Difference between revisions of "Web Resources"

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(Human Pathway/Signature genes and Interactome DBs)
(Human Variome Resources)
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== Human Variome Resources ==
 
== Human Variome Resources ==
Variation DBs
+
- Variation DBs
 
*[http://exac.broadinstitute.org/ ExAC (Exome Aggregation Consortium)] Exome variation data from >60k individuals  
 
*[http://exac.broadinstitute.org/ ExAC (Exome Aggregation Consortium)] Exome variation data from >60k individuals  
 
*[http://www.1000genomes.org/ 1000 Genome Project] Catalog of 60 million variant sites (SNV, CNV, SV), 2535 individuals from 26 populations
 
*[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://ijgvd.megabank.tohoku.ac.jp/ iJGVD] Integrative Japanese Genome Variation Database
 
*[http://ijgvd.megabank.tohoku.ac.jp/ iJGVD] Integrative Japanese Genome Variation Database
 
*[https://hgv.figshare.com/?WT.mc_id=BAN_HGV_database HGV Database] The HGV database is a fully searchable online database of genome variations published in peer-reviewed Data Reports in Human Genome Variation
 
*[https://hgv.figshare.com/?WT.mc_id=BAN_HGV_database HGV Database] The HGV database is a fully searchable online database of genome variations published in peer-reviewed Data Reports in Human Genome Variation
Variant functional effect estimation
+
 
 +
- Variant functional effect estimation
 
*[http://www.columbia.edu/~ii2135/eigen.html Eigen] Assign functional important scores on genetic variants in coding and noncoding regions (human only, unsupervised integration)
 
*[http://www.columbia.edu/~ii2135/eigen.html Eigen] Assign functional important scores on genetic variants in coding and noncoding regions (human only, unsupervised integration)
 
*[http://cadd.gs.washington.edu/home CADD: Combined Annotation Dependent Depletion] a tool for scoring the deleteriousness of SNV and indels (human only, supervised integration)
 
*[http://cadd.gs.washington.edu/home CADD: Combined Annotation Dependent Depletion] a tool for scoring the deleteriousness of SNV and indels (human only, supervised integration)

Revision as of 16:00, 19 March 2017

Contents

Human Gene/Genome Annotations

  • CCDS The concensus protein coding regions among NCBI, Ensembl, and Sanger (Havana) annotation
  • GENCODE The Encyclopedia of Genes

Human 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

- Variant functional effect estimation

Human Genotype-to-Phenotype Resources

Human Pathway/Signature genes and Interactome DBs

- 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
  • 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

- Interactome DBs

  • iRefWeb a web interface to PPI consolidated from 10 public DB (BIND, BioGRID, CORUM, DIP,IntAct, HPRD, MINT, MPact, MPPI, OPHID(predicted PPIs))
  • STRING Known and predicted PPI

Epigenomics Resources

miRNA Regulome Resources

- microRNA list and expression atlas

  • miRBase miRNA database by Manchester University
  • microRNA.org download miRNA expression atlas for human, mouse, rat

- microRNA-target links (Gold standard)

  • miRWalk2.0 Validated links from 4 databases and text minings, Predicted links from 13 prediction data sets
  • miRTarBase Manually curated microRNA-target links, miRNA-mRNA paired expression profiles, miRNA-disease links
  • miRecords Manually curated microRNA-target links + predicted links (by 11 computational algorithms)
  • miRTex Text mining system for miRNA-target, miRNA-gene/gene-miRNA regulation
  • mirSel microRNA-target links by text mining
  • Comir Combinatorial miRNA target prediction tool

- microRNA-disease

  • Human microRNA Disease Database(HMDD) Manually curated microRNA-disease links
  • miR2Disease Manually curated microRNA-target links and microRNA-disease links
  • PhenomiR A knowledgebase of miRNA expression in disease and biological processes
  • miRGator data for miRNA expression, miRNA-mRNA paired expression profile, miRNA perturbation experiments...

- Target prediction software

  • TargetScan executable PITA executable miRanda excecutable
  • miRmap target prediction by multiple algorithms, excecutable, precalculated, many other related data
  • miRDB Pre-calculated miRNA-target associations (based on SVM), not executable

-CLIP-seq database

lncRNA Regulome Resources

  • 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)

Transcriptome Analysis Resources

- Data deposit servers

  • SRA Sequence Read Archive by NCBI
  • ENA European Neucleotice Archive by EBI
  • GEO Gene Expression Omnibus (for processed data only)
  • AtGenExpress Arabidopsis gene expression DB by Weigel lab (there are unpublished non-GEO data here)
  • ImmGen Immunological Genome Project Ontogenet TF-module networks based on ImmGen data

- Expression Atlas

Phenome/Diseasome Resources

  • 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 Associationan 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 data sets
  • OGEE Online GEne Essentiality database
  • Human-Mouse Disease Connection a part of MGI

Chemical Biology and Drug Research Resources

- Drug and Bioactive chemical DBs

  • 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)

Cancer Genomics DBs

-Curated functional and clinical variants in Cancer

  • CIViC A knowledgebase for expert-crowdsourcing the clinical interpretation of variants in cancer
  • DoCM A database of curated mutations in cancer

-Catalog of Cancer genes and mutations

  • TSGene Literature curated Tumor suppressor genes (~1000 coding, ~200 non-coding); v2 paper also provides ~300 oncogenes in Supple
  • NCG The Network of Cancer Genes; a manually curated repository of cancer genes from the literature (1571 cancer genes by v5)
  • COSMIC Catalog Of Somatic Mutations In Cancer
  • CGC Cancer Gene Census

-Cancer Genomics Data Portals

-Data for survival predictions

-Cancer Genomics Data Analysis Web server

  • CRAVAT Cancer-Related Analysis of Variants ToolKit
  • IntOGen Integrative Onco Genomics

-Cancer Immunity Resource

-Cancer Pharmacogenomics

-Cancer cell essential genes

  • Achilles Project shRNA-based essential gene profiles for 216 cancer cell lines
  • COLT-cancer database shRNA-based essential gene profiles for 70 breast, pancreatic, ovarian cancer cell lines

Metagenome DBs and tools

- Metagenomic data central DB

- Human microbiome

Proteomics 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

Other Resources

- Cool software ==

  • REVIGO Visualize GO enrichment summary
  • VENNY Drawing Venn diagram

- Data-driven Omics companies

- Machine Learning

- Academic society

  • KSBSB Korean Society of Bioinformatics and Systems Biology
  • KGO Korea Genome Organization
  • KSMCB Korean Society of Molecular and Cellular Biology
  • KSBMB Korean Society of Biochemistry and Molecular Biology

- Neuroscience

- Others

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