Difference between revisions of "Web Resources"

Revision as of 13:36, 7 January 2014

Knowledgebase, GATEWAY DBs, Genome/Gene Annotations

• Scitable by Nature Learn Science at Nature Education
• Plant Physiology web
• EBI
• NCBI
• GOLD Genome Online Database-Genome project statistics and download links
• UCSC genome browser home
• ENSEMBL genome browser home
• CCDS The concensus protein coding regions among NCBI, Ensembl, and Sanger (Havana) annotation
• GENCODE The Encyclopedia of Genes
• DBTSS Transcription start site DB (with tissue specific information)
• EPD The Eukaryotic Promoter Database
• TiProD The tissue-specific Promoter DB

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

• ENCODE data summary List all released/approved experiments
• ENCODE Encyclopedia of DNA Elements project (human)
• ENCODE explore Access to collected papers exploring ENCODE data
• UWencode ENCODE (human and mouse) data browser and download site
• RNA Dashboard DB for raw transcriptome data from ENCODE
• Mouse ENCODE ENCODE for mouse
• modENCODE ENCODE for animal models (worm, fly)

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

• NCBI Variation Variation DBs (dbSNP, dbVar, dbGaP, ClinVar)
• 1000 Genome Project Deep catalog of human genetic variation
• Complete Genomics Very accurate 69 human WGS public data and more
• Exome Variant Server by NHLBI GO Exome sequencing project (ESP)

- 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

• VEP Variant Effect Predictor by EBI (very easy to install and use)
• Condel Variant effect score by integration of SIFT, Polyphen2, Massessor, MAPP, Logre
• SIFT(Sorting Intolerent from Tolerent substitution)
• PolyPhen-2 (Polymorphism Phenotyping v2)
• EvoD Evolutionary Diagnosis method
• RegulomeDB Exploring DNA functional elements for noncoding variants (by Stanford, Snyder lab)
• HaplogReg Exploring DNA functional elements for noncoding variants (by MIT, Kellis lab)

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 Central contain SNPs for any p-value
• GWAS catalog contains SNPs with p<10^-5
• COGS nature resources CollaborativeOncological Gene-environment Study (GOGS): Association study using ~211,000SNPs (iCOGS) for breast, ovarian, prostate cancers.
• 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
• GWAPP A web-based tool for GWAS in Arabidopsis

Genotype-to-Expression (eQTL) Databases

• seeQTL A DB for human eQTL
• GTEx eQTL browser genotype-to-tissue expression

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

• 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
• 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

• 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
• 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

• miRGator data for miRNA expression, miRNA-mRNA paired expression profile, miRNA perturbation experiments...
• miR2Disease Manually curated microRNA-target links and microRNA-disease links
• PhenomiR A knowledgebase of miRNA expression in disease and biological processes

-Target prediction software

• TargetScan executable PITA executable miRanda excecutable
• miRmap target prediction by multiple algorithms, excecutable, precalculated, many other related data

-CLIP-seq database

• StarBase DB for CLIP-seq data

-Plant microRNA DB

• Carrington Lab Resource Various DBs for plant miRNA

Gene Expression DBs

• GEO
• AtGenExpress Arabidopsis gene expression DB by Weigel lab (there are unpublished non-GEO data here)
• Connectivity Map Expression profiles from cultured human cells treated with bioactive small molecules
• ImmGen Immunological Genome Project Ontogenet TF-module networks based on ImmGen data
• 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
• Illumina Human Body Map Project (HBM) RNA-seq data for 16 human tissue
• GXD The mouse Gene Expression Database (by MGI)
• FlyAtlas fly gene expression in 25-17 adult and 8 larval tissues

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

• 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
• IUPHAR/BPS Guide to Pharmacology A DB of in-depth information of drug targets and ligands
• PDSP Ki DB data warehouse for published and internally-derived Ki, or affinity of drugs at targets
• Yeast Fitness DB Chemical genomics test for ~400 chemicals (Science 320-362)

Clinical Trials and Pharmaco/Toxicogenomics DBs

• ClinicalTrials.gov DB for clinical trials conducted around the world
• The Comparative Toxicogenomics database(CTD) The major DB of chemical-disease links from literature curation
• Chemical Effects in Biological Systems(CEBS) an integrated public repository for toxicogenomics data
• PharmGKB The Parmacogenomics Knowledgebase
• SIDER Side Effect Resource

Bacterial Antibiotics DBs

• Antibiotic Resistance Genes Database(ARGD)
• BacMet Antibacterial biocide and metal resistance genes database

Organism-centric DBs: Microbes

• PortEco Portal for E. coli
• Ecoli Phenome DB Mutant phenome data for 324 drug/stress conditions
• Pseudomonas Genome Database
• Bactome DB Mutant phenome data for 119 drug/stress conditions (id: pseudo, pw:Haeussler)
• Saccharomyces Genome Database
• Candida Genome Database
• Xanthobase Xanthomonas oryzae pv. oryzae Genome Database
• IMG Integrated Microbial Genomes (include metagenome data)

Organism-centric DBs: Animals

• WormBase
• FlyBase
• MGI
• Sanger mouse resource portal

Organism-centric DBs: Plants

• TAIR
• RGAP Rice Genome Annotation Project by MSU (Go get the part list here!)
• MaizeGDB
• Sol Genomics Network for Tomato
• Soybase
• Soybean functional genomics database
• Gramene
• PlantGDB Plant Genome DB

Metagenome DBs

• Human Microbiome Project (HMP)
• 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
• Genomics of Drug Sensitivity in Cancer (GDSC) The largest public DB for drug sensitivity of cancer cell line and biomarkers
• 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)

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

• COURSERA Online-course for free
• The Leading Strand CSHL meeting keynote speeches
• 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

- Neuroscience

• Allen Brain Atlas Data Potal Integrative gene expression and neuroanatomical data base
• Brainmap.org Published functional and structural neuroimaging (by functional MRI) database