Difference between revisions of "Web Resources"

Revision as of 15:01, 19 March 2017

Knowledgebase, GATEWAY DBs, Genome/Gene Annotations

• CCDS The concensus protein coding regions among NCBI, Ensembl, and Sanger (Havana) annotation
• GENCODE The Encyclopedia of Genes

NGS data public depositories

• SRA Sequence Read Archive by NCBI
• ENA European Neucleotice Archive by EBI
• GEO Gene Expression Omnibus (for processed data only)

Epigenomics and Regulomics Resources

• ENCODE Encyclopedia of DNA Elements project (human)
• Road map Epigenomics NIH Roda map Epigenomics project home
• International Human Epigenome Consortium (IHEC) The umbrella organization for international epigenomic efforts
• 4D Nucleome To understand the principles behind the 3D organization of the nucleus in space and time (the 4th dimension)
• GREAT Genomic Regions Enrichment of Annotations Tool; Predict functions for cis-regulatory regions
• CistromeMap A knowledgebase for ChIP-Seq and DNase-Seq studies in mouse and human
• Gene Regulation Info A very useful site for epigenetics and TF-DNA interaction studies (by Dr. Vladimir Teif)

Genomic Variation DBs

- Reference Human Genomics Variations

• ExAC (Exome Aggregation Consortium) Exome variation data from >60k individuals
• 1000 Genome Project Catalog of 60 million variant sites (SNV, CNV, SV), 2535 individuals from 26 populations
• UK10K Sequencing 10,000 people (4,000 healthy, 6,000 disease) in England
• Genomics England Sequencing 100,000 people in England focusing on patients with a rare disease and their families and patients with cancer.
• DiscovEHR Collaboration between the Regeneron Genetics Center (WES) and Geisinger Health System (EHR) provides the vcf by 50,000 MyCode participants
• European Variation Archive Most comprehensive and organized by studies (include Clinical variants)
• NCBI Variation Variation DBs (dbSNP, dbVar, dbGaP, ClinVar)
• iJGVD Integrative Japanese Genome Variation Database
• HGV Database The HGV database is a fully searchable online database of genome variations published in peer-reviewed Data Reports in Human Genome Variation

Genetic variant functional impact scoring Tools

• Eigen Assign functional important scores on genetic variants in coding and noncoding regions (human only, unsupervised integration)
• CADD: Combined Annotation Dependent Depletion a tool for scoring the deleteriousness of SNV and indels (human only, supervised integration)
• GWAVA: Genome Wide Annotation of VAriants a tool which aims to predict the functional impact of non-coding genetic variants (human only, supervised integration)
• 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)
• SIFT4G SIFT for many genomes
• PolyPhen-2 (Polymorphism Phenotyping v2) for human coding region only
• 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

- Human Disease-associated Genomics Variations

• CGD Clinical Genomic Database
• 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)
• 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

• UK Biobank Genotype and extensive phenotype data for ~500k UK people
• GWASdb includes moderate SNPs (p-value < 10^-3) with manual curation from original papers; manually mapped ~1600 GWAS traits to ~500 HPO terms, ~440 DO terms, ~230 DOLite terms
• European Genome-phenome Archive(EGA) Raw data of GWAS, WGS, Exome-seq. A great resource for meta-analysis
• dbGaP The database of Genotypes and Phenotypes (GWAS, WGS, Exome-seq...)
• NCBI ClinVar human variations and their relations to the human health (Not includes unreviewed data from GWAS)
• GWAS Central contain SNPs for any p-value
• GWAS catalog now maintained by EBI
• PheGenI Phenotype-Genotype Integrator
• Genome-wide Repository of Associations between SNPs and Phenotypes (GRASP) Better than GWAS catalog, including eQTL,QTLs
• COGS nature resources CollaborativeOncological Gene-environment Study (GOGS): Association study using ~211,000SNPs (iCOGS) for breast, ovarian, prostate cancers.
• 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
• PGC GWAS rawdata download contains links for other GWAS raw data
• DECIPHER Developmental Diseases to Phenotypes database with public patients (very useful for rare disease genetics research)

Genotype-to-Expression (eQTL) Databases

• GTEx Portal DB Portal for GTEx project
• GTEx eQTL browser genotype-to-tissue expression

Pathway/Signature gene set DBs

Pathway DBs

• Pathguide.org A very comprehensive list of pathway and network databases
• 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)
• SIGNOR 11000 manually-annotated causal relationships between proteins that participate in signal transduction
• 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

Signature Gene Set DBs

• MsigDB License required for redistribution
• GeneSigDB
• DSigDB Drug signature database for gene set analysis
• L1000CDS2 Return 50 signature genes for each LINCS L1000 data set using Characteristic Direction (CD) method
• CREEDS CRowd Extracted Expression of Differential Signatures: Signature gene sets from GEO selected by crowdsourcing project using CD method

Protein/Gene Interaction DBs

- PPIs by curation

• iRefWeb a web interface to PPI consolidated from 10 public DB (BIND, BioGRID, CORUM, DIP,IntAct, HPRD, MINT, MPact, MPPI, OPHID(predicted PPIs))

- Inferred gene interactions

• STRING Known and predicted PPI

TF Regulation DBs

-TFBS motif model DB

• CIS-BP (Catalog of Inferred Sequence Binding Preferences) >300 species, >250 TF families, >160,000 TFs. CisBP collects data from >25 sources, including other database such as HOCOMOCO JASPAR UNIPROBE TRANSFAC

-Tools for MOTIF discovery and searching

• MEME Suite has everything for motif based sequence analysis

-TF-target DB

• TRED a transcriptional regulatory element database (contains curated TF-target links for 36 TF families)
• ORegAnno DNA regulatory regions, TFBS, regulatory variants

-TF ChIP DB

• hmChIP TF-ChIP DB for human and mouse

-Plant TF DB

• 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

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 links (Gold standard)

• miRWalk2.0 Validated links from 4 databases and text minings, Predicted links from 13 prediction data sets
• miRTarBase Manually curated microRNA-target links, miRNA-mRNA paired expression profiles, miRNA-disease links
• miRecords Manually curated microRNA-target links + predicted links (by 11 computational algorithms)
• miRTex Text mining system for miRNA-target, miRNA-gene/gene-miRNA regulation
• mirSel microRNA-target links by text mining
• Comir Combinatorial miRNA target prediction tool

-microRNA-disease

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

-Target prediction software

• TargetScan executable PITA executable miRanda excecutable
• miRmap target prediction by multiple algorithms, excecutable, precalculated, many other related data
• miRDB Pre-calculated miRNA-target associations (based on SVM), not executable

-CLIP-seq database

• StarBase DB for CLIP-seq data

-Plant microRNA DB

• Carrington Lab Resource Various DBs for plant miRNA

ncRNA related DBs and Servers

• NONCODE Integrative annotation of long noncoding RNAs
• lncRNAdb a reference DB for long noncoding RNAs
• RAIN RNA–protein Association and Interaction Networks Intro to RAIN
• NPInter ncRNA interaction database (ncRNA and other molecules)
• RAID RNA-associated interaction DB (very comprehensive)
• LncRNADisease a DB for lncRNA associated diseases
• ncFANs a web server for functional annotation of ncRNA
• LincSNP a DB of disease-associated SNP in human lncRNA and their TFBS
• POSTAR a DB of RNA binding protein binding sites in human and mouse transcriptome (experimental and computational methods)

Gene Expression DBs (Microarray/RNA-seq)

Data deposit servers

• GEO
• AtGenExpress Arabidopsis gene expression DB by Weigel lab (there are unpublished non-GEO data here)
• ImmGen Immunological Genome Project Ontogenet TF-module networks based on ImmGen data

Expression Atlas

• TISSUE Tissue Expression Database based on text mining (by Lars Jensen)
• 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

Mass Spectrometer or Immunohistochemistry Proteomics Resources

- Human Proteome Database

• Human Proteome Map 85 samples from 17 adult tissues, 6 primary hematopoietic cells and 7 fetal tissues
• ProteomicsDB >10,000 raw data files from 60 human tissues, 147 cell lines, and 13 body fluids
• The Human Protein Atlas The tissue-based map of human proteome based on Immunohistochemistry (for 32 different tissues and organs)

- Open stand alone software for spectra database search (search engines)

• MSblender A combined search engine
• MS-GFDB: Its successor MS-GF+ is faster and more sensitive for high resolution MS data.
• X!TANDEM
• Comet: the direct descendant of Crux, which is an academic version of the commercial software SEQUEST
• MyriMatch
• OMSSA Due to budgetary constraints NCBI has discontinued OMSSA. Historical binaries are available from here.

Protein localization and Secretome DB

• Vesiclepedia A DB for all types of Extracellular Vesicles (includes Exocarta)
• Exocarta A DB for Exosome
• EVpedia A DB for Extracellular Vesicles with many analysis softwares
• SUBA SUBcellular location DB for Arabidopsis proteins

Phenotype/Disease Annotation DBs

• DisGeNET MetaDB for disease genes and variants (very comprehensive and open license)
• Open Targets Another very comprehensive DB for disease target (mostly protein coding genes) and related evidence
• denovo-db a compendium of human de novo variants
• DISEASES gene-disease association from text mining (GHR, Uniprot, textmining)
• GHR Genetics Home Reference (by NCBI)
• Disease Ontology Disease ontology files FUNDO DOLite_term-to-genes map
• Human Phenotype Ontology
• OMIM Human disease DB (needs License to distribute)
• OrphaData Open database for rare diseases and orphan drug (by Orphanet)
• 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
• GenomeRNAi v12 contains 168 human RNAi, 181 D. melanogaster RNAi screen data sets
• OGEE Online GEne Essentiality database
• Human-Mouse Disease Connection a part of MGI

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

• A curated drug-target map by curation of ChEMBL database, DrugCentral database, canSAR knowledge base (Gold Standard drug-target)
• DGIdb An integrated Drug-Gene Interaction DB (CancerCommons, ChEMBL, CIVIC, Clearity Foundation, DoCM, DrugBank, Guid To Pharmacology MyCancerGenome, PharmGKB, Targeted Agents in Lung Cancer TDG, TEND, TTD); go to help for download batch data file
• 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
• MOSAIC Chemical-genetic interaction database for 13000 compounds

Drug signature, Pharmacogenomics, Toxicogenomics, Clinical Trials

• DSigDB Drug signature database for gene set analysis
• ClinicalTrials.gov DB for clinical trials conducted around the world
• Connectivity Map (CMap) 7,000 expression profiles representing 1,309 compounds
• LINCS Library of Integrated Network-based Cellular Signatures (former Connectivity Map)
• The Comparative Toxicogenomics database(CTD) The major DB of chemical-disease links from literature curation
• TG-GATE Toxicogenomics data for >150 chemicals in rats and the primary cultured hepatocytes of rats and humans
• Chemical Effects in Biological Systems(CEBS) an integrated public repository for toxicogenomics data
• PharmGKB The Parmacogenomics Knowledgebase
• SIDER Side Effect Resource

Cancer Genomics DBs

• Cancer Program Resource Gateway by Broad

-Curated functional and clinical variants in Cancer

• CIViC A knowledgebase for expert-crowdsourcing the clinical interpretation of variants in cancer
• DoCM A database of curated mutations in cancer

-Catalog of Cancer genes and mutations

• TSGene Literature curated Tumor suppressor genes (~1000 coding, ~200 non-coding); v2 paper also provides ~300 oncogenes in Supple
• NCG The Network of Cancer Genes; a manually curated repository of cancer genes from the literature (1571 cancer genes by v5)
• COSMIC Catalog Of Somatic Mutations In Cancer
• CGC Cancer Gene Census

-Cancer Genomics Data Portals

• Synapse GENIE The largest public cancer genome data by ACCR (see ACCR GENIE project)
• Synapse TCGA-Pancancer The official resource for hosting analysis-ready TCGA Pan Cancer data
• cBioPortal Data sets from published studies including TCGA
• CGHub TCGA data portal by UCSC; TCGA The Cancer Genome Atlas project home
• TumorPortal Pan-cancer data set from many tumor types.
• ICGC data portal raw data from ICGC and TCGA
• MethHC A database of DNA Methylation and gene expression in Human Cancer (use Pan-cancer data)

-Data for survival predictions

• Synapse TCGA-Pancancer survival prediction analysis-ready TCGA data for survival prediction

-Cancer Genomics Data Analysis Web server

• CRAVAT Cancer-Related Analysis of Variants ToolKit
• IntOGen Integrative Onco Genomics

-Cancer Immunity Resource

• Cancer Immunity Resource by Cancer Immunity (now Cancer Immunology Research since 2013)

-Cancer Pharmacogenomics

• 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

-Cancer cell essential genes

• Achilles Project shRNA-based essential gene profiles for 216 cancer cell lines
• COLT-cancer database shRNA-based essential gene profiles for 70 breast, pancreatic, ovarian cancer cell lines

Metagenome DBs and tools

-Metagenomic data central DB

• EBI Metagenomics (EMG) by EBI, UK
• MG-RAST by Argonne National Laboratory, US
• IMG/MG by Joint Genome Institute of DOE, US
• iMicrobe by Gordon Betty Moore Foundation, U of Arizona

-Human microbiome

• Integrated Reference Catalog of the Human Gut Microbiome ~9.9M genes
• Human Microbiome Project (HMP)
• The integrative HMP Microbiome-host interactions during disease progression (longitudinal studies on pregnancy, IBD, T2D)
• MetaHIT Metagenomics of the human intestinal tract
• Huttenhower Lab A great resource for analysis tools

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)

Data-driven Omics companies

• Arivale Health coaching for wellness based on multi-omics analysis
• Human Longevity Inc.
• Pesonalis Genome-guided Medicine
• Calico Aging-related disease research company
• Numedii New Indications for Medicines
• Enterome Microbiome analysis for healthcare and drug development
• Second Genome Microbiome company
• Seres Health Microbiome company
• Vedanta Biosciences Microbiome company

Other Resources

-Machine Learning

• Scikit learn Open software for Machine Learning
• Machine Learning by Andrew Ng
• An Introduction To Statistical Learning Free textbook and lecture notes

- Academic society

• KSBSB Korean Society of Bioinformatics and Systems Biology
• KGO Korea Genome Organization
• KSMCB Korean Society of Molecular and Cellular Biology
• KSBMB Korean Society of Biochemistry and Molecular Biology

- Other Systems Biology Links

• DREAM Dialogue for Reverse Engineering Assessments and Methods
• Sage Bionetworks
• Assay depot Online marketplace for pharmaceutical research service
• CAGI Critical Assessment of Genome Interpretation

- Neuroscience

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

- Others

• TEDMED TEDTALK for Medicine and healthcare problems
• Retraction watch
• Conference.city Conference search site
• Yoonsup Choi's Blog

Cool Web servers

• REVIGO Visualize GO enrichment summary
• VENNY Drawing Venn diagram