Difference between revisions of "Web Resources"

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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)
 
*[http://bergelson.uchicago.edu/regmap-data/regmap.html RegMap panel] Reginal Mapping Project for Arabidopsis natural variants (by Joy Bergelson, U on Chicago)
 
*[http://www.1001genomes.org/ 1001 Genome Project] Genetic variation] of natural population of Arabidopsis (by Detlef Weigel, MPI)
 
*[http://www.1001genomes.org/ 1001 Genome Project] Genetic variation] of natural population of Arabidopsis (by Detlef Weigel, MPI)
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 +
== Epigenome, Functional DNA elements DBs ==
 +
*[http://genome.ucsc.edu/ENCODE/ ENCODE] Encyclopedia of DNA Elements project (human, mouse)
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*[http://www.uwencode.org/data UWencode] ENCODE (human and mouse) data browser and download site
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*[http://modencode.org/ modENCODE] Encyclopedia of DNA Elements project in model organisms (worm, fly)
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*[http://www.roadmapepigenomics.org/ Road map Epigenomics] NIH Roda map Epigenomics project home
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*[http://www.regulomedb.org/ RegulomeDB] Evidences from eQTL, TF binding, matched TF motif, matched DNase Footprint, DNase peak
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*[http://dbtss.hgc.jp/ DBTSS] Transcription start site DB (with tissue specific information)
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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
  
 
== Genotype-to-Phenotype Resources ==
 
== Genotype-to-Phenotype Resources ==
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*[http://mips.helmholtz-muenchen.de/proj/ppi/ MPPI] Mammalian PPI DB at MIPS
 
*[http://mips.helmholtz-muenchen.de/proj/ppi/ MPPI] Mammalian PPI DB at MIPS
 
*[http://string-db.org/ STRING] Known and predicted PPI
 
*[http://string-db.org/ STRING] Known and predicted PPI
 
== Functional DNA elements DBs ==
 
*[http://genome.ucsc.edu/ENCODE/ ENCODE] Encyclopedia of DNA Elements project (human, mouse)
 
*[http://modencode.org/ modENCODE] Encyclopedia of DNA Elements project in model organisms (worm, fly)
 
*[http://www.regulomedb.org/ RegulomeDB] Evidences from eQTL, TF binding, matched TF motif, matched DNase Footprint, DNase peak
 
*[http://dbtss.hgc.jp/ DBTSS] Transcription start site DB (with tissue specific information)
 
*[http://epd.vital-it.ch/ EPD] The Eukaryotic Promoter Database
 
*[http://tiprod.cbi.pku.edu.cn:8080/index.html TiProD] The tissue-specific Promoter DB
 
  
 
== TF Regulation DBs ==
 
== TF Regulation DBs ==

Revision as of 15:26, 27 November 2012

Contents

Knowledgebase, GATEWAY DBs, Genome Annotations

Pathway Annotation DBs

Genomic Variation DBs

  • NCBI Variation Variation DBs (dbSNP, dbVar, dbGaP, ClinVar)
  • 1000 Genome Project Deep catalog of human genetic variation
  • Exome Variant Server by NHLBI GO Exome sequencing project (ESP)
  • MutaDATABASE a centralized and standardized DNA variation DB
  • HGMD The human gene mutation database (The professional version of DB is commercial.)
  • AtPolyDB Everything about Arabidopsis natural variants (by Magnus Nordborg, GMI)
  • RegMap panel Reginal Mapping Project for Arabidopsis natural variants (by Joy Bergelson, U on Chicago)
  • 1001 Genome Project Genetic variation] of natural population of Arabidopsis (by Detlef Weigel, MPI)

Epigenome, Functional DNA elements DBs

  • ENCODE Encyclopedia of DNA Elements project (human, mouse)
  • UWencode ENCODE (human and mouse) data browser and download site
  • modENCODE Encyclopedia of DNA Elements project in model organisms (worm, fly)
  • Road map Epigenomics NIH Roda map Epigenomics project home
  • 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

Genotype-to-Phenotype Resources

Mutation Effect Prediction Tools

Gene Expression DBs

  • GEO
  • Arrayexpress
  • PLEXdb Gene expression resources for plant and plant pathogens
  • AtGenExpress Arabidopsis gene expression DB by Weigel lab
  • Connectivity Map Expression profiles from cultured human cells treated with bioactive small molecules
  • Gene Expression Atlas Gene expression atlas for many organisms collected from various experiments (by EBI)
  • GXD The mouse Gene Expression Database (by MGI)

Protein Expression DBs

  • SUBA SUBcellular location DB for Arabidopsis proteins

Protein/Gene Interaction DBs

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

  • KEGG DRUG contains information about only approved drugs
  • STITCH DB for known and predicted chemical-protein interaction
  • Drugbank A major DB of drug/target
  • Therapeutic Target Database (TTD) A major DB of drug/target
  • MATADOR Manually Annotated Targets and Drugs Online Resource
  • PDSP Ki DB data warehouse for published and internally-derived Ki, or affinity of drugs at targets

Clinical Trials and Pharmaco/Toxicogenomics DBs

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

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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