Difference between revisions of "Web Resources"
From Bioinformatics Lab
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| − | == GATEWAY | + | == GATEWAY DBs == |
*[http://www.ebi.ac.uk/ EBI] | *[http://www.ebi.ac.uk/ EBI] | ||
*[http://www.ncbi.nlm.nih.gov/ NCBI] | *[http://www.ncbi.nlm.nih.gov/ NCBI] | ||
| − | == | + | == Pathway Annotation DBs == |
*[http://www.geneontology.org/ Gene Ontology] | *[http://www.geneontology.org/ Gene Ontology] | ||
*[http://www.unipathway.org/ UniPathway] a fully manually curated resource of metabolic pathways (cross-linked to KEGG, MetaCyc) | *[http://www.unipathway.org/ UniPathway] a fully manually curated resource of metabolic pathways (cross-linked to KEGG, MetaCyc) | ||
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*[http://pid.nci.nih.gov/ Pathway Interaction Database (PID)] | *[http://pid.nci.nih.gov/ Pathway Interaction Database (PID)] | ||
| − | == | + | == Genomic Variation DBs == |
*[http://gvs.gs.washington.edu/GVS/ GVS] Genome Variation Server (meta DB containing dbSNP, HapMap phase 3) | *[http://gvs.gs.washington.edu/GVS/ GVS] Genome Variation Server (meta DB containing dbSNP, HapMap phase 3) | ||
*[http://www.ncbi.nlm.nih.gov/projects/SNP/ dbSNP] DB of short genetic variations by NCBI | *[http://www.ncbi.nlm.nih.gov/projects/SNP/ dbSNP] DB of short genetic variations by NCBI | ||
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*[http://www.1001genomes.org/ 1001 Genome Project] Genetic variation] of natural population of Arabidopsis | *[http://www.1001genomes.org/ 1001 Genome Project] Genetic variation] of natural population of Arabidopsis | ||
| − | == Prediction | + | == Genotype-to-Phenotype Resources == |
| + | *[http://www.genome.gov/gwastudies/ GWAS catalog] contains SNPs with p<10^-5 | ||
| + | *[http://jjwanglab.org:8080/gwasdb/ GWASdb] contains SNPs with p<10^-3 | ||
| + | *[http://distild.jensenlab.org/ DistiLD] Diseases and Traits in Linkage Disequilibrium Blocks | ||
| + | *[http://www.personalgenomes.org/ Personal Genome Project] | ||
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| + | == Mutation Effect Prediction Tools == | ||
*[http://sift.jcvi.org/ SIFT(Sorting Intolerent from Tolerent substitution)] | *[http://sift.jcvi.org/ SIFT(Sorting Intolerent from Tolerent substitution)] | ||
*[http://genetics.bwh.harvard.edu/pph2/ PolyPhen-2 (Polymorphism Phenotyping v2)] | *[http://genetics.bwh.harvard.edu/pph2/ PolyPhen-2 (Polymorphism Phenotyping v2)] | ||
| − | == | + | == Gene Expression DBs == |
*[http://www.ncbi.nlm.nih.gov/geo/ GEO] | *[http://www.ncbi.nlm.nih.gov/geo/ GEO] | ||
*[http://www.ebi.ac.uk/arrayexpress/ Arrayexpress] | *[http://www.ebi.ac.uk/arrayexpress/ Arrayexpress] | ||
*[http://www.plexdb.org/ PLEXdb] Gene expression resources for plant and plant pathogens | *[http://www.plexdb.org/ PLEXdb] Gene expression resources for plant and plant pathogens | ||
| − | == | + | == Protein Expression DBs == |
*[http://suba.plantenergy.uwa.edu.au/ SUBA] SUBcellular location DB for Arabidopsis proteins | *[http://suba.plantenergy.uwa.edu.au/ SUBA] SUBcellular location DB for Arabidopsis proteins | ||
| − | == | + | == Protein/Gene Interaction DBs == |
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*[http://code.google.com/p/psicquic/ Protemic Standard Initiative Common QUery InterfaCe (PSICQUIC)] | *[http://code.google.com/p/psicquic/ Protemic Standard Initiative Common QUery InterfaCe (PSICQUIC)] | ||
*[http://www.imexconsortium.org/ International Molecular Exchange Consortium (IMEx)] | *[http://www.imexconsortium.org/ International Molecular Exchange Consortium (IMEx)] | ||
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*[http://string-db.org/ STRING] Known and predicted PPI | *[http://string-db.org/ STRING] Known and predicted PPI | ||
| − | == | + | == Transcriptional Regulation DBs == |
*[http://www.bioguo.org/AnimalTFDB/ AnimalTFDB] A comprehensive manually curated animal TF DB (organized by family or species) | *[http://www.bioguo.org/AnimalTFDB/ AnimalTFDB] A comprehensive manually curated animal TF DB (organized by family or species) | ||
*[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 | ||
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*[http://jilab.biostat.jhsph.edu/database/cgi-bin/hmChIP.pl// hmChIP] DB for publicly available human and mouse ChIP-seq and ChIP-chip data | *[http://jilab.biostat.jhsph.edu/database/cgi-bin/hmChIP.pl// hmChIP] DB for publicly available human and mouse ChIP-seq and ChIP-chip data | ||
| − | == Chemical/Drug DBs == | + | == Phenotype/Disease Annotation DBs == |
| + | *[http://disease-ontology.org/ Disease Ontology] Disease ontology files [http://django.nubic.northwestern.edu/fundo/ FUNDO] DOLite_term-to-genes map | ||
| + | *[http://www.human-phenotype-ontology.org/ Human Phenotype Ontology] | ||
| + | *[http://www.omim.org/ OMIM] Human disease DB | ||
| + | *[http://www.nlm.nih.gov/research/umls/ UMLS] Unified Medical Language Systems | ||
| + | *[http://www.who.int/classifications/icd/en/ ICD] International Classification of Disease by WHO | ||
| + | *[http://genomernai.de/GenomeRNAi/ GenomeRNAi] A Phenotype DB for large-scale RNAi screens (human, mouse, fly, worm...) | ||
| + | *[http://ogeedb.embl.de OGEE] Online GEne Essentiality database | ||
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| + | == Chemical/Drug-to-Target DBs == | ||
*[http://pubchem.ncbi.nlm.nih.gov/ PubChem] by NCBI | *[http://pubchem.ncbi.nlm.nih.gov/ PubChem] by NCBI | ||
*[http://www.ebi.ac.uk/chebi/ Chemical Entities of Biological Interest] by EBI | *[http://www.ebi.ac.uk/chebi/ Chemical Entities of Biological Interest] by EBI | ||
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*[http://www.niehs.nih.gov/research/resources/databases/cebs/index.cfm CEBS] Chemical Effects in Biological Systems, an integrated public repository for toxicogenomics data | *[http://www.niehs.nih.gov/research/resources/databases/cebs/index.cfm CEBS] Chemical Effects in Biological Systems, an integrated public repository for toxicogenomics data | ||
| − | == Animal | + | == Animal Genome DBs == |
*[http://www.wormbase.org/ WormBase] | *[http://www.wormbase.org/ WormBase] | ||
*[http://flybase.org/ FlyBase] | *[http://flybase.org/ FlyBase] | ||
*[http://www.informatics.jax.org/ MGI] | *[http://www.informatics.jax.org/ MGI] | ||
| − | == Plant | + | == Plant Genome DBs == |
*[http://5e.plantphys.net/index.php Plant Physiology web] | *[http://5e.plantphys.net/index.php Plant Physiology web] | ||
*[http://www.arabidopsis.org/ TAIR] | *[http://www.arabidopsis.org/ TAIR] | ||
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*[http://www.agbase.msstate.edu/ AgBase] Curated DB for functional analysis of agriculural animals and plants | *[http://www.agbase.msstate.edu/ AgBase] Curated DB for functional analysis of agriculural animals and plants | ||
| − | == Microbial/Microbiome | + | == Microbial/Microbiome DBs == |
*[http://porteco.org/ PortEco] Portal for E. coli | *[http://porteco.org/ PortEco] Portal for E. coli | ||
*[http://www.pseudomonas.com/ Pseudomonas Genome Database] | *[http://www.pseudomonas.com/ Pseudomonas Genome Database] | ||
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*[http://www.ncbi.nlm.nih.gov/genomes/lenvs.cgi NCBI Metagenome DB] Categorized with metagenome types, sources and sequencing methods. | *[http://www.ncbi.nlm.nih.gov/genomes/lenvs.cgi NCBI Metagenome DB] Categorized with metagenome types, sources and sequencing methods. | ||
| − | == | + | == Cancer Genome/Cell Line Biology DBs == |
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*[http://cancergenome.nih.gov/ TCGA] The Cancer Genome Atlas | *[http://cancergenome.nih.gov/ TCGA] The Cancer Genome Atlas | ||
*[http://www.icgc.org/home ICGC cancer genome project] International Cancer Genome Consortium Cancer genome project | *[http://www.icgc.org/home ICGC cancer genome project] International Cancer Genome Consortium Cancer genome project | ||
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*[http://colt.ccbr.utoronto.ca/cancer/ COLT-cancer database] shRNA-based essential gene profiles for 70 breast, pancreatic, ovarian cancer cell lines | *[http://colt.ccbr.utoronto.ca/cancer/ COLT-cancer database] shRNA-based essential gene profiles for 70 breast, pancreatic, ovarian cancer cell lines | ||
| − | == Stem Cell | + | == Stem Cell Biology DBs == |
*[http://discovery.hsci.harvard.edu/ SCDE] The Stem Cell Discovery Engine | *[http://discovery.hsci.harvard.edu/ SCDE] The Stem Cell Discovery Engine | ||
| − | == Other | + | == Other Resources == |
*[http://www.genomesonline.org/ GOLD] Genome Online Database-Genome project statistics and download links | *[http://www.genomesonline.org/ GOLD] Genome Online Database-Genome project statistics and download links | ||
*[http://genomeinterpretation.org/ CAGI] Critical Assessment of Genome Interpretation | *[http://genomeinterpretation.org/ CAGI] Critical Assessment of Genome Interpretation | ||
*[http://nightscience.org/ nightscience] Collective creativity in scientific discovery games | *[http://nightscience.org/ nightscience] Collective creativity in scientific discovery games | ||
Revision as of 11:27, 13 January 2012
GATEWAY DBs
Pathway Annotation DBs
- Gene Ontology
- UniPathway a fully manually curated resource of metabolic pathways (cross-linked to KEGG, MetaCyc)
- Reactome A manually curated and peer-reviewed pathway DB
- Biocyc
- HumanCyc
- Pathway Interaction Database (PID)
Genomic Variation DBs
- GVS Genome Variation Server (meta DB containing dbSNP, HapMap phase 3)
- dbSNP DB of short genetic variations by NCBI
- 1000 Genome Project Deep catalog of human genetic variation
- HapMap Project 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.)
- 1001 Genome Project Genetic variation] of natural population of Arabidopsis
Genotype-to-Phenotype Resources
- 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
- GEO
- Arrayexpress
- PLEXdb Gene expression resources for plant and plant pathogens
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
Transcriptional Regulation DBs
- AnimalTFDB A comprehensive manually curated animal TF DB (organized by family or species)
- PlnTFDB Plant TF database by University of Potsdam, Germany
- PlantTFDB Plant TF database by Peking University, China
- AGRIS Arabidopsis Gene Regulatory Information Server (by OSU)
- miRBase miRNA database by Manchester University
- miRGator
- microRNA.org
- TargetScanHuman
- PicTar An algorithm for miRNA target scan
- Carrington Lab Resource Various DBs for plant miRNA
- hmChIP DB for publicly available human and mouse ChIP-seq and ChIP-chip data
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
Chemical/Drug-to-Target DBs
- PubChem by NCBI
- Chemical Entities of Biological Interest by EBI
- STITCH DB for known and predicted chemical-protein interaction
- Drugbank A comprehensive resource for drug and drug target information
- MATADOR Manually Annotated Targets and Drugs Online Resource
- PharmGKB The Parmacogenomics Knowledgebase
- PDSP Ki DB data warehouse for published and internally-derived Ki, or affinity of drugs at targets
- Developmental Therapeutics Program by NCI (contains NCI-60 human tumor cell-line screen data)
Side effect/Toxicogenomics DBs
- 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
- 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.
Cancer Genome/Cell Line Biology DBs
- TCGA The Cancer Genome Atlas
- ICGC cancer genome project International Cancer Genome Consortium Cancer genome project
- DTP human tumor cell line screen by NCI-60
- 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
Other Resources
- GOLD Genome Online Database-Genome project statistics and download links
- CAGI Critical Assessment of Genome Interpretation
- nightscience Collective creativity in scientific discovery games
