphically exploring an organism by means of ontologically annotated anatomical illustrationsYesOnline
SHOGoiNhttps://stemcellinformatics.org/Human omics of ips and normal cellsNoOnline
NameURLBrief descriptionDownload of dataCurrent status
SNPDelScorehttps://www.ncbi.nlm.nih.gov/research/snpdelscore/Deleterious effects of noncoding variants using a large panel of currently available methodsYesOnline
SNPxGE(2)http://lambchop.ads.uga.edu/snpxge2/index.phpHuman population gene expression and variationYesOffline
SPIKEhttps://www.cs.tau.ac.il/~spike/Curated human signaling pathwaysYesOnline
StemCellNethttp://stemcellnet.sysbiolab.eu/Molecular networks in the context of stem cell biologyYesOnline
SWATHAtlashttp://www.swathatlas.org/Immunogenetics systems biology informationYesOnline
SysteMHC Atlashttps://systemhcatlas.org/Atlas of immune peptidomics MS-relatedNoOnline
TCLPhttp://celllines.tron-mainz.de/HLA data, neo-epitopes, virus, and gene expressionYesOnline
TCRexhttps://tcrex.biodatamining.be/instructions/Recognition of pathogenic & cancer epitopes by human T cell receptors (TCR)YesOnline
TFcheckpointhttp://www.tfcheckpoint.org/Genome-scale regulatory network studiesYesOffline
The SBThttps://ftp.ncbi.nlm.nih.gov/pub/mhc/mhc/Final%20Archive/MHC human data sequencesYesOnline
VaDEhttp://bmi-tokai.jp/VaDE/Genomic polymorphisms associated to diseases, traits, and pharmacogenomicsYesOnline
VDJdb*https://vdjdb.cdr3.net/Antigen-specific TCR sequences acquired by manual processingYesOnline

Reference

Villalba, G. C., & Matte, U. (2021). Fantastic databases and where to find them: Web applications for researchers in a rush. Genetics and Molecular Biology44, e20200203.

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