Web Resources

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Contents

Knowledgebase, GATEWAY DBs, Genome/Gene Annotations


NGS data public depositories

  • SRA Sequence Read Archive by NCBI
  • ENA European Neucleotice Archive by EBI
  • GEO Gene Expression Omnibus (for processed data only)
  • ENCODE Encyclopedia of DNA Elements project (human)

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
  • IDR Reproducibility and automatic thresholding of ChIP-seq data

The Encyclopedia of DNA Element (ENCODE) Data links

Epigenomics Resources

  • CistromeMap A knowledgebase for ChIP-Seq and DNase-Seq studies in mouse and human
  • Road map Epigenomics NIH Roda map Epigenomics project home
  • BLUEPRINT epigenome Epigenome maps of >100 different blood cell types
  • Epigenie An informative web community for epigenetics-related research
  • EpGenSys European network to bring together epigenetic and systems biology
  • Gene Regulation Info A very useful site for epigenetics and TF-DNA interaction studies (by Dr. Vladimir Teif)

Genomic Variation DBs

- Human genomics variations

- Human disease associated genomics variations

  • HGMD The human gene mutation database (The professional version of DB is commercial. The public version of DB is not downloadable.)
  • COSMIC DB for somatic mutations for cancer (largely by manual curation)
  • TCGA Germline/somatic mutations for cancer are available as Mutation Analaysis file format (MAF).
  • OMIM Germline mutations for genetic diseases
  • Roche Cancer Genome Database (RCGDB) Germline/somatic mutations for cancer collected from diverse resourses (not downloadable)
  • IDbase Human Immunodeficiency-causing mutation database

- Arabidopsis genomics variations

  • 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)

Mutation Effect Prediction Tools

Genotype-to-Phenotype Resources

Genotype-to-Expression (eQTL) Databases

Pathway Annotation DBs

  • 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)
  • UniProt-GOA by EBI (support multi-species annotation)
  • UniPathway a fully manually curated resource of metabolic pathways (cross-linked to KEGG, MetaCyc)
  • Mapman Metabolic pathway databases
  • Plantcyc Plant metabolic network databases
  • Gramene A curated DB for grasses
  • agriGO A GO databases for agricultural community
  • AgBase Curated DB for functional analysis of agriculural animals and plants

Protein/Gene Interaction 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))
  • IntAct
  • BIND the Biomolecular Interaction Network Database
  • BioGRID
  • HPRD Human Protein Reference Database
  • MINT Molecular Interaction DB
  • DIP Database of Interacting Proteins
  • Mpact Representation of Interaction Data at MIPS
  • MPPI Mammalian PPI DB at MIPS

- Inferred gene interactions

  • STRING Known and predicted PPI
  • FunCoup DB of functional couplings between genes by data integration

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
  • hmChIP TF-ChIP DB for human and mouse
  • Gene Regulation Info A very useful site for epigenetics and TF-DNA interaction studies (by Dr. Vladimir Teif)

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

  • 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)
  • 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

-CLIP-seq database

-Plant microRNA DB

Gene Expression DBs

Protein Expression DBs

  • SUBA SUBcellular location DB for Arabidopsis proteins

Phenotype/Disease Annotation DBs

  • Disease Ontology Disease ontology files FUNDO DOLite_term-to-genes map
  • Human Phenotype Ontology
  • OMIM Human disease DB
  • 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
  • DISEASES gene-disease association from text mining
  • GenomeRNAi A Phenotype DB for large-scale RNAi screens (human, mouse, fly, worm...)
  • OGEE Online GEne Essentiality database

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

Clinical Trials and Pharmaco/Toxicogenomics DBs

Bacterial Antibiotics DBs

Organism-centric DBs: Microbes

Organism-centric DBs: Animals

Organism-centric DBs: Plants

Metagenomic DBs

- Project

- Database

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)

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)

Other Resources

- Neuroscience

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