Difference between revisions of "Web Resources"
From Bioinformatics Lab
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== Epigenome, Functional DNA elements DBs == | == Epigenome, Functional DNA elements DBs == | ||
| − | *[http://genome.ucsc.edu/ENCODE/ ENCODE] Encyclopedia of DNA Elements project (human | + | *[http://genome.ucsc.edu/ENCODE/ ENCODE] Encyclopedia of DNA Elements project (human) |
*[http://www.uwencode.org/data UWencode] ENCODE (human and mouse) data browser and download site | *[http://www.uwencode.org/data UWencode] ENCODE (human and mouse) data browser and download site | ||
| − | |||
*[http://www.roadmapepigenomics.org/ Road map Epigenomics] NIH Roda map Epigenomics project home | *[http://www.roadmapepigenomics.org/ Road map Epigenomics] NIH Roda map Epigenomics project home | ||
*[http://www.regulomedb.org/ RegulomeDB] Evidences from eQTL, TF binding, matched TF motif, matched DNase Footprint, DNase peak | *[http://www.regulomedb.org/ RegulomeDB] Evidences from eQTL, TF binding, matched TF motif, matched DNase Footprint, DNase peak | ||
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*[http://epd.vital-it.ch/ EPD] The Eukaryotic Promoter Database | *[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 | *[http://tiprod.cbi.pku.edu.cn:8080/index.html TiProD] The tissue-specific Promoter DB | ||
| + | *[http://www.mouseencode.org/ Mouse ENCODE] Mouse ENCODE home | ||
| + | *[http://modencode.org/ modENCODE] Encyclopedia of DNA Elements project in model organisms (worm, fly) | ||
== Genotype-to-Phenotype Resources == | == Genotype-to-Phenotype Resources == | ||
Revision as of 10:25, 14 January 2013
Knowledgebase, GATEWAY DBs, Genome Annotations
- Scitable by Nature Learn Science at Nature Education
- EBI
- NCBI
- GOLD Genome Online Database-Genome project statistics and download links
- UCSC genome browser home
Pathway Annotation DBs
- Gene Ontology by Gene Ontology Consortium
- UniProt-GOA by EBI (support multi-species annotation)
- UniPathway a fully manually curated resource of metabolic pathways (cross-linked to KEGG, MetaCyc)
- Biocyc includes Metacyc, Ecocyc, Humancyc, Aracyc, Yeastcyc
- Pathway Interaction Database (PID)
- Reactome A manually curated and peer-reviewed pathway DB
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)
- UWencode ENCODE (human and mouse) data browser and download site
- 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
- Mouse ENCODE Mouse ENCODE home
- modENCODE Encyclopedia of DNA Elements project in model organisms (worm, fly)
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
- NCBI GTex(Genotype-Tissue Expression) browser eQTL data download and analysis
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
- EBI Gene Expression Atlas Gene expression atlas for many organisms collected from various experiments
- Human Cell/tissue-specific gene expression map for 369 different cell and tissue types with 5,372 human samples from GEO
- GXD The mouse Gene Expression Database (by MGI)
Protein Expression DBs
- SUBA SUBcellular location DB for Arabidopsis proteins
Protein/Gene Interaction DBs
- Protemic Standard Initiative Common QUery InterfaCe (PSICQUIC)
- International Molecular Exchange Consortium (IMEx)
- iRefWeb a web interface to PPI consolidated from 10 public DB (BIND, BioGRID, CORUM, DIP,IntAct, HPRD, MINT, MPact, MPPI, OPHID(predicted PPIs))
- BIND the Biomolecular Interaction Network Database
- BioGRID
- CORUM Comprehensive Resource of Mammalian Protein Complexes
- DIP Database of Interacting Proteins
- IntAct
- HPRD Human Protein Reference Database
- MINT Molecular Interaction DB
- Mpact Representation of Interaction Data at MIPS
- MPPI Mammalian PPI DB at MIPS
- STRING Known and predicted PPI
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
- Disease Ontology Disease ontology files FUNDO DOLite_term-to-genes map
- 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
Animal Genome DBs
Plant Genome DBs
- Plant Physiology web
- TAIR
- Gramene
- RGAP Rice Genome Annotation Project by MSU (Go get the part list here!)
- MaizeGDB
- AgBase Curated DB for functional analysis of agriculural animals and plants
Microbial/Microbiome DBs
- PortEco Portal for E. coli
- Pseudomonas Genome Database
- Saccharomyces Genome Database
- Candida Genome Database
- IMG Integrated Microbial Genomes (include metagenome data)
- 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
- TCGA The Cancer Genome Atlas
- CGHub The Cancer Genomics Hub by UCSC (a repository for TCGA data)
- ICGC cancer genome project International Cancer Genome Consortium Cancer genome project
- PCGP The Pediatric Cancer Genome Project
- Cancer Cell line Encyclopedia (CCLE) by Broad-Novartis, 1000 cancer cell lines, ~1200 compounds and their combinations
- DTP human tumor cell line screen by NCI-60
- Developmental Therapeutics Program by NCI (contains NCI-60 human tumor cell-line screen data)
- NCI60 mutation data
- GKS Cancer Cell Line Data genomic profiles for 300 cell lines
- COLT-cancer database shRNA-based essential gene profiles for 70 breast, pancreatic, ovarian cancer cell lines
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
