Difference between revisions of "Web Resources"
From Bioinformatics Lab
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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 genomes == |
*[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] | ||
*[http://www.yeastgenome.org/ Saccharomyces Genome Database] | *[http://www.yeastgenome.org/ Saccharomyces Genome Database] | ||
| − | *[http://www.candidagenome.org/ Candida Genome Database] | + | *[http://www.candidagenome.org/ Candida Genome Database] |
| + | *[http://img.jgi.doe.gov/ IMG] Integrated Microbial Genomes (include metagenome data) | ||
| + | *[http://portal.camera.calit2.net/gridsphere/gridsphere CAMERA 2.0] Curated DB and analysis tool for metagenomes | ||
| + | *[http://www.ncbi.nlm.nih.gov/genomes/lenvs.cgi NCBI Metagenome DB] Categorized with metagenome types, sources and sequencing methods. | ||
== Protozoa genomes == | == Protozoa genomes == | ||
*[http://genome.jgi-psf.org/Naegr1/Naegr1.home.html Naegleria gruberi JGI home] | *[http://genome.jgi-psf.org/Naegr1/Naegr1.home.html Naegleria gruberi JGI home] | ||
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== Other resources == | == Other resources == | ||
Revision as of 20:37, 11 January 2012
GATEWAY DB
Ontology/Pathway
- 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)
Variome
- 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.)
- TCGA The Cancer Genome Atlas
- ICGC cancer genome project International Cancer Genome Consortium Cancer genome project
- 1001 Genome Project Genetic variation] of natural population of Arabidopsis
Prediction of deleteriousness of SNV
Transcriptome
- GEO
- Arrayexpress
- PLEXdb Gene expression resources for plant and plant pathogens
Proteome/Localisome
- SUBA SUBcellular location DB for Arabidopsis proteins
Diseasome/Phenome/Metabolome
- 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...)
- cloroplast2010 Phenome/metabolome DB for Arabidopsis clroloplast gene KO lines (by MSU)
Genotype-to-phenotype map
- GWAS catalog
- DistiLD Diseases and Traits in Linkage Disequilibrium Blocks
- Personal Genome Project
Interactome/Network
- 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/miRNA/Regulaorty network
- 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
Chemical/Drug 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 genomes
Plant genomes
- 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 genomes
- 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.
Protozoa genomes
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
