Difference between revisions of "Web Resources"

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(TF Regulation DBs)
(TF Regulation DBs)
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*[http://jaspar.cgb.ki.se/ JASPAR] TFBS(PWM)
 
*[http://jaspar.cgb.ki.se/ JASPAR] TFBS(PWM)
 
*[http://rulai.cshl.edu/cgi-bin/TRED/ TRED] a transcriptional regulatory element database (contains curated TF-target links for 36 TF families)
 
*[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://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://plntfdb.bio.uni-potsdam.de// PlnTFDB] Plant TF database by University of Potsdam, Germany

Revision as of 22:17, 9 August 2012

Contents

Knowledgebase, GATEWAY DBs, Genome Annotations

Pathway Annotation DBs

Genomic Variation DBs

Genotype-to-Phenotype Resources

  • dbGaP The database of Genotypes and Phenotypes (GWAS, WGS, Exome-seq...)
  • EGA European Genome-phenome Archive (GWAS, WGS, Exome-seq...)
  • GWAS catalog contains SNPs with p<10^-5
  • GWASdb contains SNPs with p<10^-3
  • DistiLD Diseases and Traits in Linkage Disequilibrium Blocks
  • Personal Genome Project

Mutation Effect Prediction Tools

Gene Expression DBs

Protein Expression DBs

  • SUBA SUBcellular location DB for Arabidopsis proteins

Protein/Gene Interaction DBs

Functional DNA elements DBs

  • ENCODE Encyclopedia of DNA Elements project (human, mouse)
  • modENCODE Encyclopedia of DNA Elements project in model organisms (worm, fly)
  • RegulomeDB Evidences from eQTL, TF binding, matched TF motif, matched DNase Footprint, DNase peak
  • DBTSS Transcription start site DB (with tissue specific information)
  • EPD The Eukaryotic Promoter Database
  • TiProD The tissue-specific Promoter DB

TF Regulation DBs

  • TRANSFAC TFBS(PWM) and more
  • JASPAR TFBS(PWM)
  • TRED a transcriptional regulatory element database (contains curated TF-target links for 36 TF families)
  • ORegAnno DNA regulatory regions, TFBS, regulatory variants
  • AGRIS Arabidopsis Gene Regulatory Information Server (by OSU)
  • PlnTFDB Plant TF database by University of Potsdam, Germany
  • PlantTFDB Plant TF database by Peking University, China
  • hmChIP DB for publicly available human and mouse ChIP-seq and ChIP-chip data

miRNA and target DBs

  • miRBase miRNA database by Manchester University
  • microRNA.org download miRNA expression atlas for human, mouse, rat
  • miRGator data for miRNA expression, miRNA-mRNA paired expression profile, miRNA perturbation experiments...
  • TarBase Manually curated microRNA-target links (includes high throughput evidences) download page
  • miRecords Manually curated microRNA-target links + predicted links (by 11 computational algorithms)
  • miRTarBase Manually curated microRNA-target links
  • miR2Disease Manually curated microRNA-target links and microRNA-disease links
  • Carrington Lab Resource Various DBs for plant miRNA

Phenotype/Disease Annotation DBs

Drug/Bio-active chemical DBs

  • PubChem A DB contains drug structure and function by NCBI
  • ChEMBL A DB contains drug structure and functions by EBI
  • SuperDrug A DB contains 3D-structures of drugs

Drug-Target relationship DBs

Clinical Trials and Pharmacology DBs

  • ClinicalTrials.gov DB for clinical trials conducted around the world
  • CTD The Comparative Toxicogenomics database
  • SIDER Side Effect Resource
  • CEBS Chemical Effects in Biological Systems, an integrated public repository for toxicogenomics data

Animal Genome DBs

Plant Genome DBs

Microbial/Microbiome DBs

Cancer Genome/Cell Line Biology DBs

Stem Cell Biology DBs

  • SCDE The Stem Cell Discovery Engine
  • ESCAPE Embryonic Stem Cell Atlas of Pluripotency Evidence (Many stem cell related networks)

Other Resources

  • DREAM Dialogue for Reverse Engineering Assessments and Methods
  • Sage Bionetworks
  • Assay depot Online marketplace for pharmaceutical research service
  • CAGI Critical Assessment of Genome Interpretation
  • Numedii New Indications for Medicines
  • nightscience Collective creativity in scientific discovery games
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