Difference between revisions of "Web Resources"
From Bioinformatics Lab
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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 | ||
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| + | == NGS data analysis tools == | ||
| + | *[http://code.google.com/p/bedops/ BEDOPS]A suite for common genome analysis tasks with high scalability and flexibility | ||
| + | *[http://code.google.com/p/bedtools/ BEDTools] A suite for BED (Browser Extensible Data) and GFF (General Feature Format) format. | ||
| + | *[http://samtools.sourceforge.net/ SAMtools] A suite for SAM (Sequence Alignment/Map) format | ||
| + | *[http://biowhat.ucsd.edu/homer/ Homer] A suite of tools for Motif Discovery and NGS (ChIP-Seq, RNA-Seq, DNase-Seq, Hi-C). Excellent documentation! | ||
| + | *[http://fureylab.web.unc.edu/software/fseq/ F-Seq] A Feature Density Estimator for High-Throughput Sequence Tags | ||
| + | *[https://sites.google.com/site/anshulkundaje/projects/idr IDR] Reproducibility and automatic thresholding of ChIP-seq data | ||
== The Encyclopedia of DNA Element (ENCODE) Data links == | == The Encyclopedia of DNA Element (ENCODE) Data links == | ||
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*[http://modencode.org/ modENCODE] ENCODE for animal models (worm, fly) | *[http://modencode.org/ modENCODE] ENCODE for animal models (worm, fly) | ||
| − | == | + | == Epigenomics Resources == |
| − | *[http:// | + | *[http://www.roadmapepigenomics.org/ Road map Epigenomics] NIH Roda map Epigenomics project home |
| − | *[http:// | + | *[http://www.blueprint-epigenome.eu/ BLUEPRINT epigenome] Epigenome maps of >100 different blood cell types |
| − | *[http:// | + | *[http://epigenie.com/ Epigenie] An informative web community for epigenetics-related research |
| − | + | *[http://www.epigenesys.eu/ EpGenSys] European network to bring together epigenetic and systems biology | |
| − | + | *[http://www.generegulation.info/ Gene Regulation Info] A very useful site for epigenetics and TF-DNA interaction studies (by Dr. Vladimir Teif) | |
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== Genomic Variation DBs == | == Genomic Variation DBs == | ||
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*[http://www.1001genomes.org/ 1001 Genome Project] Genetic variation] of natural population of Arabidopsis (by Detlef Weigel, MPI) | *[http://www.1001genomes.org/ 1001 Genome Project] Genetic variation] of natural population of Arabidopsis (by Detlef Weigel, MPI) | ||
| − | == | + | == Mutation Effect Prediction Tools == |
| − | *[http:// | + | *[http://asia.ensembl.org/info/docs/variation/vep/index.html VEP] Variant Effect Predictor by EBI (very easy to install and use) |
| − | *[http:// | + | *[http://bg.upf.edu/condel/home Condel] Variant effect score by integration of SIFT, Polyphen2, Massessor, MAPP, Logre |
| − | *[http:// | + | *[http://sift.jcvi.org/ SIFT(Sorting Intolerent from Tolerent substitution)] |
| − | *[http:// | + | *[http://genetics.bwh.harvard.edu/pph2/ PolyPhen-2 (Polymorphism Phenotyping v2)] |
| − | *[http://www. | + | *[http://barn.asu.edu/EvoD/ EvoD] Evolutionary Diagnosis method |
| + | *[http://www.regulomedb.org/ RegulomeDB] Exploring DNA functional elements for noncoding variants (by Stanford, Snyder lab) | ||
| + | *[http://www.broadinstitute.org/mammals/haploreg HaplogReg] Exploring DNA functional elements for noncoding variants (by MIT, Kellis lab) | ||
== Genotype-to-Phenotype Resources == | == Genotype-to-Phenotype Resources == | ||
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*[https://cynin.gmi.oeaw.ac.at/home/resources/gwapp/gwapp GWAPP] A web-based tool for GWAS in Arabidopsis | *[https://cynin.gmi.oeaw.ac.at/home/resources/gwapp/gwapp GWAPP] A web-based tool for GWAS in Arabidopsis | ||
| − | == | + | == Pathway Annotation DBs == |
| − | *[http:// | + | *[http://www.geneontology.org/ Gene Ontology] by Gene Ontology Consortium |
| − | *[http:// | + | *[http://www.genome.jp/kegg/ KEGG] pathways and many more |
| − | *[http:// | + | *[http://biocyc.org/ Biocyc] includes Metacyc, Ecocyc, Humancyc, Aracyc, Yeastcyc |
| − | *[http:// | + | *[http://www.reactome.org/ Reactome] A manually curated and peer-reviewed pathway DB |
| − | *[http:// | + | *[http://pid.nci.nih.gov/ Pathway Interaction Database (PID)] Human pathways curated by NCI-Nature/imported from BioCarta/Reactome |
| − | + | *[http://mips.helmholtz-muenchen.de/genre/proj/corum/index.html CORUM] Comprehensive Resource of Mammalian Protein Complexes | |
| − | *[http://www. | + | *[http://www.netpath.org/ NetPath] A database for signaling pathways (cancer/immune signaling pathways) |
| − | + | *[http://www.ebi.ac.uk/GOA/ UniProt-GOA] by EBI (support multi-species annotation) | |
| − | + | *[http://www.unipathway.org/ UniPathway] a fully manually curated resource of metabolic pathways (cross-linked to KEGG, MetaCyc) | |
| − | *[http://www. | + | *[http://mapman.gabipd.org Mapman] Metabolic pathway databases |
| − | *[http://www. | + | *[http://www.plantcyc.org/ Plantcyc] Plant metabolic network databases |
| − | *[http:// | + | *[http://www.gramene.org/ Gramene] A curated DB for grasses |
| − | *[http://www. | + | *[http://bioinfo.cau.edu.cn/agriGO agriGO] A GO databases for agricultural community |
| − | *[http://www. | + | *[http://www.agbase.msstate.edu/ AgBase] Curated DB for functional analysis of agriculural animals and plants |
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== Protein/Gene Interaction DBs == | == Protein/Gene Interaction DBs == | ||
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*[http://cegg.unige.ch/mirmap/ miRmap] target prediction by multiple algorithms, excecutable, precalculated, many other related data | *[http://cegg.unige.ch/mirmap/ miRmap] target prediction by multiple algorithms, excecutable, precalculated, many other related data | ||
*[http://jcclab.science.oregonstate.edu// Carrington Lab Resource] Various DBs for plant miRNA | *[http://jcclab.science.oregonstate.edu// Carrington Lab Resource] Various DBs for plant miRNA | ||
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| + | == Gene Expression DBs == | ||
| + | *[http://www.ncbi.nlm.nih.gov/geo/ GEO] | ||
| + | *[http://www.weigelworld.org/resources/microarray/AtGenExpress/ AtGenExpress] Arabidopsis gene expression DB by Weigel lab (there are unpublished non-GEO data here) | ||
| + | *[http://www.broadinstitute.org/cmap/ Connectivity Map] Expression profiles from cultured human cells treated with bioactive small molecules | ||
| + | *[http://www.immgen.org/ ImmGen] Immunological Genome Project [http://www.immgen.org/ModsRegs/modules.html Ontogenet] TF-module networks based on ImmGen data | ||
| + | *[http://www.ebi.ac.uk/gxa/ EBI Gene Expression Atlas] Gene expression atlas for many organisms collected from various experiments | ||
| + | *[http://www.ebi.ac.uk/gxa/array/U133A Human Cell/tissue-specific gene expression map] for 369 different cell and tissue types with 5,372 human samples from GEO | ||
| + | *[http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE30611 Illumina Human Body Map Project (HBM)] RNA-seq data for 16 human tissue | ||
| + | *[http://www.informatics.jax.org/expression.shtml GXD] The mouse Gene Expression Database (by MGI) | ||
| + | *[http://flyatlas.org/ FlyAtlas] fly gene expression in 25-17 adult and 8 larval tissues | ||
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| + | == Protein Expression DBs == | ||
| + | *[http://suba.plantenergy.uwa.edu.au/ SUBA] SUBcellular location DB for Arabidopsis proteins | ||
== Phenotype/Disease Annotation DBs == | == Phenotype/Disease Annotation DBs == | ||
Revision as of 20:36, 6 November 2013
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 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
- 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
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 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
- miRTarBase Manually curated microRNA-target links
- miR2Disease Manually curated microRNA-target links and microRNA-disease links
- miRecords Manually curated microRNA-target links + predicted links (by 11 computational algorithms)
- Comir Combinatorial miRNA target prediction tool
- TargetScan executable PITA executable miRanda excecutable
- miRmap target prediction by multiple algorithms, excecutable, precalculated, many other related data
- 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
- DGA Disease and Gene Annotation, an integrative set of disease-to-gene, gene-to-gene, disease-to-disease relationships
- 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/ 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
- 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
- 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
Organism-centric DBs: Microbes
- PortEco Portal for E. coli
- Pseudomonas Genome Database
- Saccharomyces Genome Database
- Candida Genome Database
- Xanthobase Xanthomonas oryzae pv. oryzae Genome Database
- IMG Integrated Microbial Genomes (include metagenome data)
Organism-centric DBs: Animals
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)
Neuroscience DBs
- Allen Brain Atlas Data Potal Integrative gene expression and neuroanatomical data base
- Brainmap.org Published functional and structural neuroimaging (by functional MRI) database
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
- 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
