Difference between revisions of "Web Resources"

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== Knowledgebase, GATEWAY DBs, Genome/Gene Annotations ==
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== Google DataSet Search Engine ==
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*[http://www.nature.com/scitable Scitable by Nature] Learn Science at Nature Education
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*[https://toolbox.google.com/datasetsearch Google Dataset Search]
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*[http://5e.plantphys.net/index.php Plant Physiology web]
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== Gene/Genome Annotations ==
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*[http://www.ebi.ac.uk/ EBI]
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*[http://www.ncbi.nlm.nih.gov/ NCBI]
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*[http://www.genomesonline.org/ GOLD] Genome Online Database-Genome project statistics and download links
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*[http://genome.ucsc.edu/ UCSC genome browser home]
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*[http://asia.ensembl.org/ ENSEMBL genome browser home]
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*[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
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*[http://dbtss.hgc.jp/ DBTSS] Transcription start site DB (with tissue specific information)
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*[https://metascape.org/ Metasape] Gene annotation and Enrichment analysis resource by NIH
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*[http://epd.vital-it.ch/ EPD] The Eukaryotic Promoter Database
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*[http://tiprod.cbi.pku.edu.cn:8080/index.html TiProD] The tissue-specific Promoter DB
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== The Encyclopedia of DNA Element (ENCODE) Data links ==
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== Variome Resources ==
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*[http://genome.ucsc.edu/ENCODE/dataSummary.html ENCODE data summary] List all released/approved experiments
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- Variation DBs
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*[http://genome.ucsc.edu/ENCODE/ ENCODE] Encyclopedia of DNA Elements project (human)
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*[http://exac.broadinstitute.org/ ExAC (Exome Aggregation Consortium)] Exome variation data from >60k individuals
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*[http://www.nature.com/encode/ ENCODE explore] Access to collected papers exploring ENCODE data
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*[http://www.1000genomes.org/ 1000 Genome Project] Catalog of 60 million variant sites (SNV, CNV, SV), 2535 individuals from 26 populations
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*[http://www.uwencode.org/data UWencode] ENCODE (human and mouse) data browser and download site
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*[http://www.uk10k.org/ UK10K] Sequencing 10,000 people (4,000 healthy, 6,000 disease) in England
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*[http://genome.crg.cat/encode_RNA_dashboard/ RNA Dashboard] DB for raw transcriptome data from ENCODE
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*[http://www.genomicsengland.co.uk/ Genomics England] Sequencing 100,000 people in England focusing on patients with a rare disease and their families and patients with cancer.
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*[http://www.mouseencode.org/ Mouse ENCODE] ENCODE for mouse
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*[http://www.discovehrshare.com/ DiscovEHR] Collaboration between the Regeneron Genetics Center (WES) and Geisinger Health System (EHR) provides the vcf by 50,000 MyCode participants
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*[http://modencode.org/ modENCODE] ENCODE for animal models (worm, fly)
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*[http://www.ebi.ac.uk/eva/ European Variation Archive] Most comprehensive and organized by studies (include Clinical variants)
 +
*[http://www.ncbi.nlm.nih.gov/variation/ NCBI Variation] Variation DBs (dbSNP, dbVar, dbGaP, ClinVar)
 +
*[http://ijgvd.megabank.tohoku.ac.jp/ iJGVD] Integrative Japanese Genome Variation Database
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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
  
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== NGS data analysis tools ==
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- Functional significance of variants
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*[http://code.google.com/p/bedops/ BEDOPS]A suite for common genome analysis tasks with high scalability and flexibility
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*[http://www.columbia.edu/~ii2135/eigen.html Eigen] Assign functional important scores on genetic variants in coding and noncoding regions (human only, unsupervised integration)
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*[http://code.google.com/p/bedtools/ BEDTools] A suite for BED (Browser Extensible Data) and GFF (General Feature Format) format.
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*[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://samtools.sourceforge.net/ SAMtools] A suite for SAM (Sequence Alignment/Map) format
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*[https://www.sanger.ac.uk/sanger/StatGen_Gwava GWAVA: Genome Wide Annotation of VAriants] a tool which aims to predict the functional impact of non-coding genetic variants (human only, supervised integration)
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*[http://biowhat.ucsd.edu/homer/ Homer] A suite of tools for Motif Discovery and NGS (ChIP-Seq, RNA-Seq, DNase-Seq, Hi-C). Excellent documentation!
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*[http://asia.ensembl.org/info/docs/variation/vep/index.html VEP] Variant Effect Predictor by EBI (very easy to install and use)
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*[http://fureylab.web.unc.edu/software/fseq/ F-Seq] A Feature Density Estimator for High-Throughput Sequence Tags
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*[http://bg.upf.edu/condel/home Condel] Variant effect score by integration of SIFT, Polyphen2, Massessor, MAPP, Logre
 +
*[http://sift.jcvi.org/ SIFT(Sorting Intolerent from Tolerent substitution)]
 +
*[http://sift.bii.a-star.edu.sg/sift4g/ SIFT4G] SIFT for many genomes
 +
*[http://genetics.bwh.harvard.edu/pph2/ PolyPhen-2 (Polymorphism Phenotyping v2)] for human coding region only
 +
*[http://www.regulomedb.org/ RegulomeDB] Exploring DNA functional elements for noncoding variants (by Stanford, Snyder lab)
 +
*[http://www.broadinstitute.org/mammals/haploreg HaplogReg] Exploring DNA functional elements for noncoding variants (by MIT, Kellis lab)
  
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== Pathway Annotation DBs ==
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== Phenome/Diseasome Resources ==
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- 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
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*[http://diseases.jensenlab.org/ DISEASES] gene-disease association from text mining (GHR, Uniprot, textmining)
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*[https://ghr.nlm.nih.gov/ GHR] Genetics Home Reference (by NCBI)
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*[http://disease-ontology.org/ Disease Ontology] Disease ontology files [http://django.nubic.northwestern.edu/fundo/ FUNDO] DOLite_term-to-genes map
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*[http://www.human-phenotype-ontology.org/ Human Phenotype Ontology]
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*[http://www.omim.org/ OMIM] Human disease DB (needs License to distribute)
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*[http://www.orphadata.org OrphaData] Open database for rare diseases and orphan drug (by Orphanet)
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*[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
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*[http://www.who.int/classifications/icd/en/ ICD] International Classification of Disease by WHO
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*[http://dga.nubic.northwestern.edu DGA] Disease and Gene Annotation, an integrative set of disease-to-gene, gene-to-gene, disease-to-disease relationships
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*[http://genomernai.de/GenomeRNAi/ GenomeRNAi] v12 contains 168 human RNAi, 181 D. melanogaster RNAi screen datasets
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*[http://ogeedb.embl.de OGEE] Online GEne Essentiality database
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*[http://www.informatics.jax.org/humanDisease.shtml Human-Mouse Disease Connection] a part of MGI
 +
 
 +
- QTL depositories
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*[https://www.gtexportal.org/home/ GTEx Portal] eQTL for ~50 different tissue types in humans
 +
 
 +
- GWAS resources
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*[https://www.covid19hg.org/results/ COVID-19 Host Genetics Inititative]COVID-19 GWAS regulsts
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*[https://atlas.ctglab.nl/ GWAS ATLAS] Atlas of GWAS Summary Statistics (most comprehensive!)
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*[http://www.ebi.ac.uk/gwas/ GWAS catalog] Disease-associated variants; Now providing GWAS summary stat data
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*[http://geneatlas.roslin.ed.ac.uk/ GeneATLAS] GWAS for ~780 traits using 452,264 UK Biobank White British individuals
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*[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)
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*[http://ldsc.broadinstitute.org/ldhub/ LDHUB] a centralized database of summary-level GWAS results
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*[http://apps.nhlbi.nih.gov/Grasp/ Genome-wide Repository of Associations between SNPs and Phenotypes (GRASP)] Better than GWAS catalog, including eQTL,QTLs
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*[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
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*[http://distild.jensenlab.org/ DistiLD] Diseases and Traits in Linkage Disequilibrium Blocks
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- Genotype raw data depositories
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*[http://www.humanfunctionalgenomics.org Human Functional Genomics Project] Raw data are available from [https://hfgp.bbmri.nl/ BBMRI-NL data infrastructure]
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*[http://www.ukbiobank.ac.uk/ UK Biobank] Genotype and extensive phenotype data for ~500k UK people
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*[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...)
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- Clinical/Disease variant databases
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*[http://research.nhgri.nih.gov/CGD/ CGD] Clinical Genomic Database
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*[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://www.ncbi.nlm.nih.gov/omim OMIM] Germline mutations for genetic diseases
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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)
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*[http://bioinf.uta.fi/base_root/ IDbase] Human Immunodeficiency-causing mutation database
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*[http://www.ncbi.nlm.nih.gov/clinvar/ NCBI ClinVar] human variations and their relations to the human health (Not includes unreviewed data from GWAS)
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- Others
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*[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://www.personalgenomes.org/ Personal Genome Project]
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*[https://decipher.sanger.ac.uk/ DECIPHER] Developmental Diseases to Phenotypes database with public patients (very useful for rare disease genetics research)
 +
 
 +
== Interactome, Pathway/Signature Resources ==
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- Interactome DBs
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*[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.
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*[http://string-db.org/ STRING] Known and predicted PPI
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*[http://interactome.baderlab.org/ Human Reference Interactome Project] Y2H-based human protein interactions
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 +
- Pathway DBs
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*[http://pathguide.org/ Pathguide.org] A very comprehensive list of pathway and network databases
 
*[http://www.geneontology.org/ Gene Ontology] by Gene Ontology Consortium
 
*[http://www.geneontology.org/ Gene Ontology] by Gene Ontology Consortium
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*[http://www.agbase.msstate.edu/ AgBase] Curated DB for functional analysis of agriculural animals and plants
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*[http://www.genome.jp/kegg/ KEGG] pathways and many more
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*[http://www.ebi.ac.uk/GOA/ UniProt-GOA] by EBI (support multi-species annotation)
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*[http://www.unipathway.org/ UniPathway] a fully manually curated resource of metabolic pathways (cross-linked to KEGG, MetaCyc)
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*[http://biocyc.org/ Biocyc] includes Metacyc, Ecocyc, Humancyc, Aracyc, Yeastcyc
 
*[http://biocyc.org/ Biocyc] includes Metacyc, Ecocyc, Humancyc, Aracyc, Yeastcyc
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*[http://pid.nci.nih.gov/ Pathway Interaction Database (PID)]
 
 
*[http://www.reactome.org/ Reactome] A manually curated and peer-reviewed pathway DB
 
*[http://www.reactome.org/ Reactome] A manually curated and peer-reviewed pathway DB
 +
*[http://pid.nci.nih.gov/ Pathway Interaction Database (PID)] Human pathways curated by NCI-Nature/imported from BioCarta/Reactome
 +
*[http://mips.helmholtz-muenchen.de/genre/proj/corum/index.html CORUM] Comprehensive Resource of Mammalian Protein Complexes
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*[http://www.netpath.org/ NetPath] A database for signaling pathways (cancer/immune signaling pathways)
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*[http://signor.uniroma2.it/index.jsp SIGNOR] 11000 manually-annotated causal relationships between proteins that participate in signal transduction
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*[http://www.ebi.ac.uk/GOA/ UniProt-GOA] by EBI (support multi-species annotation)
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*[http://www.unipathway.org/ UniPathway] a fully manually curated resource of metabolic pathways (cross-linked to KEGG, MetaCyc)
  
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== Genomic Variation DBs ==
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- Signature Gene Set DBs
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*[http://www.ncbi.nlm.nih.gov/variation/ NCBI Variation] Variation DBs (dbSNP, dbVar, dbGaP, ClinVar)
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*[http://software.broadinstitute.org/gsea/msigdb MsigDB] License required for redistribution
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*[http://www.1000genomes.org/ 1000 Genome Project] Deep catalog of human genetic variation
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*[http://www.genesigdb.org/genesigdb/ GeneSigDB] Manually curated gene sets from Pubmed literature
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*[http://www.completegenomics.com/ Complete Genomics] Very accurate 69 human WGS public data and more
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*[https://www.immunespace.org/announcements/home/thread.view?rowId=50 ImmnuneSigDB] Compendium of immune signatures (now available from MsigDB)
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*[http://evs.gs.washington.edu/EVS/ Exome Variant Server] by NHLBI GO Exome sequencing project (ESP)
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*[http://biocc.hrbmu.edu.cn/CancerSEA/goDownload CancerSEA] which provides 14 signature profiles for characterization of cancer cells
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*[http://www.mutadatabase.org/ MutaDATABASE] a centralized and standardized DNA variation DB
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*[http://tanlab.ucdenver.edu/DSigDB/DSigDBv1.0/ DSigDB] Drug signature database for gene set analysis
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*[http://www.hgmd.org/ HGMD] The human gene mutation database (The professional version of DB is commercial.)
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*[http://amp.pharm.mssm.edu/L1000CDS2/help/ L1000CDS2] Return 50 signature genes for each LINCS L1000 data set using Characteristic Direction (CD) method
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*[https://cynin.gmi.oeaw.ac.at/home/resources/atpolydb AtPolyDB] Everything about Arabidopsis natural variants (by Magnus Nordborg, GMI)
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*[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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*[http://bergelson.uchicago.edu/regmap-data/regmap.html RegMap panel] Reginal Mapping Project for Arabidopsis natural variants (by Joy Bergelson, U on Chicago)
+
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*[http://www.1001genomes.org/ 1001 Genome Project] Genetic variation] of natural population of Arabidopsis (by Detlef Weigel, MPI)
+
  
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== Epigenomics Resources ==
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== Regulome Resources ==
 +
- TF and motif DB
 +
*[http://humantfs.ccbr.utoronto.ca/ The Human Transcription Factors] 2765 putative TFs and 1639 confident TFs by manual curation
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*[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 Consortium projects
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*[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
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*[http://epigenie.com/ Epigenie] An informative web community for epigenetics-related research
+
*[http://ihec-epigenomes.org/ International Human Epigenome Consortium (IHEC)] The umbrella organization for international epigenomic efforts
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*[http://www.epigenesys.eu/ EpGenSys] European network to bring together epigenetic and systems biology
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*[http://www.4dnucleome.org/ 4D Nucleome] To understand the principles behind the 3D organization of the nucleus in space and time (the 4th dimension) 
  
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== Genotype-to-Phenotype Resources ==
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- Promoter DB
−
*[http://www.ncbi.nlm.nih.gov/gap dbGaP] The database of Genotypes and Phenotypes (GWAS, WGS, Exome-seq...)
+
*[http://epd.vital-it.ch/ EPD] Eukaryotic Promoter Database; Databases of experimentally validated (by either publication or in-house assay) promoters in various organisms
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*[https://www.ebi.ac.uk/ega/ EGA] European Genome-phenome Archive (GWAS, WGS, Exome-seq...)
+
−
*[http://www.genome.gov/gwastudies/ GWAS catalog] contains SNPs with p<10^-5
+
−
*[http://jjwanglab.org:8080/gwasdb/ GWASdb] contains SNPs with p<10^-3
+
−
*[http://distild.jensenlab.org/ DistiLD] Diseases and Traits in Linkage Disequilibrium Blocks
+
−
*[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
+
  
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== Mutation Effect Prediction Tools ==
+
- Enhancer DB
−
*[http://sift.jcvi.org/ SIFT(Sorting Intolerent from Tolerent substitution)]
+
*[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://genetics.bwh.harvard.edu/pph2/ PolyPhen-2 (Polymorphism Phenotyping v2)]
+
*[http://bioinfo.au.tsinghua.edu.cn/dbsuper/ dbSUPER] contains 82,234 super-enhancers in 102 human and 25 mouse tissue/cell types
−
*[http://www.regulomedb.org/ RegulomeDB] Exploring DNA functional elements for noncoding variants (by Stanford, Snyder lab)
+
*[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://www.broadinstitute.org/mammals/haploreg HaplogReg] Exploring DNA functional elements for noncoding variants (by MIT, Kellis lab)
+
*[http://biocc.hrbmu.edu.cn/DiseaseEnhancer/ DiseaseEnhancer] manual curation of disease-associated enhancers
  
−
== Gene Expression DBs ==
+
- Transcriptional Start Site (TSS) DB
−
*[http://www.ncbi.nlm.nih.gov/geo/ GEO]
+
*[http://dbtss.hgc.jp/ DBTTS] contains 491 million TSS tag sequences for 20 tissues and 7 cell cultures in human and mouse
−
*[http://www.ebi.ac.uk/arrayexpress/ Arrayexpress]
+
−
*[http://www.plexdb.org/ PLEXdb] Gene expression resources for plant and plant pathogens
+
−
*[http://www.weigelworld.org/resources/microarray/AtGenExpress/ AtGenExpress] Arabidopsis gene expression DB by Weigel lab
+
−
*[http://www.broadinstitute.org/cmap/ Connectivity Map] Expression profiles from cultured human cells treated with bioactive small molecules
+
−
*[http://www.ebi.ac.uk/gxa/ EBI Gene Expression Atlas] Gene expression atlas for many organisms collected from various experiments
+
−
*[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
+
−
*[http://www.informatics.jax.org/expression.shtml GXD] The mouse Gene Expression Database (by MGI)
+
−
*[http://flyatlas.org/ FlyAtlas] fly gene expression in 25-17 adult and 8 larval tissues
+
  
−
== Protein Expression DBs ==
+
- Chip-seq/DNase-seq DB
−
*[http://suba.plantenergy.uwa.edu.au/ SUBA] SUBcellular location DB for Arabidopsis proteins
+
*[http://cistrome.org Cistrome DB] the most comprehensive DB for Chip-seq and DNase-seq data
  
−
== Protein/Gene Interaction DBs ==
+
- Enhancer-Promoter Interaction DB
−
*[http://code.google.com/p/psicquic/ Protemic Standard Initiative Common QUery InterfaCe (PSICQUIC)]
+
*[http://yiplab.cse.cuhk.edu.hk/jeme/ JEME] Computationally inferred EPI networks for 935 human primary cells, tissues, and cell lines
−
*[http://www.imexconsortium.org/ International Molecular Exchange Consortium (IMEx)]
+
−
*[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))
+
−
*[http://bond.unleashedinformatics.com/ BIND] the Biomolecular Interaction Network Database
+
−
*[http://thebiogrid.org/ BioGRID]
+
−
*[http://mips.helmholtz-muenchen.de/genre/proj/corum/index.html CORUM] Comprehensive Resource of Mammalian Protein Complexes
+
−
*[http://dip.doe-mbi.ucla.edu/dip/ DIP] Database of Interacting Proteins
+
−
*[http://www.ebi.ac.uk/intact/ IntAct]
+
−
*[http://www.hprd.org/ HPRD] Human Protein Reference Database
+
−
*[http://mint.bio.uniroma2.it/mint/ MINT] Molecular Interaction DB
+
−
*[http://mips.helmholtz-muenchen.de/genre/proj/mpact Mpact] Representation of Interaction Data at MIPS
+
−
*[http://mips.helmholtz-muenchen.de/proj/ppi/ MPPI] Mammalian PPI DB at MIPS
+
−
*[http://string-db.org/ STRING] Known and predicted PPI
+
−
 
+
−
== TF Regulation DBs ==
+
−
*[http://autosome.ru/HOCOMOCO/ HOCOMOCO] Homo sapiencs comprehensive (TFBS) model collection (include TRANSFAC, JASPAR, ENCODE, other literatures)
+
−
*[http://www.gene-regulation.com/pub/databases.html TRANSFAC] TFBS(PWM) and more
+
−
*[http://jaspar.cgb.ki.se/ JASPAR] TFBS(PWM)
+
−
*[http://the_brain.bwh.harvard.edu/uniprobe/ UNIPROBE] Universal protein-binding motif inferred from Protein-binding Array experiments
+
−
*[http://rulai.cshl.edu/cgi-bin/TRED/ TRED] a transcriptional regulatory element database (contains curated TF-target links for 36 TF families)
+
−
*[http://www.oreganno.org/oregano/ ORegAnno] DNA regulatory regions, TFBS, regulatory variants
+
−
*[http://arabidopsis.med.ohio-state.edu/ AGRIS] Arabidopsis Gene Regulatory Information Server (by OSU)
+
−
*[http://plntfdb.bio.uni-potsdam.de// PlnTFDB] Plant TF database by University of Potsdam, Germany
+
−
*[http://planttfdb.cbi.pku.edu.cn// PlantTFDB] Plant TF database by Peking University, China
+
  
−
== miRNA and target/ long noncoding RNA DBs ==
+
- 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
−
*[http://miRGator.kobic.re.kr miRGator] data for miRNA expression, miRNA-mRNA paired expression profile, miRNA perturbation experiments...
+
*[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
−
*[http://www.microrna.gr/tarbase TarBase] Manually curated microRNA-target links (includes high throughput evidences) [http://diana.cslab.ece.ntua.gr/tarbase/tarbase_download.php download page]
+
−
*[http://miRecords.umn.edu/miRecords miRecords] Manually curated microRNA-target links + predicted links (by 11 computational algorithms)
+
−
*[http://mirtarbase.mbc.nctu.edu.tw/ miRTarBase] Manually curated microRNA-target links
+
−
*[http://www.mir2disease.org/ miR2Disease] Manually curated microRNA-target links and microRNA-disease links
+
−
*[http://jcclab.science.oregonstate.edu// Carrington Lab Resource]  Various DBs for plant miRNA
+
−
*[http://noncode.org/NONCODERv3/ NONCODER] A DB for all ncRNAs
+
−
*[http://www.lncrnadb.org/ lncran DB] A DB for long non-coding RNAs
+
  
−
== Phenotype/Disease Annotation DBs ==
+
- microRNA-target links (Gold standard)
−
*[http://disease-ontology.org/ Disease Ontology] Disease ontology files [http://django.nubic.northwestern.edu/fundo/ FUNDO] DOLite_term-to-genes map
+
*[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://dga.nubic.northwestern.edu DGA] Disease and Gene Annotation, an integrative set of disease-to-gene, gene-to-gene, disease-to-disease relationships
+
*[http://mirtarbase.mbc.nctu.edu.tw/ miRTarBase] Experimental-based microRNA-target links (most popular)
−
*[http://www.human-phenotype-ontology.org/ Human Phenotype Ontology]
+
−
*[http://www.omim.org/ OMIM] Human disease DB
+
−
*[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://genomernai.de/GenomeRNAi/ GenomeRNAi] A Phenotype DB for large-scale RNAi screens (human, mouse, fly, worm...)
+
−
*[http://ogeedb.embl.de OGEE] Online GEne Essentiality database
+
  
−
== Drug/Bio-active chemical DBs ==
+
- microRNA-disease
 +
*[http://202.38.126.151/hmdd/tools/hmdd2.html Human microRNA Disease Database(HMDD)] Manually curated microRNA-disease links (most comprehensive)
 +
*[http://mips.helmholtz-muenchen.de/phenomir/ PhenomiR] DB for dysregulated miRNA in diseases
 +
*[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...
 +
 
 +
- miRNA Target predictions
 +
*[http://ophid.utoronto.ca/mirDIP/ mirDIP] >150M human miRNA-target predictions collected from 30 resources with integrative score
 +
 
 +
- CLIP-seq database
 +
*[http://starbase.sysu.edu.cn/ StarBase] DB for CLIP-seq data
 +
 
 +
- 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.lncrnadb.org/ lncRNAdb] a reference DB for long noncoding RNAs
 +
*[http://rth.dk/resources/rain/ RAIN] RNA–protein Association and Interaction Networks [http://benasque.org/2015rna/talks_contr/283_20150728-RAIN-Benasque.pdf Intro to RAIN]
 +
*[http://www.bioinfo.org/NPInter/ NPInter] ncRNA interaction database (ncRNA and other molecules)
 +
*[http://www.rna-society.org/raid/ RAID] RNA-associated interaction DB (very comprehensive)
 +
*[http://cmbi.bjmu.edu.cn/lncrnadisease LncRNADisease] a DB for lncRNA associated diseases
 +
*[http://www.bioinfo.org/ncfans/ ncFANs] a web server for functional annotation of ncRNA
 +
*[http://210.46.80.146/lincsnp/ LincSNP] a DB of disease-associated SNP in human lncRNA and their TFBS
 +
*[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)
 +
 
 +
== Single Cell Analysis Resources ==
 +
- Spatial Omics Resources
 +
*[https://github.com/crazyhottommy/awesome_spatial_omics awesome_spatial_omics]
 +
- Human Cell Atlas
 +
*[https://www.humancellatlas.org/ HCA]
 +
*[https://chanzuckerberg.com/science/programs-resources/humancellatlas/ Chan Zukerburg Initiative HCA seed networks]
 +
*[https://www.covid19cellatlas.org/ COVID-19 Cell Atlas] Data portal by HCA
 +
- scRNA-seq data analysis resources
 +
*[https://satijalab.org/seurat/ Seurat] The package for scRNA-seq data analysis
 +
*[https://velocyto.org Velocyto] RNA Velocity analysis with steady-state model
 +
*[https://scvelo.org scVelo] Generalized RNA Velocity analysis through dynamic modeling
 +
*[https://www.sanger.ac.uk/science/tools/scrna-seq-analysis-course scRNA-seq analysis course by Sanger]
 +
*[https://www.cellphonedb.org/ CellPhoneDB] A repository of curated receptors, ligands and their interactions.
 +
*[https://github.com/seandavi/awesome-single-cell Awesome single cell]
 +
*[https://www.scrna-tools.org/ scRNA-tools DB]
 +
- Depositories for scRNA-seq data
 +
*[https://portals.broadinstitute.org/single_cell Single Cell Portal] scRNA-seq database by Broad Institute
 +
*[https://bioinfo.uth.edu/scrnaseqdb/ scRNASeqDB] scRNA-seq database by UTHSC
 +
*[http://imlspenticton.uzh.ch:3838/conquer/ conquer] A repository of consistently processed, analysis-ready single-cell RNA-seq data sets
 +
*[http://jinglebells.bgu.ac.il/ Jinglebells] A repository of standardized single cell RNA-Seq datasets for analysis and visualization at the single cell level
 +
*[http://single-cell.clst.riken.jp/ SCPortalen] human and mouse single-cell centric database
 +
*[https://support.10xgenomics.com/single-cell-gene-expression/datasets 10X Genomics Datasets] by 10X Genomics
 +
 
 +
==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
 +
*[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://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
 
*[https://www.ebi.ac.uk/chembl/ ChEMBL] A DB contains drug structure and functions by EBI
 
*[https://www.ebi.ac.uk/chembl/ ChEMBL] A DB contains drug structure and functions by EBI
 +
*[http://www.accessdata.fda.gov/scripts/cder/drugsatfda/ Drugs@FDA] A DB for FDA approved drugs
 +
*[http://dailymed.nlm.nih.gov/dailymed/ DailyMed] High quality Information about marketed drugs by NCBI
 
*[http://bioinf.charite.de/superdrug/ SuperDrug] A DB contains 3D-structures of drugs
 
*[http://bioinf.charite.de/superdrug/ SuperDrug] A DB contains 3D-structures of drugs
  
−
== Drug-Target relationship DBs ==
+
- Clinical Trial Information
 +
*[http://clinicaltrials.gov/ ClinicalTrials.gov] DB for clinical trials conducted around the world
 +
 
 +
- 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)
 
*[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 142: Line 218:
 
*[http://bidd.nus.edu.sg/group/ttd/ttd.asp Therapeutic Target Database (TTD)] A major DB of drug/target
 
*[http://bidd.nus.edu.sg/group/ttd/ttd.asp Therapeutic Target Database (TTD)] A major DB of drug/target
 
*[http://matador.embl.de/ MATADOR] Manually Annotated Targets and Drugs Online Resource
 
*[http://matador.embl.de/ MATADOR] Manually Annotated Targets and Drugs Online Resource
 +
*[http://www.guidetopharmacology.org/ IUPHAR/BPS Guide to Pharmacology] A DB of in-depth information of drug targets and ligands
 
*[http://pdsp.med.unc.edu/kidb.php PDSP Ki DB] data warehouse for published and internally-derived Ki, or affinity of drugs at targets
 
*[http://pdsp.med.unc.edu/kidb.php PDSP Ki DB] data warehouse for published and internally-derived Ki, or affinity of drugs at targets
  
−
== Clinical Trials and Pharmaco/Toxicogenomics DBs ==
+
- Drug signature, Pharmacogenomics, Toxicogenomics DBs
−
*[http://clinicaltrials.gov/ ClinicalTrials.gov] DB for clinical trials conducted around the world
+
*[http://tanlab.ucdenver.edu/DSigDB/DSigDBv1.0/ DSigDB] Drug signature database for gene set analysis
−
*[http://ctd.mdibl.org/ CTD] The Comparative Toxicogenomics database
+
*[https://clue.io/ CLUE] The expanded CMap including 1.3M L1000 profiles for 27,927 perturbagens (476,251 expressions)
−
*[http://www.niehs.nih.gov/research/resources/databases/cebs/index.cfm CEBS] Chemical Effects in Biological Systems, an integrated public repository for toxicogenomics data
+
*[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
 +
*[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://www.niehs.nih.gov/research/resources/databases/cebs/index.cfm Chemical Effects in Biological Systems(CEBS)] an integrated public repository for toxicogenomics data
 
*[http://www.pharmgkb.org/ PharmGKB] The Parmacogenomics Knowledgebase
 
*[http://www.pharmgkb.org/ PharmGKB] The Parmacogenomics Knowledgebase
 
*[http://sideeffects.embl.de/ SIDER] Side Effect Resource
 
*[http://sideeffects.embl.de/ SIDER] Side Effect Resource
  
−
== Organism-centric DBs ==
+
- Drug-Gene Interaction DBs
−
*[http://www.wormbase.org/ WormBase]
+
*[http://mosaic.cs.umn.edu/ MOSAIC] Chemical-genetic interactions in Yeast (cover >13000 compounds)
−
*[http://flybase.org/ FlyBase]
+
−
*[http://www.informatics.jax.org/ MGI]
+
−
*[http://www.arabidopsis.org/ TAIR]
+
−
*[http://www.gramene.org/ Gramene]
+
−
*[http://rice.plantbiology.msu.edu/ RGAP] Rice Genome Annotation Project by MSU (Go get the part list here!)
+
−
*[http://www.maizegdb.org/ MaizeGDB]
+
−
*[http://porteco.org/ PortEco] Portal for E. coli
+
−
*[http://www.pseudomonas.com/ Pseudomonas Genome Database]
+
−
*[http://www.yeastgenome.org/ Saccharomyces Genome Database]
+
−
*[http://www.candidagenome.org/ Candida Genome Database]
+
−
*[http://img.jgi.doe.gov/ IMG] Integrated Microbial Genomes (include metagenome data)  
+
  
−
== Metagenome DBs ==
+
== Cancer Biology Resources ==
−
*[http://portal.camera.calit2.net/gridsphere/gridsphere CAMERA 2.0] Curated DB and analysis tool for metagenomes
+
- Cancer Somatic Mutations DBs
−
*[http://www.ncbi.nlm.nih.gov/genomes/lenvs.cgi NCBI Metagenome DB] Categorized with metagenome types, sources and sequencing methods.
+
*[https://search.cancervariants.org/ meta-knowledgebase of somatic variants] Harmonized integration of Cancer Genome Interpreter, CIVIC, JAX-CKB, MolecularMatch, OncoKB, PMKB
−
*[http://www.openmicrobiome.org/ OMI] Open Microbiome Initiative
+
*[http://cancer.sanger.ac.uk/cancergenome/projects/cosmic/ COSMIC(The Catalog Of Somatic Mutations In Cancer)] By Sanger with expert curation
−
*[http://www.earthmicrobiome.org/ EMP] Earh Microbiome Project will sequence 10,000 metagenomes in an year, 200,000 metagenomes in 3 years
+
*[http://docm.info DoCM] A database of functional variants validated in cancer
 +
*[http://civicdb.org CIViC] A knowledgebase for expert-crowdsourcing the clinical interpretation of variants in cancer
  
−
== Cancer Genome/Cell Line Biology DBs ==
+
- Cancer Somatic Mutation Visualization
−
*[http://cancergenome.nih.gov/ TCGA] The Cancer Genome Atlas
+
*[https://pecan.stjude.cloud/proteinpaint Proteinpaint] Exploring genomic alteration in pediatric cancer
−
*[https://cghub.ucsc.edu/ CGHub] The Cancer Genomics Hub by UCSC (a repository for TCGA data)
+
 
−
*[http://www.icgc.org/home ICGC cancer genome project] International Cancer Genome Consortium Cancer genome project
+
- Cancer Gene DBs  
−
*[http://www.pediatriccancergenomeproject.org/ PCGP] The Pediatric Cancer Genome Project
+
*[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)
−
*[http://www.cancerrxgene.org/ Genomics of Drug Sensitivity in Cancer (GDSC)] The largest public DB for drug sensitivity of cancer cell line and biomarkers
+
*[https://www.ncbi.nlm.nih.gov/pubmed/23539594 125 mutation-based drivers] see Supple TableS2A (71 TSG and 54 OG by 20/20 rule)
−
*[http://www.broadinstitute.org/ccle/home Cancer Cell line Encyclopedia (CCLE)] by Broad-Novartis, 1000 cancer cell lines, ~1200 compounds and their combinations
+
*[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://dtp.nci.nih.gov/docs/cancer/cancer_data.html DTP human tumor cell line screen] by NCI-60
+
*[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
−
*[http://dtp.nci.nih.gov/ Developmental Therapeutics Program] by NCI (contains NCI-60 human tumor cell-line screen data)
+
*[https://www.nature.com/articles/nrc2771 77 Cancer Genes by amplification and overexpression] see Supple TableS2
−
*[http://www.sanger.ac.uk/genetics/CGP/NCI60/ NCI60 mutation data]
+
*[http://ncg.kcl.ac.uk/ NCG(The Network of Cancer Genes)] (~500) CGC + (~1000) Candidate genes from Panel Seq, WES, WGS studies
−
*[https://cabig.nci.nih.gov/caArray_GSKdata/ GKS Cancer Cell Line Data] genomic profiles for 300 cell lines
+
 
 +
- 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.broadinstitute.org/software/cprg/ Cancer Program Resource Gateway] by Broad
 +
 
 +
- Cancer Genomics Data Analysis Cloud Platforms
 +
*[http://xena.ucsc.edu/ UCSC Xena] An online exploration tool for public (TCGA, ICGC and more) and private, multi-omic and clinical/phenotype data
 +
*[http://cgc.systemsbiology.net/ ISB-CGC] Cancer Genomics Cloud by ISB
 +
*[http://mev.tm4.org WebMeV] Analysis of large genomic data, particularly for RNASeq and microarray data (TCGA, GEO, or user-uploaded).
 +
 
 +
- Tumor Microenvironment Analysis tools
 +
*[https://cistrome.shinyapps.io/timer/ TIMER] Web server for a comprehensive TME analysis
 +
*[http://xcell.ucsf.edu/ xCell] Tumor cellular heterogeneity analysis web server; R package is also available from [https://github.com/dviraran/xCell github]
 +
 
 +
- Cancer Pharmacogenomics
 +
*[https://pharmacodb.pmgenomics.ca/ PharmacoDB] Integrative database for cancer pharmacogenomics (CCLE, GDSC, CTRP, and more)
 +
*[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)] (~250 drugs x ~1110 cell lines)
 +
*[http://www.broadinstitute.org/ccle/home Cancer Cell line Encyclopedia (CCLE)] (~20 drugs x ~1060 cell lines)
 +
 
 +
- Cancer cell essential genes
 +
*[http://genomecrispr.dkfz.de GenomeCRISPR] A database for high-throughput CRISPR/Cas9 screening experiments
 +
*[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)
 
*[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
  
−
== Stem Cell Biology DBs ==
+
== Immunogenetics DBs and tools  ==
−
*[http://discovery.hsci.harvard.edu/ SCDE] The Stem Cell Discovery Engine
+
*[https://www.iedb.org/ Immune Epitope Database] The most comprehensive (immunogenic and pathogenic) epitope database
−
*[http://www.maayanlab.net/ESCAPE/ ESCAPE] Embryonic Stem Cell Atlas of Pluripotency Evidence (Many stem cell related networks)
+
*[http://projects.met-hilab.org/tadb/ TANTIGEN] Tumor T-cell Antigen database (>1000 peptides by literature curation)
 +
*[https://caped.icp.ucl.ac.be/about Cancer Antigenic Peptide Database] ~400 peptides by literature curation
 +
 
 +
== Microbiomics DBs and tools  ==
 +
- Gut microbial biobank by Automated culturomics
 +
*[http://microbial-culturomics.com/] CAMII biobank
 +
 
 +
- Microbiome Data Analysis Resources
 +
*[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
 +
*[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]
 +
 
 +
== Proteome Resources ==
 +
- Human Proteome Database
 +
*[http://www.humanproteomemap.org/ Human Proteome Map] 85 samples from 17 adult tissues, 6 primary hematopoietic cells and 7 fetal tissues
 +
*[https://www.proteomicsdb.org ProteomicsDB] >10,000 raw data files from 60 human tissues, 147 cell lines, and 13 body fluids
 +
*[http://www.proteinatlas.org/ 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)
 +
*[http://www.marcottelab.org/index.php/MSblender MSblender] A combined search engine
 +
*[http://proteomics.ucsd.edu/Software/MSGFDB/ MS-GFDB]: Its successor [http://proteomics.ucsd.edu/Software/MSGFPlus/ MS-GF+] is faster and more sensitive for high-resolution MS data.
 +
*[http://www.thegpm.org/TANDEM/ X!TANDEM]
 +
*[http://comet-ms.sourceforge.net/ Comet]: the direct descendant of [http://noble.gs.washington.edu/proj/crux/ Crux], which is an academic version of the commercial software SEQUEST
 +
*[http://fenchurch.mc.vanderbilt.edu/software.php MyriMatch]
 +
*[http://pubchem.ncbi.nlm.nih.gov/omssa/ OMSSA] Due to budgetary constraints NCBI has discontinued OMSSA. Historical binaries are available from here.
 +
- Protein localization and Secretome DB
 +
*[http://microvesicles.org/ Vesiclepedia] A DB for all types of Extracellular Vesicles (includes Exocarta)
 +
*[http://www.exocarta.org/ Exocarta] A DB for Exosome
 +
*[http://evpedia.info EVpedia] A DB for Extracellular Vesicles with many analysis software
 +
 
 +
== AI, 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
 +
*[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
  
 
== Other Resources ==
 
== Other Resources ==
−
*[https://www.coursera.org/ COURSERA] Online-course for free
+
- 특허
−
*[http://www.the-dream-project.org/ DREAM] Dialogue for Reverse Engineering Assessments and Methods
+
*[https://ysis2.yonsei.ac.kr/ 연세대특허관리시스템]
−
*[http://sagebase.org/ Sage Bionetworks]
+
*[https://www.ripis.or.kr/U_Ntis.do?method=m01 과제정보검색] by 정부R&D 특허성과관리시스템
−
*[https://www.assaydepot.com/ Assay depot] Online marketplace for pharmaceutical research service
+
- Contract Research Organization (CRO)
−
*[http://genomeinterpretation.org/ CAGI] Critical Assessment of Genome Interpretation
+
*[https://www.bioneer.co.kr/20-s-2500.html Standard Protein Synthesis Service] by BIONEER
−
*[http://numedii.com/ Numedii] New Indications for Medicines
+
- IRB (Institutional Review Board, 의학연구윤리심의위원회)
−
*[http://nightscience.org/ nightscience] Collective creativity in scientific discovery games
+
*[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.secondgenome.com/ Second Genome] Microbiome company
 +
*[http://www.serestherapeutics.com/ Seres Health] Microbiome company
 +
*[http://www.vedantabio.com/ Vedanta Biosciences] Microbiome company
 +
*[https://www.hempharma.bio/ HEM Pharma]
 +
 
 +
- Precision Medicine Biotech company
 +
*[https://celsiustx.com/ Celsius Terapeutics] Novel targets and biomarker identified through single-cell RNA sequencing analysis
 +
*[http://www.humanlongevity.com/ Human Longevity Inc.]
 +
*[http://www.personalis.com/ Pesonalis] Genome-guided Medicine
 +
*[http://www.calicolabs.com/ Calico] Aging-related disease research company
 +
*[https://bostongene.com/ BostonGene] Tumor Portrait technology for Precision Oncology
 +
 
 +
- Others
 +
*[https://dna.macrogen.com/ Macrogen] 
 +
*[http://www.tedmed.com/ TEDMED] TEDTALK for Medicine and healthcare problems
 +
*[http://retractionwatch.com/ Retraction watch]
 +
*[https://thevc.kr/] TheVC

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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