Difference between revisions of "Web Resources"

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== Knowledgebase, GATEWAY DBs, Genome/Gene Annotations ==
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== Human 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

Revision as of 15:18, 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

Epigenomics and Regulomics Resources

  • ENCODE Encyclopedia of DNA Elements project (human)
  • Road map Epigenomics NIH Roda map Epigenomics project home
  • International Human Epigenome Consortium (IHEC) The umbrella organization for international epigenomic efforts
  • 4D Nucleome To understand the principles behind the 3D organization of the nucleus in space and time (the 4th dimension)
  • GREAT Genomic Regions Enrichment of Annotations Tool; Predict functions for cis-regulatory regions
  • CistromeMap A knowledgebase for ChIP-Seq and DNase-Seq studies in mouse and human
  • Gene Regulation Info A very useful site for epigenetics and TF-DNA interaction studies (by Dr. Vladimir Teif)

Human Genomic 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

Genetic variant functional impact scoring Tools

Genotype-to-Phenotype Resources

Pathway/Signature gene set 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

- PPIs by curation

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

- Inferred gene interactions

  • STRING Known and predicted PPI

TF binding site motif DBs

-TFBS motif model DB

-Tools for MOTIF discovery and searching

  • MEME Suite has everything for motif based sequence analysis

miRNA DBs and target prediction tools

-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

ncRNA related DBs and Servers

  • 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)

Gene Expression DBs (Microarray/RNA-seq)

Data deposit servers

NGS data public depositories

  • SRA Sequence Read Archive by NCBI
  • ENA European Neucleotice Archive by EBI
  • GEO Gene Expression Omnibus (for processed data only)
  • GEO
  • 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

Mass Spectrometer or Immunohistochemistry 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 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 softwares
  • SUBA SUBcellular location DB for Arabidopsis proteins

Phenotype/Disease Annotation 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 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

Drug/Bio-active 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

Drug-Target relationship/ Chemical genomics DBs

Drug signature, Pharmacogenomics, Toxicogenomics, Clinical Trials

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

Genome Engineering Resources

  • Addgene Plasmids for Genome Engineering
  • Zhang Lab Feng Zhang at MIT (CRISPR resource, Optic control)
  • Joung Lab Keith Joung at Harvard (TALEN resource, CRISPR resource)

Data-driven Omics companies

Other Resources

-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

- Other Systems Biology Links

  • DREAM Dialogue for Reverse Engineering Assessments and Methods
  • Sage Bionetworks
  • Assay depot Online marketplace for pharmaceutical research service
  • CAGI Critical Assessment of Genome Interpretation

- Neuroscience

- Others

Cool Web servers

  • REVIGO Visualize GO enrichment summary
  • VENNY Drawing Venn diagram
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