Web Resources

GATEWAY DB

• EBI
• NCBI

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

• SIFT(Sorting Intolerent from Tolerent substitution)
• PolyPhen-2 (Polymorphism Phenotyping v2)

Transcriptome

• GEO
• Arrayexpress
• PLEXdb Gene expression resources for plant and plant pathogens

Proteome/Localisome

• SUBA SUBcellular location DB for Arabidopsis proteins

Diseasome/Phenome

• 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

Genotype-to-phenotype map

• 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

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

• 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

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

• WormBase
• FlyBase
• MGI

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

• Naegleria gruberi JGI home

Cancer, Cell Line Profiles

• TCGA The Cancer Genome Atlas
• 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 Line Profiles

• 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