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Contents

Knowledgebase, GATEWAY DBs, Genome/Gene Annotations

The Encyclopedia of DNA Element (ENCODE) Data links

NGS data analysis tools

  • BEDOPSA suite for common genome analysis tasks with high scalability and flexibility
  • BEDTools A suite for BED (Browser Extensible Data) and GFF (General Feature Format) format.
  • SAMtools A suite for SAM (Sequence Alignment/Map) format
  • Homer A suite of tools for Motif Discovery and NGS (ChIP-Seq, RNA-Seq, DNase-Seq, Hi-C). Excellent documentation!
  • F-Seq A Feature Density Estimator for High-Throughput Sequence Tags

Pathway Annotation DBs

Genomic Variation DBs

  • NCBI Variation Variation DBs (dbSNP, dbVar, dbGaP, ClinVar)
  • 1000 Genome Project Deep catalog of human genetic variation
  • Complete Genomics Very accurate 69 human WGS public data and more
  • 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)

Epigenomics Resources

Genotype-to-Phenotype Resources

Mutation Effect Prediction Tools

Gene Expression DBs

Protein Expression DBs

  • SUBA SUBcellular location DB for Arabidopsis proteins

Protein/Gene Interaction DBs

TF Regulation DBs

  • HOCOMOCO Homo sapiencs comprehensive (TFBS) model collection (include TRANSFAC, JASPAR, ENCODE, other literatures)
  • TRANSFAC TFBS(PWM) and more
  • JASPAR TFBS(PWM)
  • UNIPROBE Universal protein-binding motif inferred from Protein-binding Array experiments
  • 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

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

  • Disease Ontology Disease ontology files FUNDO DOLite_term-to-genes map
  • DGA Disease and Gene Annotation, an integrative set of disease-to-gene, gene-to-gene, disease-to-disease relationships
  • Human Phenotype Ontology
  • OMIM Human disease DB
  • UMLS Unified Medical Language Systems
  • ICD International Classification of Disease by WHO
  • GenomeRNAi A Phenotype DB for large-scale RNAi screens (human, mouse, fly, worm...)
  • OGEE Online GEne Essentiality database

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

Organism-centric DBs

Metagenome DBs

  • CAMERA 2.0 Curated DB and analysis tool for metagenomes
  • NCBI Metagenome DB Categorized with metagenome types, sources and sequencing methods.
  • OMI Open Microbiome Initiative
  • EMP Earh Microbiome Project will sequence 10,000 metagenomes in an year, 200,000 metagenomes in 3 years

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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