Difference between revisions of "Web Resources"

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== Google DataSet Search Engine ==
 +
*[https://toolbox.google.com/datasetsearch Google Dataset Search]
 
== Gene/Genome Annotations ==
 
== 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
  
 
== Variome Resources ==
 
== Variome Resources ==
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- GWAS resources
 
- GWAS resources
−
*[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)  
+
*[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://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://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://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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== Interactome, Pathway/Signature Resources ==
 
== Interactome, Pathway/Signature Resources ==
 
- Interactome DBs
 
- Interactome DBs
−
*[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))
+
*[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://string-db.org/ STRING] Known and predicted PPI
 
*[http://interactome.baderlab.org/ Human Reference Interactome Project] Y2H-based human protein interactions
 
*[http://interactome.baderlab.org/ Human Reference Interactome Project] Y2H-based human protein interactions
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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]
+
*[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
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- Epigenomics Consortium projects
 
- 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
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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)
  
−
== Single Cell Genomics Resources ==  
+
== Single Cell Analysis Resources ==
−
*[https://github.com/seandavi/awesome-single-cell Awesome single cell] List of software packages for single-cell data analysis, including RNA-seq, ATAC-seq, etc (GitHub)
+
- 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://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
 
*[https://bioinfo.uth.edu/scrnaseqdb/ scRNASeqDB] scRNA-seq database by UTHSC
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==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)  
 
*[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)  
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- 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
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== Cancer Biology Resources  ==
 
== Cancer Biology Resources  ==
 
- Cancer Somatic Mutations DBs
 
- Cancer Somatic Mutations DBs
 +
*[https://search.cancervariants.org/ meta-knowledgebase of somatic variants] Harmonized integration of Cancer Genome Interpreter, CIVIC, JAX-CKB, MolecularMatch, OncoKB, PMKB
 
*[http://cancer.sanger.ac.uk/cancergenome/projects/cosmic/ COSMIC(The Catalog Of Somatic Mutations In Cancer)] By Sanger with expert curation
 
*[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 functional variants validated in cancer  
 
*[http://docm.info DoCM] A database of functional variants validated in cancer  
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- Cancer Genomics Data Analysis Cloud Platforms
 
- 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://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).
 
*[http://mev.tm4.org WebMeV] Analysis of large genomic data, particularly for RNASeq and microarray data (TCGA, GEO, or user-uploaded).
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*[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]
  
 
== Proteome Resources ==
 
== Proteome Resources ==
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*[http://www.exocarta.org/ Exocarta] A DB for Exosome
 
*[http://www.exocarta.org/ Exocarta] A DB for Exosome
 
*[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
 +
 +
== 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 ==
−
- Academic society
+
- 특허
 +
*[https://ysis2.yonsei.ac.kr/ 연세대특허관리시스템]
 +
*[https://www.ripis.or.kr/U_Ntis.do?method=m01 과제정보검색] by 정부R&D 특허성과관리시스템
 +
- Contract Research Organization (CRO)
 +
*[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.ashg.org/ ASHG] American Society of Human Genetics
 
*[http://www.aacr.org AACR] American Association for Cancer Research
 
*[http://www.aacr.org AACR] American Association for Cancer Research
 
*[http://www.human-microbiome.org/ IHMC] The International Human Microbiome Consortium
 
*[http://www.human-microbiome.org/ IHMC] The International Human Microbiome Consortium
−
*[http://www.ksbi.or.kr/ KSBI] Korean Society of Bioinformatics
 
 
*[http://www.cancer.or.kr KCA] Korean Cancer Association
 
*[http://www.cancer.or.kr KCA] Korean Cancer Association
 
*[http://www.kogo.or.kr KOGO] Korea Genome Organization
 
*[http://www.kogo.or.kr KOGO] Korea Genome Organization
 
*[http://www.ksmcb.or.kr/ KSMCB] Korean Society of Molecular and Cellular Biology
 
*[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://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]
  
−
- Cool software
+
- Cancer Immunology Biotech company
−
*[http://revigo.irb.hr/ REVIGO] Visualize GO enrichment summary
+
*[https://gv20oncotherapy.com/ GV20] AI-based cancer immunotherapy development
−
*[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]  
+
*[https://fortugabio.com/ FortugaBio] Cancer Immunotherapy
−
*[http://bioinfogp.cnb.csic.es/tools/venny/ VENNY] Drawing Venn diagram
+
*[http://www.eutilex.com/ Eutilex] Cancer Immunotherapy
  
−
- Data-driven Omics companies
+
- Microbiome Biotech company
−
*[https://www.arivale.com/ Arivale] Health coaching for wellness based on multi-omics analysis
+
*[https://microba.com/ MICROBA] Precision microbiome profiling and drug discovery
−
*[http://www.humanlongevity.com/ Human Longevity Inc.]
+
*[https://microbiotica.com/ Microbiotica] Microbiome-based therapeutics and biomarker discovery
−
*[http://www.personalis.com/ Pesonalis] Genome-guided Medicine
+
*[https://clinical-microbiomics.com/ Clinical Microbiomics] offer expert microbiome analysis for clinical, pre-clinical studies
−
*[http://www.calicolabs.com/ Calico] Aging-related disease research company
+
−
*[http://numedii.com/ Numedii] New Indications for Medicines
+
 
*[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
−
- Neuroscience
+
*[https://bostongene.com/ BostonGene] Tumor Portrait technology for Precision Oncology
−
*[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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