Difference between revisions of "Web Resources"

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== Human Gene/Genome Annotations ==
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== Google DataSet Search Engine ==
 +
*[https://toolbox.google.com/datasetsearch Google Dataset Search]
 +
== Gene/Genome Annotations ==
 
*[http://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi CCDS] The concensus protein coding regions among NCBI, Ensembl, and Sanger (Havana) annotation  
 
*[http://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi CCDS] The concensus protein coding regions among NCBI, Ensembl, and Sanger (Havana) annotation  
 
*[http://www.gencodegenes.org/ GENCODE] The Encyclopedia of Genes
 
*[http://www.gencodegenes.org/ GENCODE] The Encyclopedia of Genes
 +
*[https://metascape.org/ Metasape] Gene annotation and Enrichment analysis resource by NIH
  
−
== Human Variome Resources ==
+
== Variome Resources ==
 
- Variation DBs
 
- Variation DBs
 
*[http://exac.broadinstitute.org/ ExAC (Exome Aggregation Consortium)] Exome variation data from >60k individuals  
 
*[http://exac.broadinstitute.org/ ExAC (Exome Aggregation Consortium)] Exome variation data from >60k individuals  
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*[https://hgv.figshare.com/?WT.mc_id=BAN_HGV_database HGV Database] The HGV database is a fully searchable online database of genome variations published in peer-reviewed Data Reports in Human Genome Variation
 
*[https://hgv.figshare.com/?WT.mc_id=BAN_HGV_database HGV Database] The HGV database is a fully searchable online database of genome variations published in peer-reviewed Data Reports in Human Genome Variation
  
−
- Variant functional effect estimation
+
- Functional significance of variants
 
*[http://www.columbia.edu/~ii2135/eigen.html Eigen] Assign functional important scores on genetic variants in coding and noncoding regions (human only, unsupervised integration)
 
*[http://www.columbia.edu/~ii2135/eigen.html Eigen] Assign functional important scores on genetic variants in coding and noncoding regions (human only, unsupervised integration)
 
*[http://cadd.gs.washington.edu/home CADD: Combined Annotation Dependent Depletion] a tool for scoring the deleteriousness of SNV and indels (human only, supervised integration)
 
*[http://cadd.gs.washington.edu/home CADD: Combined Annotation Dependent Depletion] a tool for scoring the deleteriousness of SNV and indels (human only, supervised integration)
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*[http://www.broadinstitute.org/mammals/haploreg HaplogReg] Exploring DNA functional elements for noncoding variants (by MIT, Kellis lab)
 
*[http://www.broadinstitute.org/mammals/haploreg HaplogReg] Exploring DNA functional elements for noncoding variants (by MIT, Kellis lab)
  
−
== Human Genotype-to-Phenotype Resources ==
+
== Phenome/Diseasome Resources ==
 +
- Human Disease DBs
 +
*[http://www.disgenet.org/web/DisGeNET DisGeNET] MetaDB for disease genes and variants (very comprehensive and open license)
 +
*[https://www.opentargets.org/ Open Targets] Another very comprehensive DB for disease target (mostly protein-coding genes) and related evidence
 +
*[http://denovo-db.gs.washington.edu/denovo-db/ denovo-db] a compendium of human de novo variants
 +
*[http://diseases.jensenlab.org/ DISEASES] gene-disease association from text mining (GHR, Uniprot, textmining)
 +
*[https://ghr.nlm.nih.gov/ GHR] Genetics Home Reference (by NCBI)
 +
*[http://disease-ontology.org/ Disease Ontology] Disease ontology files [http://django.nubic.northwestern.edu/fundo/ FUNDO] DOLite_term-to-genes map
 +
*[http://www.human-phenotype-ontology.org/ Human Phenotype Ontology]
 +
*[http://www.omim.org/ OMIM] Human disease DB (needs License to distribute)
 +
*[http://www.orphadata.org OrphaData] Open database for rare diseases and orphan drug (by Orphanet)
 +
*[http://geneticassociationdb.nih.gov/ GAD] Genetic Association Database: archive of human genetic association studies of complex diseases and disorders (includes summary data extracted from published candidate gene and GWAS studies).
 +
*[http://www.nlm.nih.gov/research/umls/ UMLS] Unified Medical Language Systems
 +
*[http://www.who.int/classifications/icd/en/ ICD] International Classification of Disease by WHO
 +
*[http://dga.nubic.northwestern.edu DGA] Disease and Gene Annotation, an integrative set of disease-to-gene, gene-to-gene, disease-to-disease relationships
 +
*[http://genomernai.de/GenomeRNAi/ GenomeRNAi] v12 contains 168 human RNAi, 181 D. melanogaster RNAi screen datasets
 +
*[http://ogeedb.embl.de OGEE] Online GEne Essentiality database
 +
*[http://www.informatics.jax.org/humanDisease.shtml Human-Mouse Disease Connection] a part of MGI
 +
 
 +
- QTL depositories
 +
*[https://www.gtexportal.org/home/ GTEx Portal] eQTL for ~50 different tissue types in humans
 +
 
 +
- GWAS resources
 +
*[https://www.covid19hg.org/results/ COVID-19 Host Genetics Inititative]COVID-19 GWAS regulsts
 +
*[https://atlas.ctglab.nl/ GWAS ATLAS] Atlas of GWAS Summary Statistics (most comprehensive!)
 +
*[http://www.ebi.ac.uk/gwas/ GWAS catalog] Disease-associated variants; Now providing GWAS summary stat data
 +
*[http://geneatlas.roslin.ed.ac.uk/ GeneATLAS] GWAS for ~780 traits using 452,264 UK Biobank White British individuals
 +
*[http://www.ncbi.nlm.nih.gov/gap/phegeni PheGenI] Phenotype-Genotype Integrator: For a query trait, it return GWAS loci collected from all available data resources (very convenient to make a single GWAS data set for each trait)
 +
*[http://ldsc.broadinstitute.org/ldhub/ LDHUB] a centralized database of summary-level GWAS results
 +
*[http://apps.nhlbi.nih.gov/Grasp/ Genome-wide Repository of Associations between SNPs and Phenotypes (GRASP)] Better than GWAS catalog, including eQTL,QTLs
 +
*[http://jjwanglab.org:8080/gwasdb/ GWASdb] includes moderate SNPs (p-value < 10^-3) with manual curation from original papers; manually mapped ~1600 GWAS traits to ~500 HPO terms, ~440 DO terms, ~230 DOLite terms
 +
*[http://distild.jensenlab.org/ DistiLD] Diseases and Traits in Linkage Disequilibrium Blocks
 +
 
 +
- Genotype raw data depositories
 +
*[http://www.humanfunctionalgenomics.org Human Functional Genomics Project] Raw data are available from [https://hfgp.bbmri.nl/ BBMRI-NL data infrastructure]
 +
*[http://www.ukbiobank.ac.uk/ UK Biobank] Genotype and extensive phenotype data for ~500k UK people
 +
*[https://www.ebi.ac.uk/ega/ European Genome-phenome Archive(EGA)] Raw data of GWAS, WGS, Exome-seq. A great resource for meta-analysis
 +
*[http://www.ncbi.nlm.nih.gov/gap dbGaP] The database of Genotypes and Phenotypes (GWAS, WGS, Exome-seq...)
 +
 
 +
- Clinical/Disease variant databases
 
*[http://research.nhgri.nih.gov/CGD/ CGD] Clinical Genomic Database
 
*[http://research.nhgri.nih.gov/CGD/ CGD] Clinical Genomic Database
 
*[http://www.hgmd.org/ HGMD] The human gene mutation database (The professional version of DB is commercial. The public version of DB is not downloadable.)
 
*[http://www.hgmd.org/ HGMD] The human gene mutation database (The professional version of DB is commercial. The public version of DB is not downloadable.)
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*[http://rcgdb.bioinf.uni-sb.de/MutomeWeb/ Roche Cancer Genome Database (RCGDB)] Germline/somatic mutations for cancer collected from diverse resourses (not downloadable)
 
*[http://rcgdb.bioinf.uni-sb.de/MutomeWeb/ Roche Cancer Genome Database (RCGDB)] Germline/somatic mutations for cancer collected from diverse resourses (not downloadable)
 
*[http://bioinf.uta.fi/base_root/ IDbase] Human Immunodeficiency-causing mutation database
 
*[http://bioinf.uta.fi/base_root/ IDbase] Human Immunodeficiency-causing mutation database
−
*[http://www.ukbiobank.ac.uk/ UK Biobank] Genotype and extensive phenotype data for ~500k UK people
 
−
*[http://jjwanglab.org:8080/gwasdb/ GWASdb] includes moderate SNPs (p-value < 10^-3) with manual curation from original papers; manually mapped ~1600 GWAS traits to ~500 HPO terms, ~440 DO terms, ~230 DOLite terms
 
−
*[https://www.ebi.ac.uk/ega/ European Genome-phenome Archive(EGA)] Raw data of GWAS, WGS, Exome-seq. A great resource for meta-analysis
 
−
*[http://www.ncbi.nlm.nih.gov/gap dbGaP] The database of Genotypes and Phenotypes (GWAS, WGS, Exome-seq...)
 
 
*[http://www.ncbi.nlm.nih.gov/clinvar/ NCBI ClinVar] human variations and their relations to the human health (Not includes unreviewed data from GWAS)
 
*[http://www.ncbi.nlm.nih.gov/clinvar/ NCBI ClinVar] human variations and their relations to the human health (Not includes unreviewed data from GWAS)
−
*[http://www.ebi.ac.uk/gwas/ GWAS catalog] now maintained by EBI
+
 
−
*[http://www.ncbi.nlm.nih.gov/gap/phegeni PheGenI] Phenotype-Genotype Integrator
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- Others
−
*[http://apps.nhlbi.nih.gov/Grasp/ Genome-wide Repository of Associations between SNPs and Phenotypes (GRASP)] Better than GWAS catalog, including eQTL,QTLs
+
 
*[http://www.nature.com/icogs/ COGS nature resources] CollaborativeOncological Gene-environment Study (GOGS): Association study using ~211,000SNPs (iCOGS) for breast, ovarian, prostate cancers.
 
*[http://www.nature.com/icogs/ COGS nature resources] CollaborativeOncological Gene-environment Study (GOGS): Association study using ~211,000SNPs (iCOGS) for breast, ovarian, prostate cancers.
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*[http://distild.jensenlab.org/ DistiLD] Diseases and Traits in Linkage Disequilibrium Blocks
 
 
*[http://www.personalgenomes.org/ Personal Genome Project]
 
*[http://www.personalgenomes.org/ Personal Genome Project]
−
*[http://www.ncbi.nlm.nih.gov/gtex/GTEX2/gtex.cgi NCBI GTex(Genotype-Tissue Expression) browser] eQTL data download and analysis
 
−
*[https://www.med.unc.edu/pgc/downloads PGC GWAS rawdata download] contains links for other GWAS raw data
 
 
*[https://decipher.sanger.ac.uk/ DECIPHER] Developmental Diseases to Phenotypes database with public patients (very useful for rare disease genetics research)
 
*[https://decipher.sanger.ac.uk/ DECIPHER] Developmental Diseases to Phenotypes database with public patients (very useful for rare disease genetics research)
  
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== Human Pathway/Signature genes and Interactome DBs ==
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== Interactome, Pathway/Signature Resources ==
 +
- Interactome DBs
 +
*[https://irefindex.vib.be/wiki/index.php/iRefIndex iRefIndex] provides an index of protein interactions available in a number of primary interaction databases including BIND, BioGRID, CORUM, DIP, HPRD, InnateDB, IntAct, MatrixDB, MINT, MPact, MPIDB, MPPI, Reactome, VirHostnet, and QuickGO.
 +
*[http://string-db.org/ STRING] Known and predicted PPI
 +
*[http://interactome.baderlab.org/ Human Reference Interactome Project] Y2H-based human protein interactions
 +
 
 
- Pathway DBs
 
- Pathway DBs
 
*[http://pathguide.org/ Pathguide.org] A very comprehensive list of pathway and network databases
 
*[http://pathguide.org/ Pathguide.org] A very comprehensive list of pathway and network databases
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- Signature Gene Set DBs
 
- Signature Gene Set DBs
 
*[http://software.broadinstitute.org/gsea/msigdb MsigDB] License required for redistribution
 
*[http://software.broadinstitute.org/gsea/msigdb MsigDB] License required for redistribution
−
*[http://www.genesigdb.org/genesigdb/ GeneSigDB]
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*[http://www.genesigdb.org/genesigdb/ GeneSigDB] Manually curated gene sets from Pubmed literature
 +
*[https://www.immunespace.org/announcements/home/thread.view?rowId=50 ImmnuneSigDB] Compendium of immune signatures (now available from MsigDB)
 +
*[http://biocc.hrbmu.edu.cn/CancerSEA/goDownload CancerSEA] which provides 14 signature profiles for characterization of cancer cells
 
*[http://tanlab.ucdenver.edu/DSigDB/DSigDBv1.0/ DSigDB] Drug signature database for gene set analysis
 
*[http://tanlab.ucdenver.edu/DSigDB/DSigDBv1.0/ DSigDB] Drug signature database for gene set analysis
 
*[http://amp.pharm.mssm.edu/L1000CDS2/help/ L1000CDS2] Return 50 signature genes for each LINCS L1000 data set using Characteristic Direction (CD) method
 
*[http://amp.pharm.mssm.edu/L1000CDS2/help/ L1000CDS2] Return 50 signature genes for each LINCS L1000 data set using Characteristic Direction (CD) method
 
*[http://amp.pharm.mssm.edu/creeds/ CREEDS] CRowd Extracted Expression of Differential Signatures: Signature gene sets from GEO selected by crowdsourcing project using CD method
 
*[http://amp.pharm.mssm.edu/creeds/ CREEDS] CRowd Extracted Expression of Differential Signatures: Signature gene sets from GEO selected by crowdsourcing project using CD method
  
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- Interactome DBs
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== Regulome Resources ==
−
*[http://wodaklab.org/iRefWeb/ iRefWeb] a web interface to PPI consolidated from 10 public DB (BIND, BioGRID, CORUM, DIP,IntAct, HPRD, MINT, MPact, MPPI, OPHID(predicted PPIs))
+
- TF and motif DB
−
*[http://string-db.org/ STRING] Known and predicted PPI
+
*[http://humantfs.ccbr.utoronto.ca/ The Human Transcription Factors] 2765 putative TFs and 1639 confident TFs by manual curation
 +
*[http://cisbp.ccbr.utoronto.ca/ CIS-BP (Catalog of Inferred Sequence Binding Preferences)] >300 species, >250 TF families, >160,000 TFs. CisBP collects data from >25 sources, including other database such as [http://autosome.ru/HOCOMOCO/ HOCOMOCO] [http://jaspar.genereg.net JASPAR] [http://the_brain.bwh.harvard.edu/uniprobe/ UNIPROBE] [http://www.gene-regulation.com/pub/databases.html TRANSFAC]  
  
−
== Epigenomics Resources ==
+
- Epigenomics Consortium projects
−
*[http://genome.ucsc.edu/ENCODE/ ENCODE] Encyclopedia of DNA Elements project (human)
+
*[https://www.encodeproject.org/ ENCODE] Encyclopedia of DNA Elements project portal
 
*[http://www.roadmapepigenomics.org/ Road map Epigenomics] NIH Roda map Epigenomics project home
 
*[http://www.roadmapepigenomics.org/ Road map Epigenomics] NIH Roda map Epigenomics project home
 
*[http://ihec-epigenomes.org/ International Human Epigenome Consortium (IHEC)] The umbrella organization for international epigenomic efforts
 
*[http://ihec-epigenomes.org/ International Human Epigenome Consortium (IHEC)] The umbrella organization for international epigenomic efforts
 
*[http://www.4dnucleome.org/ 4D Nucleome] To understand the principles behind the 3D organization of the nucleus in space and time (the 4th dimension)   
 
*[http://www.4dnucleome.org/ 4D Nucleome] To understand the principles behind the 3D organization of the nucleus in space and time (the 4th dimension)   
−
*[http://bejerano.stanford.edu/great/public/html/ GREAT] Genomic Regions Enrichment of Annotations Tool; Predict functions for cis-regulatory regions
 
−
*[http://cistrome.org/pc/ CistromeMap] A knowledgebase for ChIP-Seq and DNase-Seq studies in mouse and human
 
−
*[http://www.generegulation.info/ Gene Regulation Info] A very useful site for epigenetics and TF-DNA interaction studies (by Dr. Vladimir Teif)
 
−
*[http://cisbp.ccbr.utoronto.ca/ CIS-BP (Catalog of Inferred Sequence Binding Preferences)] >300 species, >250 TF families, >160,000 TFs. CisBP collects data from >25 sources, including other database such as [http://autosome.ru/HOCOMOCO/ HOCOMOCO] [http://jaspar.genereg.net JASPAR] [http://the_brain.bwh.harvard.edu/uniprobe/ UNIPROBE] [http://www.gene-regulation.com/pub/databases.html TRANSFAC]
 
−
*[http://meme.nbcr.net/meme/intro.html MEME Suite] has everything for motif based sequence analysis
 
  
−
== miRNA Regulome Resources ==
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- Promoter DB
 +
*[http://epd.vital-it.ch/ EPD] Eukaryotic Promoter Database; Databases of experimentally validated (by either publication or in-house assay) promoters in various organisms
 +
 
 +
- Enhancer DB
 +
*[http://enhanceratlas.org/ Enhancer Atlas] Human enhancers based on >=3 independent high-throughput experimental datasets (contains 2,534,123 enhancers for 76 cell lines and 29 tissues)
 +
*[http://bioinfo.au.tsinghua.edu.cn/dbsuper/ dbSUPER] contains 82,234 super-enhancers in 102 human and 25 mouse tissue/cell types
 +
*[http://zdzlab.einstein.yu.edu/1/hedd.php HEDD] Human Enhancer Disease Database (~2.8M enhancers from ENCODE, FANTOM5, RoadMap and annotations for disease, target, variant, conservation)
 +
*[http://biocc.hrbmu.edu.cn/DiseaseEnhancer/ DiseaseEnhancer] manual curation of disease-associated enhancers
 +
 
 +
- Transcriptional Start Site (TSS) DB
 +
*[http://dbtss.hgc.jp/ DBTTS] contains 491 million TSS tag sequences for 20 tissues and 7 cell cultures in human and mouse
 +
 
 +
- Chip-seq/DNase-seq DB
 +
*[http://cistrome.org Cistrome DB] the most comprehensive DB for Chip-seq and DNase-seq data
 +
 
 +
- Enhancer-Promoter Interaction DB
 +
*[http://yiplab.cse.cuhk.edu.hk/jeme/ JEME] Computationally inferred EPI networks for 935 human primary cells, tissues, and cell lines
 +
 
 
- microRNA list and expression atlas
 
- microRNA list and expression atlas
 
*[http://mirbase.org// miRBase] miRNA database by Manchester University
 
*[http://mirbase.org// miRBase] miRNA database by Manchester University
 
*[http://www.microrna.org microRNA.org] download miRNA expression atlas for human, mouse, rat
 
*[http://www.microrna.org microRNA.org] download miRNA expression atlas for human, mouse, rat
 +
*[https://bioconductor.org/packages/devel/data/experiment/html/microRNAome.html microRNAome] microRNA RNA-seq based atlas for 46 primary cell types and 42 cancer or immortalized cell lines
  
 
- microRNA-target links (Gold standard)
 
- microRNA-target links (Gold standard)
 
*[http://zmf.umm.uni-heidelberg.de/apps/zmf/mirwalk2 miRWalk2.0] Validated links from 4 databases and text minings, Predicted links from 13 prediction data sets
 
*[http://zmf.umm.uni-heidelberg.de/apps/zmf/mirwalk2 miRWalk2.0] Validated links from 4 databases and text minings, Predicted links from 13 prediction data sets
−
*[http://mirtarbase.mbc.nctu.edu.tw/ miRTarBase] Manually curated microRNA-target links, miRNA-mRNA paired expression profiles, miRNA-disease links
+
*[http://mirtarbase.mbc.nctu.edu.tw/ miRTarBase] Experimental-based microRNA-target links (most popular)
−
*[http://miRecords.umn.edu/miRecords miRecords] Manually curated microRNA-target links + predicted links (by 11 computational algorithms)
+
−
*[http://research.bioinformatics.udel.edu/miRTex/ miRTex] Text mining system for miRNA-target, miRNA-gene/gene-miRNA regulation
+
−
*[http://services.bio.ifi.lmu.de/mirsel/ mirSel] microRNA-target links by text mining
+
−
*[http://www.benoslab.pitt.edu/comir/ Comir] Combinatorial miRNA target prediction tool
+
  
 
- microRNA-disease
 
- microRNA-disease
−
*[http://202.38.126.151/hmdd/tools/hmdd2.html Human microRNA Disease Database(HMDD)] Manually curated microRNA-disease links
+
*[http://202.38.126.151/hmdd/tools/hmdd2.html Human microRNA Disease Database(HMDD)] Manually curated microRNA-disease links (most comprehensive)
−
*[http://www.mir2disease.org/ miR2Disease] Manually curated microRNA-target links and microRNA-disease links
+
*[http://mips.helmholtz-muenchen.de/phenomir/ PhenomiR] DB for dysregulated miRNA in diseases
−
*[http://mips.helmholtz-muenchen.de/phenomir/ PhenomiR] A knowledgebase of miRNA expression in disease and biological processes
+
*[http://www.picb.ac.cn/dbDEMC/ dbDEMC] DB for dysregulated miRNA in Cancer
 
*[http://miRGator.kobic.re.kr miRGator] data for miRNA expression, miRNA-mRNA paired expression profile, miRNA perturbation experiments...  
 
*[http://miRGator.kobic.re.kr miRGator] data for miRNA expression, miRNA-mRNA paired expression profile, miRNA perturbation experiments...  
  
−
- Target prediction software
+
- miRNA Target predictions
−
*[http://www.targetscan.org/ TargetScan] executable [http://genie.weizmann.ac.il/pubs/mir07/index.html PITA] executable [http://www.microrna.org/microrna/getDownloads.do miRanda] excecutable
+
*[http://ophid.utoronto.ca/mirDIP/ mirDIP] >150M human miRNA-target predictions collected from 30 resources with integrative score
−
*[http://cegg.unige.ch/mirmap/ miRmap] target prediction by multiple algorithms, excecutable, precalculated, many other related data
+
 
−
*[http://mirdb.org/miRDB/ miRDB] Pre-calculated miRNA-target associations (based on SVM), not executable
+
- CLIP-seq database
−
-CLIP-seq database
+
 
*[http://starbase.sysu.edu.cn/ StarBase] DB for CLIP-seq data
 
*[http://starbase.sysu.edu.cn/ StarBase] DB for CLIP-seq data
  
−
== lncRNA Regulome Resources ==
+
- lncRNA Resources
 +
*[http://fantom.gsc.riken.jp/cat/ FANTOM-CAT] An atlas of human long non-coding RNAs with accurate 5' ends
 
*[http://www.noncode.org/ NONCODE] Integrative annotation of long noncoding RNAs
 
*[http://www.noncode.org/ NONCODE] Integrative annotation of long noncoding RNAs
 
*[http://www.lncrnadb.org/ lncRNAdb] a reference DB for long noncoding RNAs
 
*[http://www.lncrnadb.org/ lncRNAdb] a reference DB for long noncoding RNAs
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*[http://lulab.life.tsinghua.edu.cn/postar/ POSTAR] a DB of RNA binding protein binding sites in human and mouse transcriptome (experimental and computational methods)
 
*[http://lulab.life.tsinghua.edu.cn/postar/ POSTAR] a DB of RNA binding protein binding sites in human and mouse transcriptome (experimental and computational methods)
  
−
== Transcriptome Analysis Resources ==
+
== Single Cell Analysis Resources ==
−
- Data deposit servers
+
- Spatial Omics Resources
−
*[http://www.ncbi.nlm.nih.gov/sra SRA] Sequence Read Archive by NCBI
+
*[https://github.com/crazyhottommy/awesome_spatial_omics awesome_spatial_omics]
−
*[http://www.ebi.ac.uk/ena/ ENA] European Neucleotice Archive by EBI
+
- Human Cell Atlas
−
*[http://www.ncbi.nlm.nih.gov/geo/ GEO] Gene Expression Omnibus (for processed data only)
+
*[https://www.humancellatlas.org/ HCA]
−
*[http://www.weigelworld.org/resources/microarray/AtGenExpress/ AtGenExpress] Arabidopsis gene expression DB by Weigel lab (there are unpublished non-GEO data here)
+
*[https://chanzuckerberg.com/science/programs-resources/humancellatlas/ Chan Zukerburg Initiative HCA seed networks]
−
*[http://www.immgen.org/ ImmGen] Immunological Genome Project [http://www.immgen.org/ModsRegs/modules.html Ontogenet] TF-module networks based on ImmGen data
+
*[https://www.covid19cellatlas.org/ COVID-19 Cell Atlas] Data portal by HCA
−
 
+
- scRNA-seq data analysis resources
−
- Expression Atlas
+
*[https://satijalab.org/seurat/ Seurat] The package for scRNA-seq data analysis
−
*[http://tissues.jensenlab.org/ TISSUE] Tissue Expression Database based on text mining (by Lars Jensen)
+
*[https://velocyto.org Velocyto] RNA Velocity analysis with steady-state model
−
*[http://www.ebi.ac.uk/gxa/ EBI Gene Expression Atlas] Gene expression atlas for many organisms collected from various experiments
+
*[https://scvelo.org scVelo] Generalized RNA Velocity analysis through dynamic modeling
−
*[http://www.ebi.ac.uk/gxa/array/U133A Human Cell/tissue-specific gene expression map] for 369 different cell and tissue types with 5,372 human samples from GEO
+
*[https://www.sanger.ac.uk/science/tools/scrna-seq-analysis-course scRNA-seq analysis course by Sanger]
−
*[http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE30611 Illumina Human Body Map Project (HBM)] RNA-seq data for 16 human tissue
+
*[https://www.cellphonedb.org/ CellPhoneDB] A repository of curated receptors, ligands and their interactions.
−
*[http://www.informatics.jax.org/expression.shtml GXD] The mouse Gene Expression Database (by MGI)
+
*[https://github.com/seandavi/awesome-single-cell Awesome single cell]  
−
 
+
*[https://www.scrna-tools.org/ scRNA-tools DB]
−
== Phenome/Diseasome Resources ==
+
- Depositories for scRNA-seq data
−
*[http://www.disgenet.org/web/DisGeNET DisGeNET] MetaDB for disease genes and variants (very comprehensive and open license)
+
*[https://portals.broadinstitute.org/single_cell Single Cell Portal] scRNA-seq database by Broad Institute
−
*[https://www.opentargets.org/ Open Targets] Another very comprehensive DB for disease target (mostly protein coding genes) and related evidence
+
*[https://bioinfo.uth.edu/scrnaseqdb/ scRNASeqDB] scRNA-seq database by UTHSC
−
*[http://denovo-db.gs.washington.edu/denovo-db/ denovo-db] a compendium of human de novo variants
+
*[http://imlspenticton.uzh.ch:3838/conquer/ conquer] A repository of consistently processed, analysis-ready single-cell RNA-seq data sets
−
*[http://diseases.jensenlab.org/ DISEASES] gene-disease association from text mining (GHR, Uniprot, textmining)
+
*[http://jinglebells.bgu.ac.il/ Jinglebells] A repository of standardized single cell RNA-Seq datasets for analysis and visualization at the single cell level
−
*[https://ghr.nlm.nih.gov/ GHR] Genetics Home Reference (by NCBI)
+
*[http://single-cell.clst.riken.jp/ SCPortalen] human and mouse single-cell centric database
−
*[http://disease-ontology.org/ Disease Ontology] Disease ontology files [http://django.nubic.northwestern.edu/fundo/ FUNDO] DOLite_term-to-genes map
+
*[https://support.10xgenomics.com/single-cell-gene-expression/datasets 10X Genomics Datasets] by 10X Genomics
−
*[http://www.human-phenotype-ontology.org/ Human Phenotype Ontology]
+
−
*[http://www.omim.org/ OMIM] Human disease DB (needs License to distribute)
+
−
*[http://www.orphadata.org OrphaData] Open database for rare diseases and orphan drug (by Orphanet)
+
−
*[http://geneticassociationdb.nih.gov/ GAD] Genetic Associationan Database: archive of human genetic association studies of complex diseases and disorders (includes summary data extracted from published candidate gene and GWAS studies).
+
−
*[http://www.nlm.nih.gov/research/umls/ UMLS] Unified Medical Language Systems
+
−
*[http://www.who.int/classifications/icd/en/ ICD] International Classification of Disease by WHO
+
−
*[http://dga.nubic.northwestern.edu DGA] Disease and Gene Annotation, an integrative set of disease-to-gene, gene-to-gene, disease-to-disease relationships
+
−
*[http://genomernai.de/GenomeRNAi/ GenomeRNAi] v12 contains 168 human RNAi, 181 D. melanogaster RNAi screen data sets
+
−
*[http://ogeedb.embl.de OGEE] Online GEne Essentiality database
+
−
*[http://www.informatics.jax.org/humanDisease.shtml Human-Mouse Disease Connection] a part of MGI
+
  
 
==Chemical Biology and Drug Research Resources==
 
==Chemical Biology and Drug Research Resources==
 +
- Prioritizing Drugs for target gene regulation
 +
*[https://maayanlab.cloud/DGB/ Drug Gene Budger] based on LINCS, GEO, CMAP data [https://pubmed.ncbi.nlm.nih.gov/30169739/ DGB reference]
 
- Drug and Bioactive chemical DBs
 
- Drug and Bioactive chemical DBs
 +
*[https://clue.io/repurposing Drug Repurposing Hub] a best-in-class drug screening collection of >3,000 clinical drugs and their annotation (structure, MoA, protein targets)
 
*[http://drugable.com/ Drugable.com] by National Library of Medicine, ~1 million chemicals, ~7000 structural pockets, ~4 millions of drug-protein interactions by docking model
 
*[http://drugable.com/ Drugable.com] by National Library of Medicine, ~1 million chemicals, ~7000 structural pockets, ~4 millions of drug-protein interactions by docking model
 
*[http://pubchem.ncbi.nlm.nih.gov/ PubChem] A DB contains drug structure and function by NCBI
 
*[http://pubchem.ncbi.nlm.nih.gov/ PubChem] A DB contains drug structure and function by NCBI
Line 167: Line 211:
  
 
- Drug Target DBs
 
- Drug Target DBs
 +
*[https://www.dgidb.org/ DGIdb] An integrated Drug-Gene Interaction DB
 
*[https://www.ncbi.nlm.nih.gov/pubmed/27910877 A curated drug-target map] by curation of [https://www.ebi.ac.uk/chembl/ ChEMBL database], [http://drugcentral.org/ DrugCentral database], [https://cansar.icr.ac.uk/ canSAR knowledge base] (Gold Standard drug-target)
 
*[https://www.ncbi.nlm.nih.gov/pubmed/27910877 A curated drug-target map] by curation of [https://www.ebi.ac.uk/chembl/ ChEMBL database], [http://drugcentral.org/ DrugCentral database], [https://cansar.icr.ac.uk/ canSAR knowledge base] (Gold Standard drug-target)
−
*[http://dgidb.genome.wustl.edu/ DGIdb] An integrated Drug-Gene Interaction DB (CancerCommons, ChEMBL, CIVIC, Clearity Foundation, DoCM, DrugBank, Guid To Pharmacology MyCancerGenome, PharmGKB, Targeted Agents in Lung Cancer TDG, TEND, TTD); go to help for download batch data file
 
 
*[http://www.genome.jp/kegg/drug/ KEGG DRUG] contains information about only approved drugs
 
*[http://www.genome.jp/kegg/drug/ KEGG DRUG] contains information about only approved drugs
 
*[http://stitch.embl.de/ STITCH] DB for known and predicted chemical-protein interaction
 
*[http://stitch.embl.de/ STITCH] DB for known and predicted chemical-protein interaction
Line 179: Line 223:
 
- Drug signature, Pharmacogenomics, Toxicogenomics DBs
 
- Drug signature, Pharmacogenomics, Toxicogenomics DBs
 
*[http://tanlab.ucdenver.edu/DSigDB/DSigDBv1.0/ DSigDB] Drug signature database for gene set analysis
 
*[http://tanlab.ucdenver.edu/DSigDB/DSigDBv1.0/ DSigDB] Drug signature database for gene set analysis
 +
*[https://clue.io/ CLUE] The expanded CMap including 1.3M L1000 profiles for 27,927 perturbagens (476,251 expressions)
 +
*[http://www.ilincs.org iLINCS] Integrated System to Analyze LINCS and other data
 
*[https://www.broadinstitute.org/cmap/ Connectivity Map (CMap)]  7,000 expression profiles representing 1,309 compounds
 
*[https://www.broadinstitute.org/cmap/ Connectivity Map (CMap)]  7,000 expression profiles representing 1,309 compounds
−
*[http://lincscloud.org/ LINCS] Library of Integrated Network-based Cellular Signatures (former Connectivity Map)
 
 
*[http://ctd.mdibl.org/ The Comparative Toxicogenomics database(CTD)] The major DB of chemical-disease links from literature curation  
 
*[http://ctd.mdibl.org/ The Comparative Toxicogenomics database(CTD)] The major DB of chemical-disease links from literature curation  
 
*[http://toxico.nibio.go.jp/english/index.html TG-GATE] Toxicogenomics data for >150 chemicals in rats and the primary cultured hepatocytes of rats and humans
 
*[http://toxico.nibio.go.jp/english/index.html TG-GATE] Toxicogenomics data for >150 chemicals in rats and the primary cultured hepatocytes of rats and humans
Line 190: Line 235:
 
*[http://mosaic.cs.umn.edu/ MOSAIC] Chemical-genetic interactions in Yeast (cover >13000 compounds)
 
*[http://mosaic.cs.umn.edu/ MOSAIC] Chemical-genetic interactions in Yeast (cover >13000 compounds)
  
−
== Cancer Genomics DBs ==
+
== Cancer Biology Resources ==
−
*[https://www.broadinstitute.org/software/cprg/ Cancer Program Resource Gateway] by Broad
+
- Cancer Somatic Mutations DBs
−
-Curated functional and clinical variants in Cancer
+
*[https://search.cancervariants.org/ meta-knowledgebase of somatic variants] Harmonized integration of Cancer Genome Interpreter, CIVIC, JAX-CKB, MolecularMatch, OncoKB, PMKB
−
*[http://civicdb.org CIViC] A knowledgebase for expert-crowdsourcing the clinical interpretation of variants in cancer
+
*[http://cancer.sanger.ac.uk/cancergenome/projects/cosmic/ COSMIC(The Catalog Of Somatic Mutations In Cancer)] By Sanger with expert curation
−
*[http://docm.info DoCM] A database of curated mutations in cancer
+
*[http://docm.info DoCM] A database of functional variants validated in cancer
−
-Catalog of Cancer genes and mutations
+
*[http://civicdb.org CIViC] A knowledgebase for expert-crowdsourcing the clinical interpretation of variants in cancer  
−
*[http://bioinfo.mc.vanderbilt.edu/TSGene/ TSGene] Literature curated Tumor suppressor genes (~1000 coding, ~200 non-coding); v2 paper also provides ~300 oncogenes in Supple
+
 
−
*[http://ncg.kcl.ac.uk/ NCG] The Network of Cancer Genes; a manually curated repository of cancer genes from the literature (1571 cancer genes by v5)
+
- Cancer Somatic Mutation Visualization
−
*[http://cancer.sanger.ac.uk/cancergenome/projects/cosmic/ COSMIC] Catalog Of Somatic Mutations In Cancer
+
*[https://pecan.stjude.cloud/proteinpaint Proteinpaint] Exploring genomic alteration in pediatric cancer
−
*[http://cancer.sanger.ac.uk/cancergenome/projects/census/ CGC] Cancer Gene Census 
+
 
−
-Cancer Genomics Data Portals
+
- Cancer Gene DBs
 +
*[http://cancer.sanger.ac.uk/cancergenome/projects/census/ CGC(Cancer Gene Census}] A catalog of genes with mutations that are causally implicated in cancer (by COSMIC)
 +
*[https://www.ncbi.nlm.nih.gov/pubmed/23539594 125 mutation-based drivers] see Supple TableS2A (71 TSG and 54 OG by 20/20 rule)
 +
*[https://bioinfo.uth.edu/TSGene/ TSGene] Literature-curated 1217 human TSGs (1018 protein-coding and 199 non-coding genes) and 320 protein-coding oncogenes
 +
*[http://ccgd-starrlab.oit.umn.edu CCGD(Candidate Cancer Gene Database)]A database of cancer driver genes from transposon-based forward genetic screens in mice
 +
*[https://www.nature.com/articles/nrc2771 77 Cancer Genes by amplification and overexpression] see Supple TableS2
 +
*[http://ncg.kcl.ac.uk/ NCG(The Network of Cancer Genes)] (~500) CGC + (~1000) Candidate genes from Panel Seq, WES, WGS studies
 +
 
 +
- Cancer Genomics Research Gateway
 +
*[https://gdc.cancer.gov/ NCI Genomic Data Commons] GDC provides the cancer research community with a unified data repository that enables data sharing across cancer genomic studies.
 +
*[https://dcc.icgc.org/ ICGC data portal] raw data from '''ICGC''' and '''TCGA'''
 +
*[https://ocg.cancer.gov/programs/target TARGET(Therapeutically Applicable Research To Generate Effective Treatments)] '''Childhood Cancer''' Genome Project by NCI
 +
*[https://www.pedpancan.com/pedpancan/ PedPanCan(A Pan-Cancer Study of '''Childhood Cancers''')] by Multi-Institutes including St. Jude Children's Research Hospital
 +
*[https://ocg.cancer.gov/ NCI Office of Cancer Genomics] OCG is dedicated to supporting cancer genomics research by sharing molecular data from its programs to enhance understanding of cancer.
 +
*[https://ocg.cancer.gov/programs/ctd2/data-portal CTD2 data portal] Data Portal of [https://ocg.cancer.gov/programs/ctd2/overview Cancer Target Discovery and Development] program which strives to functionally validate discoveries from large-scale genomic initiatives.
 
*[https://www.synapse.org/#!Synapse:syn7222066/wiki/405659 Synapse GENIE] The largest public cancer genome data by ACCR (see [http://www.aacr.org/Research/Research/Pages/aacr-project-genie.aspx#.WJv3szuLSUk ACCR GENIE project])   
 
*[https://www.synapse.org/#!Synapse:syn7222066/wiki/405659 Synapse GENIE] The largest public cancer genome data by ACCR (see [http://www.aacr.org/Research/Research/Pages/aacr-project-genie.aspx#.WJv3szuLSUk ACCR GENIE project])   
−
*[https://www.synapse.org/#!Synapse:syn300013 Synapse TCGA-Pancancer] The official resource for hosting analysis-ready TCGA Pan Cancer data
+
*[https://www.broadinstitute.org/software/cprg/ Cancer Program Resource Gateway] by Broad
−
*[http://www.cbioportal.org/ cBioPortal] Data sets from published studies including TCGA
+
 
−
*[https://cghub.ucsc.edu/ CGHub] TCGA data portal by UCSC; [http://cancergenome.nih.gov/ TCGA] The Cancer Genome Atlas project home
+
- Cancer Genomics Data Analysis Cloud Platforms
−
*[http://cancergenome.broadinstitute.org/ TumorPortal] Pan-cancer data set from many tumor types.
+
*[http://xena.ucsc.edu/ UCSC Xena] An online exploration tool for public (TCGA, ICGC and more) and private, multi-omic and clinical/phenotype data
−
*[https://dcc.icgc.org/ ICGC data portal] raw data from ICGC and TCGA
+
*[http://cgc.systemsbiology.net/ ISB-CGC] Cancer Genomics Cloud by ISB
−
*[http://methhc.mbc.nctu.edu.tw/ MethHC] A database of DNA Methylation and gene expression in Human Cancer (use Pan-cancer data)
+
*[http://mev.tm4.org WebMeV] Analysis of large genomic data, particularly for RNASeq and microarray data (TCGA, GEO, or user-uploaded).
−
-Data for survival predictions
+
 
−
*[https://www.synapse.org/#!Synapse:syn1710282 Synapse TCGA-Pancancer survival prediction] analysis-ready TCGA data for survival prediction
+
- Tumor Microenvironment Analysis tools
−
-Cancer Genomics Data Analysis Web server
+
*[https://cistrome.shinyapps.io/timer/ TIMER] Web server for a comprehensive TME analysis
−
*[http://www.cravat.us/ CRAVAT] Cancer-Related Analysis of Variants ToolKit
+
*[http://xcell.ucsf.edu/ xCell] Tumor cellular heterogeneity analysis web server; R package is also available from [https://github.com/dviraran/xCell github]
−
*[http://www.intogen.org/ IntOGen] Integrative Onco Genomics
+
 
−
-Cancer Immunity Resource
+
- Cancer Pharmacogenomics
−
*[http://cancerimmunity.org/resources/ Cancer Immunity Resource] by Cancer Immunity (now Cancer Immunology Research since 2013)
+
*[https://pharmacodb.pmgenomics.ca/ PharmacoDB] Integrative database for cancer pharmacogenomics (CCLE, GDSC, CTRP, and more)
−
-Cancer Pharmacogenomics
+
*[https://portals.broadinstitute.org/ctrp/ CTRP] The Cancer Therapeutics Response Portal (~550 drugs x ~890 cell lines)
−
*[http://www.cancerrxgene.org/ Genomics of Drug Sensitivity in Cancer (GDSC)] The largest public DB for drug sensitivity of cancer cell line and biomarkers
+
*[http://www.cancerrxgene.org/ Genomics of Drug Sensitivity in Cancer (GDSC)] (~250 drugs x ~1110 cell lines)
−
*[http://www.broadinstitute.org/ccle/home Cancer Cell line Encyclopedia (CCLE)] by Broad-Novartis, 1000 cancer cell lines, ~1200 compounds and their combinations
+
*[http://www.broadinstitute.org/ccle/home Cancer Cell line Encyclopedia (CCLE)] (~20 drugs x ~1060 cell lines)
−
*[http://dtp.nci.nih.gov/docs/cancer/cancer_data.html DTP human tumor cell line screen] by NCI-60
+
 
−
*[http://dtp.nci.nih.gov/ Developmental Therapeutics Program] by NCI (contains NCI-60 human tumor cell-line screen data)
+
- Cancer cell essential genes
−
*[http://www.sanger.ac.uk/genetics/CGP/NCI60/ NCI60 mutation data]
+
*[http://genomecrispr.dkfz.de GenomeCRISPR] A database for high-throughput CRISPR/Cas9 screening experiments
−
*[https://cabig.nci.nih.gov/caArray_GSKdata/ GKS Cancer Cell Line Data] genomic profiles for 300 cell lines
+
*[http://www.broadinstitute.org/achilles Achilles Project] shRNA-based screen for 216 cancer cell lines (v2.4.3) and CRISPR-based screen for 33 cancer cell lines (v3.3.8)
−
-Cancer cell essential genes
+
−
*[http://www.broadinstitute.org/achilles Achilles Project] shRNA-based essential gene profiles for 216 cancer cell lines
+
 
*[http://colt.ccbr.utoronto.ca/cancer/ COLT-cancer database] shRNA-based essential gene profiles for 70 breast, pancreatic, ovarian cancer cell lines
 
*[http://colt.ccbr.utoronto.ca/cancer/ COLT-cancer database] shRNA-based essential gene profiles for 70 breast, pancreatic, ovarian cancer cell lines
  
−
== Metagenome DBs and tools  ==
+
== Immunogenetics DBs and tools  ==
−
- Metagenomic data central DB
+
*[https://www.iedb.org/ Immune Epitope Database] The most comprehensive (immunogenic and pathogenic) epitope database
−
*[https://www.ebi.ac.uk/metagenomics/ EBI Metagenomics (EMG)] by EBI, UK
+
*[http://projects.met-hilab.org/tadb/ TANTIGEN] Tumor T-cell Antigen database (>1000 peptides by literature curation)
−
*[http://metagenomics.anl.gov/ MG-RAST] by Argonne National Laboratory, US
+
*[https://caped.icp.ucl.ac.be/about Cancer Antigenic Peptide Database] ~400 peptides by literature curation
−
*[https://img.jgi.doe.gov/cgi-bin/m/main.cgi IMG/MG] by Joint Genome Institute of DOE, US
+
 
−
*[http://imicrobe.us/ iMicrobe] by Gordon Betty Moore Foundation, U of Arizona
+
== Microbiomics DBs and tools ==
−
- Human microbiome
+
- Gut microbial biobank by Automated culturomics
−
*[http://meta.genomics.cn/ Integrated Reference Catalog of the Human Gut Microbiome] ~9.9M genes
+
*[http://microbial-culturomics.com/] CAMII biobank
−
*[http://www.hmpdacc.org/ Human Microbiome Project (HMP)]
+
 
−
*[http://hmp2.org/ The integrative HMP] Microbiome-host interactions during disease progression (longitudinal studies on pregnancy, IBD, T2D)
+
- Microbiome Data Analysis Resources
−
*[http://www.metahit.eu/ MetaHIT] Metagenomics of the human intestinal tract
+
*[https://www.youtube.com/playlist?list=PLOPiWVjg6aTzsA53N19YqJQeZpSCH9QPc Microbiome Discovery] Awesome Lectures by Dan Knight
 
*[http://huttenhower.sph.harvard.edu/ Huttenhower Lab] A great resource for analysis tools
 
*[http://huttenhower.sph.harvard.edu/ Huttenhower Lab] A great resource for analysis tools
 +
*[https://hcmph.sph.harvard.edu/ Harvard Chan Microbiome in Public Health Center (HCMPH)]
 +
 +
- Microbiome Catalogs and Taxonomy
 +
*[https://gtdb.ecogenomic.org/ GTDB] BACTERIAL GENOME TAXONOMY DATABASE
 +
*[https://www.mbiomenet.org/HRGM/ HRGM] Human Reference Gut Microbiome by Yonsei University
 +
*[https://www.ebi.ac.uk/metagenomics/genomes UHGG] Unified Human Gastrointestinal Genome by EBI
 +
*[http://gmgc.embl.de/ GMGC] Global Microbial Gene Catalog by EMBL
 +
 +
-Microbiome-Disease(drug, diet) interaction DBs
 +
*[https://disbiome.ugent.be/ Disbiome] Microbe-Disease interactions
 +
*[http://www.aiddlab.com/MASI/ MASI] Microbe-Drug(Disease, Diet) interactions
 +
*[http://bio-annotation.cn/gutMDisorder/ gutMDisorder] Microbe-Disease(Diet) interactions
 +
 +
- Metagenomic DB
 +
*[https://www.ebi.ac.uk/metagenomics/ MGnify] by EBI, UK
 +
*[https://img.jgi.doe.gov/cgi-bin/m/main.cgi IMG] Integrated Microbial Genomes by Joint Genome Institute of DOE, US
 +
*[http://hmp2.org/ The integrative HMP]
 +
 +
- Bacterial Culture Collection
 +
*[https://kctc.kribb.re.kr/kctc.aspx KCTC] Korean Collection for Type Cultures
 +
*[https://www.atcc.org/ ATCC Microbiology collection]
 +
*[https://www.dsmz.de/ DSMZ] German Collection of Microorganisms
 +
 +
- Human Microbiome Bioactive Molecules (including Metabolites) DB & Analysis Tools
 +
*[https://www.microbiome-bioactives.org/ HMBR] THE HUMAN MICROBIOME BIOACTIVES RESOURCE
 +
*[http://huttenhower.sph.harvard.edu/metawibele MetaWIBELE] A workflow to prioritize potentially bioactive gene products in microbial communities
 +
*[http://huttenhower.sph.harvard.edu/macarron/ MACARRoN] A tool for systematic analysis of microbiome-associated metabolomes for identification of novel, potentially bioactive small moleculeshttps
 +
 +
- Mouse Diet Resource
 +
*[https://researchdiets.com/ Research Diet]
  
−
== Proteomics Resources ==
+
== Proteome Resources ==
 
- Human Proteome Database
 
- Human Proteome Database
 
*[http://www.humanproteomemap.org/ Human Proteome Map] 85 samples from 17 adult tissues, 6 primary hematopoietic cells and 7 fetal tissues
 
*[http://www.humanproteomemap.org/ Human Proteome Map] 85 samples from 17 adult tissues, 6 primary hematopoietic cells and 7 fetal tissues
Line 256: Line 343:
 
*[http://evpedia.info EVpedia] A DB for Extracellular Vesicles with many analysis software
 
*[http://evpedia.info EVpedia] A DB for Extracellular Vesicles with many analysis software
  
−
== Other Resources ==
+
== AI, Software ==
−
- Cool software ==
+
- AI for Biomedicine
 +
*[https://www.youtube.com/channel/UCtYLUTtgS3k1Fg4y5tAhLbw StatQuest] Excellent tutorial movies for learning machine learning and more (by Josh Starmer at UNC)
 +
*[http://scikit-learn.org/ Scikit learn] Open software for Machine Learning
 +
*[https://www.coursera.org/course/ml?from_restricted_preview=1&course_id=971489&r=https%3A%2F%2Fclass.coursera.org%2Fml-004 Machine Learning by Andrew Ng]
 +
*[http://www-bcf.usc.edu/~gareth/ISL/ An Introduction To Statistical Learning] Free textbook and lecture notes
 +
*[https://github.com/Jianing-Qiu/Awesome-Healthcare-Foundation-Models Foundation Models in Biomedicine]
 +
 
 +
- Cool software
 +
*[https://cmdcolin.github.io/awesome-genome-visualization/?latest=true Awesome genome visualization] Genome visualization software depository
 
*[http://revigo.irb.hr/ REVIGO] Visualize GO enrichment summary
 
*[http://revigo.irb.hr/ REVIGO] Visualize GO enrichment summary
 +
*[https://gehlenborglab.shinyapps.io/upsetr/ UpSetR Shiny App] Visualizes set intersections in a matrix layout and introduces aggregates based on groupings and queries; R package is also available from [https://github.com/hms-dbmi/UpSetR github]
 
*[http://bioinfogp.cnb.csic.es/tools/venny/ VENNY] Drawing Venn diagram
 
*[http://bioinfogp.cnb.csic.es/tools/venny/ VENNY] Drawing Venn diagram
  
−
- Data-driven Omics companies
+
== Other Resources ==
−
*[https://www.arivale.com/ Arivale] Health coaching for wellness based on multi-omics analysis
+
- 특허
−
*[http://www.humanlongevity.com/ Human Longevity Inc.]
+
*[https://ysis2.yonsei.ac.kr/ 연세대특허관리시스템]
−
*[http://www.personalis.com/ Pesonalis] Genome-guided Medicine  
+
*[https://www.ripis.or.kr/U_Ntis.do?method=m01 과제정보검색] by 정부R&D 특허성과관리시스템
−
*[http://www.calicolabs.com/ Calico] Aging-related disease research company
+
- Contract Research Organization (CRO)
−
*[http://numedii.com/ Numedii] New Indications for Medicines
+
*[https://www.bioneer.co.kr/20-s-2500.html Standard Protein Synthesis Service] by BIONEER
 +
- IRB (Institutional Review Board, 의학연구윤리심의위원회)
 +
*[https://irb.yonsei.ac.kr/ 연세e-IRB]
 +
*[https://edu.kdca.go.kr/edu/index.html 질병관리청 IRB 교육사이트]
 +
*[https://citiprogram.org CITI-program IRB education]
 +
- Academic society & Research Center
 +
*[http://www.ksbi.or.kr/ KSBI] Korean Society of Bioinformatics
 +
*[http://www.ashg.org/ ASHG] American Society of Human Genetics
 +
*[http://www.aacr.org AACR] American Association for Cancer Research
 +
*[http://www.human-microbiome.org/ IHMC] The International Human Microbiome Consortium
 +
*[http://www.cancer.or.kr KCA] Korean Cancer Association
 +
*[http://www.kogo.or.kr KOGO] Korea Genome Organization
 +
*[http://www.ksmcb.or.kr/ KSMCB] Korean Society of Molecular and Cellular Biology
 +
*[http://new.ksbmb.or.kr/ KSBMB] Korean Society of Biochemistry and Molecular Biology
 +
*[http://www.kormb.or.kr/ KMB] The Korean Society of Microbiology and Biotechnology
 +
*[http://www.msk.or.kr/msk/ MSK] The Microbiological Society of Korea
 +
*[http://mrc-systemsmed.org/ Yonsei Medical Research Center for Systems Medicine]
 +
 
 +
- Cancer Immunology Biotech company
 +
*[https://gv20oncotherapy.com/ GV20] AI-based cancer immunotherapy development
 +
*[https://fortugabio.com/ FortugaBio] Cancer Immunotherapy
 +
*[http://www.eutilex.com/ Eutilex] Cancer Immunotherapy
 +
 
 +
- Microbiome Biotech company
 +
*[https://microba.com/ MICROBA] Precision microbiome profiling and drug discovery
 +
*[https://microbiotica.com/ Microbiotica] Microbiome-based therapeutics and biomarker discovery
 +
*[https://clinical-microbiomics.com/ Clinical Microbiomics] offer expert microbiome analysis for clinical, pre-clinical studies
 
*[http://www.enterome.fr/ Enterome] Microbiome analysis for healthcare and drug development
 
*[http://www.enterome.fr/ Enterome] Microbiome analysis for healthcare and drug development
 
*[http://www.secondgenome.com/ Second Genome] Microbiome company
 
*[http://www.secondgenome.com/ Second Genome] Microbiome company
 
*[http://www.serestherapeutics.com/ Seres Health] Microbiome company
 
*[http://www.serestherapeutics.com/ Seres Health] Microbiome company
 
*[http://www.vedantabio.com/ Vedanta Biosciences] Microbiome company
 
*[http://www.vedantabio.com/ Vedanta Biosciences] Microbiome company
 +
*[https://www.hempharma.bio/ HEM Pharma]
  
−
- Machine Learning
+
- Precision Medicine Biotech company
−
*[http://scikit-learn.org/ Scikit learn] Open software for Machine Learning
+
*[https://celsiustx.com/ Celsius Terapeutics] Novel targets and biomarker identified through single-cell RNA sequencing analysis
−
*[https://www.coursera.org/course/ml?from_restricted_preview=1&course_id=971489&r=https%3A%2F%2Fclass.coursera.org%2Fml-004 Machine Learning by Andrew Ng]
+
*[http://www.humanlongevity.com/ Human Longevity Inc.]
−
*[http://www-bcf.usc.edu/~gareth/ISL/ An Introduction To Statistical Learning] Free textbook and lecture notes
+
*[http://www.personalis.com/ Pesonalis] Genome-guided Medicine
−
 
+
*[http://www.calicolabs.com/ Calico] Aging-related disease research company
−
- Academic society
+
*[https://bostongene.com/ BostonGene] Tumor Portrait technology for Precision Oncology
−
*[http://www.ksbsb.or.kr/ KSBSB] Korean Society of Bioinformatics and Systems Biology
+
−
*[http://www.kogo.or.kr/webapp/ KGO] Korea Genome Organization
+
−
*[http://www.ksmcb.or.kr/ KSMCB] Korean Society of Molecular and Cellular Biology
+
−
*[http://new.ksbmb.or.kr/ KSBMB] Korean Society of Biochemistry and Molecular Biology
+
−
 
+
−
- Neuroscience
+
−
*[http://www.brain-map.org/ Allen Brain Atlas Data Potal] Integrative gene expression and neuroanatomical data base
+
−
*[http://www.brainmap.org/ Brainmap.org] Published functional and structural neuroimaging (by functional MRI) database
+
  
 
- Others
 
- Others
 +
*[https://dna.macrogen.com/ Macrogen] 
 
*[http://www.tedmed.com/ TEDMED] TEDTALK for Medicine and healthcare problems
 
*[http://www.tedmed.com/ TEDMED] TEDTALK for Medicine and healthcare problems
 
*[http://retractionwatch.com/ Retraction watch]
 
*[http://retractionwatch.com/ Retraction watch]
−
*[http://www.conference.city/ Conference.city] Conference search site
+
*[https://thevc.kr/] TheVC
−
*[http://www.yoonsupchoi.com/ Yoonsup Choi's Blog]
+

Latest revision as of 20:23, 8 July 2024

Contents

[edit] Google DataSet Search Engine

[edit] Gene/Genome Annotations

  • CCDS The concensus protein coding regions among NCBI, Ensembl, and Sanger (Havana) annotation
  • GENCODE The Encyclopedia of Genes
  • Metasape Gene annotation and Enrichment analysis resource by NIH

[edit] Variome Resources

- Variation DBs

  • ExAC (Exome Aggregation Consortium) Exome variation data from >60k individuals
  • 1000 Genome Project Catalog of 60 million variant sites (SNV, CNV, SV), 2535 individuals from 26 populations
  • UK10K Sequencing 10,000 people (4,000 healthy, 6,000 disease) in England
  • Genomics England Sequencing 100,000 people in England focusing on patients with a rare disease and their families and patients with cancer.
  • DiscovEHR Collaboration between the Regeneron Genetics Center (WES) and Geisinger Health System (EHR) provides the vcf by 50,000 MyCode participants
  • European Variation Archive Most comprehensive and organized by studies (include Clinical variants)
  • NCBI Variation Variation DBs (dbSNP, dbVar, dbGaP, ClinVar)
  • iJGVD Integrative Japanese Genome Variation Database
  • HGV Database The HGV database is a fully searchable online database of genome variations published in peer-reviewed Data Reports in Human Genome Variation

- Functional significance of variants

[edit] Phenome/Diseasome Resources

- Human Disease DBs

  • DisGeNET MetaDB for disease genes and variants (very comprehensive and open license)
  • Open Targets Another very comprehensive DB for disease target (mostly protein-coding genes) and related evidence
  • denovo-db a compendium of human de novo variants
  • DISEASES gene-disease association from text mining (GHR, Uniprot, textmining)
  • GHR Genetics Home Reference (by NCBI)
  • Disease Ontology Disease ontology files FUNDO DOLite_term-to-genes map
  • Human Phenotype Ontology
  • OMIM Human disease DB (needs License to distribute)
  • OrphaData Open database for rare diseases and orphan drug (by Orphanet)
  • GAD Genetic Association Database: archive of human genetic association studies of complex diseases and disorders (includes summary data extracted from published candidate gene and GWAS studies).
  • UMLS Unified Medical Language Systems
  • ICD International Classification of Disease by WHO
  • DGA Disease and Gene Annotation, an integrative set of disease-to-gene, gene-to-gene, disease-to-disease relationships
  • GenomeRNAi v12 contains 168 human RNAi, 181 D. melanogaster RNAi screen datasets
  • OGEE Online GEne Essentiality database
  • Human-Mouse Disease Connection a part of MGI

- QTL depositories

  • GTEx Portal eQTL for ~50 different tissue types in humans

- GWAS resources

  • COVID-19 Host Genetics InititativeCOVID-19 GWAS regulsts
  • GWAS ATLAS Atlas of GWAS Summary Statistics (most comprehensive!)
  • GWAS catalog Disease-associated variants; Now providing GWAS summary stat data
  • GeneATLAS GWAS for ~780 traits using 452,264 UK Biobank White British individuals
  • PheGenI Phenotype-Genotype Integrator: For a query trait, it return GWAS loci collected from all available data resources (very convenient to make a single GWAS data set for each trait)
  • LDHUB a centralized database of summary-level GWAS results
  • Genome-wide Repository of Associations between SNPs and Phenotypes (GRASP) Better than GWAS catalog, including eQTL,QTLs
  • GWASdb includes moderate SNPs (p-value < 10^-3) with manual curation from original papers; manually mapped ~1600 GWAS traits to ~500 HPO terms, ~440 DO terms, ~230 DOLite terms
  • DistiLD Diseases and Traits in Linkage Disequilibrium Blocks

- Genotype raw data depositories

- Clinical/Disease variant databases

  • CGD Clinical Genomic Database
  • HGMD The human gene mutation database (The professional version of DB is commercial. The public version of DB is not downloadable.)
  • OMIM Germline mutations for genetic diseases
  • Roche Cancer Genome Database (RCGDB) Germline/somatic mutations for cancer collected from diverse resourses (not downloadable)
  • IDbase Human Immunodeficiency-causing mutation database
  • NCBI ClinVar human variations and their relations to the human health (Not includes unreviewed data from GWAS)

- Others

  • COGS nature resources CollaborativeOncological Gene-environment Study (GOGS): Association study using ~211,000SNPs (iCOGS) for breast, ovarian, prostate cancers.
  • Personal Genome Project
  • DECIPHER Developmental Diseases to Phenotypes database with public patients (very useful for rare disease genetics research)

[edit] Interactome, Pathway/Signature Resources

- Interactome DBs

  • iRefIndex provides an index of protein interactions available in a number of primary interaction databases including BIND, BioGRID, CORUM, DIP, HPRD, InnateDB, IntAct, MatrixDB, MINT, MPact, MPIDB, MPPI, Reactome, VirHostnet, and QuickGO.
  • STRING Known and predicted PPI
  • Human Reference Interactome Project Y2H-based human protein interactions

- Pathway DBs

  • Pathguide.org A very comprehensive list of pathway and network databases
  • Gene Ontology by Gene Ontology Consortium
  • KEGG pathways and many more
  • Biocyc includes Metacyc, Ecocyc, Humancyc, Aracyc, Yeastcyc
  • Reactome A manually curated and peer-reviewed pathway DB
  • Pathway Interaction Database (PID) Human pathways curated by NCI-Nature/imported from BioCarta/Reactome
  • CORUM Comprehensive Resource of Mammalian Protein Complexes
  • NetPath A database for signaling pathways (cancer/immune signaling pathways)
  • SIGNOR 11000 manually-annotated causal relationships between proteins that participate in signal transduction
  • UniProt-GOA by EBI (support multi-species annotation)
  • UniPathway a fully manually curated resource of metabolic pathways (cross-linked to KEGG, MetaCyc)

- Signature Gene Set DBs

  • MsigDB License required for redistribution
  • GeneSigDB Manually curated gene sets from Pubmed literature
  • ImmnuneSigDB Compendium of immune signatures (now available from MsigDB)
  • CancerSEA which provides 14 signature profiles for characterization of cancer cells
  • DSigDB Drug signature database for gene set analysis
  • L1000CDS2 Return 50 signature genes for each LINCS L1000 data set using Characteristic Direction (CD) method
  • CREEDS CRowd Extracted Expression of Differential Signatures: Signature gene sets from GEO selected by crowdsourcing project using CD method

[edit] Regulome Resources

- TF and motif DB

- Epigenomics Consortium projects

- Promoter DB

  • EPD Eukaryotic Promoter Database; Databases of experimentally validated (by either publication or in-house assay) promoters in various organisms

- Enhancer DB

  • Enhancer Atlas Human enhancers based on >=3 independent high-throughput experimental datasets (contains 2,534,123 enhancers for 76 cell lines and 29 tissues)
  • dbSUPER contains 82,234 super-enhancers in 102 human and 25 mouse tissue/cell types
  • HEDD Human Enhancer Disease Database (~2.8M enhancers from ENCODE, FANTOM5, RoadMap and annotations for disease, target, variant, conservation)
  • DiseaseEnhancer manual curation of disease-associated enhancers

- Transcriptional Start Site (TSS) DB

  • DBTTS contains 491 million TSS tag sequences for 20 tissues and 7 cell cultures in human and mouse

- Chip-seq/DNase-seq DB

  • Cistrome DB the most comprehensive DB for Chip-seq and DNase-seq data

- Enhancer-Promoter Interaction DB

  • JEME Computationally inferred EPI networks for 935 human primary cells, tissues, and cell lines

- microRNA list and expression atlas

  • miRBase miRNA database by Manchester University
  • microRNA.org download miRNA expression atlas for human, mouse, rat
  • microRNAome microRNA RNA-seq based atlas for 46 primary cell types and 42 cancer or immortalized cell lines

- microRNA-target links (Gold standard)

  • miRWalk2.0 Validated links from 4 databases and text minings, Predicted links from 13 prediction data sets
  • miRTarBase Experimental-based microRNA-target links (most popular)

- microRNA-disease

  • Human microRNA Disease Database(HMDD) Manually curated microRNA-disease links (most comprehensive)
  • PhenomiR DB for dysregulated miRNA in diseases
  • dbDEMC DB for dysregulated miRNA in Cancer
  • miRGator data for miRNA expression, miRNA-mRNA paired expression profile, miRNA perturbation experiments...

- miRNA Target predictions

  • mirDIP >150M human miRNA-target predictions collected from 30 resources with integrative score

- CLIP-seq database

- lncRNA Resources

  • FANTOM-CAT An atlas of human long non-coding RNAs with accurate 5' ends
  • NONCODE Integrative annotation of long noncoding RNAs
  • lncRNAdb a reference DB for long noncoding RNAs
  • RAIN RNA–protein Association and Interaction Networks Intro to RAIN
  • NPInter ncRNA interaction database (ncRNA and other molecules)
  • RAID RNA-associated interaction DB (very comprehensive)
  • LncRNADisease a DB for lncRNA associated diseases
  • ncFANs a web server for functional annotation of ncRNA
  • LincSNP a DB of disease-associated SNP in human lncRNA and their TFBS
  • POSTAR a DB of RNA binding protein binding sites in human and mouse transcriptome (experimental and computational methods)

[edit] Single Cell Analysis Resources

- Spatial Omics Resources

- Human Cell Atlas

- scRNA-seq data analysis resources

- Depositories for scRNA-seq data

  • Single Cell Portal scRNA-seq database by Broad Institute
  • scRNASeqDB scRNA-seq database by UTHSC
  • conquer A repository of consistently processed, analysis-ready single-cell RNA-seq data sets
  • Jinglebells A repository of standardized single cell RNA-Seq datasets for analysis and visualization at the single cell level
  • SCPortalen human and mouse single-cell centric database
  • 10X Genomics Datasets by 10X Genomics

[edit] Chemical Biology and Drug Research Resources

- Prioritizing Drugs for target gene regulation

- Drug and Bioactive chemical DBs

  • Drug Repurposing Hub a best-in-class drug screening collection of >3,000 clinical drugs and their annotation (structure, MoA, protein targets)
  • Drugable.com by National Library of Medicine, ~1 million chemicals, ~7000 structural pockets, ~4 millions of drug-protein interactions by docking model
  • PubChem A DB contains drug structure and function by NCBI
  • ChEMBL A DB contains drug structure and functions by EBI
  • Drugs@FDA A DB for FDA approved drugs
  • DailyMed High quality Information about marketed drugs by NCBI
  • SuperDrug A DB contains 3D-structures of drugs

- Clinical Trial Information

- Drug Target DBs

- Drug signature, Pharmacogenomics, Toxicogenomics DBs

- Drug-Gene Interaction DBs

  • MOSAIC Chemical-genetic interactions in Yeast (cover >13000 compounds)

[edit] Cancer Biology Resources

- Cancer Somatic Mutations DBs

- Cancer Somatic Mutation Visualization

  • Proteinpaint Exploring genomic alteration in pediatric cancer

- Cancer Gene DBs

- Cancer Genomics Research Gateway

- Cancer Genomics Data Analysis Cloud Platforms

  • UCSC Xena An online exploration tool for public (TCGA, ICGC and more) and private, multi-omic and clinical/phenotype data
  • ISB-CGC Cancer Genomics Cloud by ISB
  • WebMeV Analysis of large genomic data, particularly for RNASeq and microarray data (TCGA, GEO, or user-uploaded).

- Tumor Microenvironment Analysis tools

  • TIMER Web server for a comprehensive TME analysis
  • xCell Tumor cellular heterogeneity analysis web server; R package is also available from github

- Cancer Pharmacogenomics

- Cancer cell essential genes

  • GenomeCRISPR A database for high-throughput CRISPR/Cas9 screening experiments
  • Achilles Project shRNA-based screen for 216 cancer cell lines (v2.4.3) and CRISPR-based screen for 33 cancer cell lines (v3.3.8)
  • COLT-cancer database shRNA-based essential gene profiles for 70 breast, pancreatic, ovarian cancer cell lines

[edit] Immunogenetics DBs and tools

[edit] Microbiomics DBs and tools

- Gut microbial biobank by Automated culturomics

  • [1] CAMII biobank

- Microbiome Data Analysis Resources

- Microbiome Catalogs and Taxonomy

  • GTDB BACTERIAL GENOME TAXONOMY DATABASE
  • HRGM Human Reference Gut Microbiome by Yonsei University
  • UHGG Unified Human Gastrointestinal Genome by EBI
  • GMGC Global Microbial Gene Catalog by EMBL

-Microbiome-Disease(drug, diet) interaction DBs

  • Disbiome Microbe-Disease interactions
  • MASI Microbe-Drug(Disease, Diet) interactions
  • gutMDisorder Microbe-Disease(Diet) interactions

- Metagenomic DB

- Bacterial Culture Collection

- Human Microbiome Bioactive Molecules (including Metabolites) DB & Analysis Tools

  • HMBR THE HUMAN MICROBIOME BIOACTIVES RESOURCE
  • MetaWIBELE A workflow to prioritize potentially bioactive gene products in microbial communities
  • MACARRoN A tool for systematic analysis of microbiome-associated metabolomes for identification of novel, potentially bioactive small moleculeshttps

- Mouse Diet Resource

[edit] Proteome Resources

- Human Proteome Database

  • Human Proteome Map 85 samples from 17 adult tissues, 6 primary hematopoietic cells and 7 fetal tissues
  • ProteomicsDB >10,000 raw data files from 60 human tissues, 147 cell lines, and 13 body fluids
  • The Human Protein Atlas The tissue-based map of human proteome based on Immunohistochemistry (for 32 different tissues and organs)

- Open stand-alone software for mass spectra database search (search engines)

  • MSblender A combined search engine
  • MS-GFDB: Its successor MS-GF+ is faster and more sensitive for high-resolution MS data.
  • X!TANDEM
  • Comet: the direct descendant of Crux, which is an academic version of the commercial software SEQUEST
  • MyriMatch
  • OMSSA Due to budgetary constraints NCBI has discontinued OMSSA. Historical binaries are available from here.

- Protein localization and Secretome DB

  • Vesiclepedia A DB for all types of Extracellular Vesicles (includes Exocarta)
  • Exocarta A DB for Exosome
  • EVpedia A DB for Extracellular Vesicles with many analysis software

[edit] AI, Software

- AI for Biomedicine

- Cool software

[edit] Other Resources

- 특허

- Contract Research Organization (CRO)

- IRB (Institutional Review Board, 의학연구윤리심의위원회)

- Academic society & Research Center

  • KSBI Korean Society of Bioinformatics
  • ASHG American Society of Human Genetics
  • AACR American Association for Cancer Research
  • IHMC The International Human Microbiome Consortium
  • KCA Korean Cancer Association
  • KOGO Korea Genome Organization
  • KSMCB Korean Society of Molecular and Cellular Biology
  • KSBMB Korean Society of Biochemistry and Molecular Biology
  • KMB The Korean Society of Microbiology and Biotechnology
  • MSK The Microbiological Society of Korea
  • Yonsei Medical Research Center for Systems Medicine

- Cancer Immunology Biotech company

  • GV20 AI-based cancer immunotherapy development
  • FortugaBio Cancer Immunotherapy
  • Eutilex Cancer Immunotherapy

- Microbiome Biotech company

- Precision Medicine Biotech company

- Others

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