Genome Biology     Genetics     Biostatistics     Population Genetics    Genetic Epidemiology     HLA     MHC     Homepage

 

BIOINFORMATICS TOOLS

(for Genetic Epidemiologists)

Mehmet Tevfik DORAK, MD, PhD

 

Open Access Reviews / Journals

ENCODE Resources (Pazin MJ. CSHP 2015); Database Tools (Bianco, Genomics 2013; Zou, 2015); UCSC Browser (Mangan, 2014)

JournalsNucleic Acids Research: Database Issue (2018)Web Server Issue (2017);  Database: Biomart IssueEnsembl Issue

 Nucleic Acids Research Databases Catalog

Scientific Data

 

Article Collections

 ENCODE (Web Focus)     FANTOM5 (RIKEN)    IHEC    Epigenome RoadMap     TCGA     GTEx

 

Societies

ISCB     ISMB    AMIA   ECCB

 

Online Suites

Galaxy (101 - Support)   ExPASy (ref)   Taverna 2.5.0/Archive (ref)   Apache-Taverna   BioMart (ref)   Artemis (manual)   Babelomics (ref / tutorial)  

Bioconductor (manual)   BioPython (tutorial & cookbook / PDF)

EDGE: Empowering the Development of Genomics Expertise (ref)

 

Biomarts

Ensembl BioMart (YouTube tutorial)   UCSC Table Browser   GWAS Central GWAS Mart (tutorial)   SPS Mart (allele freqs)  Fantom5

 

Genome Browsers

 UCSC Human Genome BioInformatics    GENCODE    FANTOM5 (ref / tutorial / wiki / user guide (pp.12-19)) - ZENBU - SLIDEBASE (tutorial)

Ensembl Genome Browser (Human)   Vega Genome Browser (Human)

NIH RoadMap Epigenomic Browser (tutorial)   WashU EpiGenome   Human Epigenome Atlas   NCBI Epigenomics (help)   NGSmethDB (ref)

1KG (Browser - Quick Start Guide)-(NCBI)   PopHuman (ref)

  UK10K (ref)   GENCODE Browser   SNiPA   ExAc (ref(gnomAD) genome Aggregation Browser (ref)

CNV Browser  DECIPHER  eQTL Browser  seeQTL  GTEx eQTL Browser

StarBase (tutorial / ref)   lncRNome   lncRBase   NonCode   FANTOM CAT (lncRNA Atlas) Browser (ref)   Integrative Genomics  

VISTA Enhancer Browser    Swiss Regulon    Reactome Pathway Browser   ImmunoBase Browser   ImmunPop Browser (ref)

 

 General Resources

NCBI Global Search   GoPubMed  HuGE  LabMeeting   NCBI Tutorials / Handbook / Help Manual   NIH Helix   NCBI Tools for Data Mining  NCI Data Analysis Tools

Sanger: Software / Databases & Tools     EMBL-EBI    Swiss Institute of Bioinformatics: ExPASy   JJ Wang Lab

NCBI Gene .. GeneCards .. GeneMap .. GenAtlas .. GenCanVas .. iHOP .. NetAffX .. BioGPS Gene Annotation .. Harmonizome (ref)

NCBI (tutorials on YouTube) .. BLAST .. MimicMe (ref) .. e-PCR .. In Silico PCR .. GeneNote .. GeneLoc .. CGAP-GAI .. Aceview

ENCODE (ref / tutorial1 / tutorial2 / cell types)   GENCODE    RegulomeDB   FANTOM/Gateway (papers / software)

Database of Genomic Variants (CNV)   CNV inspector   Copy Number Variation Resources   DECIPHER (ref)

OMIM .. OMIM Map .. NCBI Genetic Association Database (GAD) .. HuGE Navigator .. Variant Name Mapper  

Gene Exp Omnibus -GEO (NCBI) .. NCBI dbGaP .. ArrayExpress (EBI) .. BioGPS .. SOURCE (genomics tool)

Comparative Toxicogenomics Database (CTD)    CHE Toxicant & Disease Database  

  NIEHS SNPs    RNA-seq Atlas (ref)   NGSmethDB (ref)  

Genomic coordinate conversion: Ensembl Assembly Converter   Kaviar

rsID to VCF conversion: dbSNP  

Harmonizome (ref)

 

 SNP Resources (variation & functional annotation)

GENEPI TOOLBOX (ref)   Endeavour

dbSNP .. dbSNP Tutorial    Variation Discovery Resource UW-FHCRC (Seattle SNPs): VG2 (Visual Genotypes)    LOVD (ref)

NCBI Variation Viewer   NCBI ClinVar (ref)  NHGRI Clin Genomic DB   GeneSNPs   PharmGKB   HGMD

 Ensembl Variant Effect Predictor (VEP)     AVIA  (ref / tutorial)     wANNOVAR (tutorial)    FunSeq2 (ref)

rVarBase (ref / tutorial)   SNiPA (ref)   mQTLdb (ref)   BIOS QTL Browser (ref1 / ref2)

SNPnexus (guide) .. PheGenI (tutorial) .. HaploReg v4 (ref) .. HumanMine (ref) .. CoreMine .. VaDE .. SNVrap/QUICKrap (ref)  

FUN-LDA (ref)   CADD (ref) .. DANN (ref) .. EIGEN (ref) .. FATHMM (ref) .. GWAVA (ref) .. SusPect (ref) .. RegulomeDB (GWAS) .. DeepSEA (ref)

FATHMM-XF (ref)  PhD-SNPg (refPredictSNP2 (refSNPDelScore (ref)  ClinGen Pathogenicity Calculator (ref)

 RVS / Reference Variant Store (ref)     Structure PPi (ref)     GenoCanyon (ref)

VarioWatch .. SNPedia .. NextBio .. SNPwatch .. MutaGeneSys .. LS-SNP/PDB .. LS-SNP (ref)

dSysMap (ref / tutorial)    PsyGeNET (ref1/ref2)

  rSNP Guide .. SNPLogic .. SPSMart (comparative frequencies)

DistiLD .. SNPEffect .. SNPfunc (ref) .. GRAIL (ref)

PopHuman (ref)   Haplotter   HGDP Selection Browser   Selectome - A Database of Positive Selection   dbPSHP (ref)   GERP (ref1 / ref2)

RVIS Genic Intolerance (ref)

 FERRET for 1KG SNP Data Download (ref)

Harmonizome (ref)

 

Proxy Search

NCI LDLink (refNCI LDAssoc (ref)

ssSNPer .. SNAP .. SNPSnap (ref / guide) .. SPOT (ref / user guide) .. HaploReg v4 .. CandiSNPer (ref)  

SNP Data Analysis (including HWE): SNPStats    OEGE HWE Calculator

 

eQTL / meQTL Resources

GTEx .. NCBI Molecular QTL Browser (ref) .. SCAN (tutorial) .. PheGenI .. QTLminer (ref) .. eQTL Databases  

eQTL Resources @ Pritchard Lab (browser) .. Blood eQTL Browser .. BIOS QTL Browser (ref1 / ref2) .. eQTL Catalog (NESDA/NTR) (Ref)

CAGE eQTL Browser (ref)   ImmunPop eQTL Browser (ref)   GWAS2Genes (ref)    GEUVADIS/1KG (ref; data download)

 mQTLdb (ref) .. e/meQTL .. reQTL (ref) .. HSM (Haplotype-specific Methylation-associated SNPs) (ref)

seeQTL (help / ref)   Plateletomics (Platelet transcriptomics by gender)  ImmGen eQTL Browser (mouse)   

FIRE (Functional Inference of genetic variants that Regulate gene Expression) (ref)

eCAVIAR: colocalization of GWAS signals and eQTLs (ref / manual)   PancanQTL (ref)

DIVAN (ref)

 

Splice Site SNPs

ssSNPTarget (ref) .. AASsites (ref) .. AS-ALPS (ref)  

EC Gene (alternative splicing) .. NNSplice (splice site prediction on genomic sequence)

 

Coding SNP Annotation

genome Aggregation (gnomAD) Browser (formerly ExAc Browser) (ref)

 SNPs3D .. dbNSFP (ref) .. SNPdbe (ref) .. PolyPhen-2 .. SIFT (by SNP ID) .. PolyDoms .. KD4v (ref)

 MutDB .. HGMD .. Panther (download) .. FannsDB (Condel & TransFIC) .. Mutation Assessor (ref) .. MutPred .. PMut (ref)

 

GWAS Resources

 GWASdb v2 (JJ Wang Lab)   Catalog (NHGRI-EBI)   GWAS Central   HuGE GWAS Integrator

PhenoScanner (manual)    GRASP (ref / overview / user guide)    GWATCH (ref / tutorial)    

GWAS4D (ref / help)    FUMA GWAS (ref)  LocusZoom (ref)

HaploReg v4 (ref)    RegulomeDB (GWAS)

 WGAviewer (ref / workshop notes)   GenAMap (ref / tutorial)   SNPTrack (ref)

OMICtools    GWAS Diagram Browser   SIB Association Viewer (ref)

SNP Imputability   HLA-IMP (tutorial/ref)

CAPE: CellulAr dePendent dEactivating mutations predictor (ref

GARLIC: GWAS-based Prediction Toolkit for Connecting Diseases and Cell Types (ref)  

LD Hub (ref)    easyGWAS (ref / tutorial)     MR-Base (ref1 / ref2)

 HESS: Heritability Estimation from Summary Statistics of GWAS (ref)   UKBB Heritability Browser

LDGIdb (Linkage-Disequilibrium-based Gene Interaction database) (ref)

Breast Cancer GWAS: GAME-ON   CGEMS   (KM Plotter)  Human Protein Atlas KM Plotter (ref

GeneAtlas (UK Biobank)   GeneAtlas/PheWAS   PheWAS Catalog    PheWeb (UK Biobank) (unpublished)

  Metabolomics GWAS    PGWAS: Proteomics GWAS (ref)

NHGRI GWAS Catalog as a Table (2015)

eCAVIAR: colocalization of GWAS signals and eQTLs (ref / manual)

 

Epigenetics

NIH RoadMap Epigenomic Browser (tutorial / cell types)   WashU EpiGenome   Human Epigenome Atlas   NCBI Epigenomics (help)  

Int Hum Epigenet Cons (IHEC)   IHEC Data Portal  

HEDD (Human Epigenetic Drug Database) (ref)

CpG sites list

 

Chromatin Features Databases

HEDD (Human Enhancer Disease Database) (ref)   DiseaseEnhancer (Disease-associated enhancers) (ref)   GeneHancer (ref)

SlideBase (FANTOM Enhancers) (tutorial)

Cistrome DB (for chromatin features) (ref)   NHGRI HistoneDB v.2 (ref

3DIV (3D-genome Interaction Viewer and Database) (ref / tutorial)  

3D Genome Browsers:  Yue Lab (ref / tutorial)    HUGIn (ref / tutorial)    3DGB/McGill (ref)    3Disease Browser (ref / tutorial)

 4D Genome (ref)   3CDB (ref)   CCSI/obsolete (ref)

Human Histone Modification Database (HHMD) (ref)

 

ncRNA (microRNA/lncRNA) & Pseudogene Resources

EpiGenie Epigenetics Tools

NONCODE (ref)   NPInter v3 (ref)   ncRNA Databases Resource (NRDR)   ChIPBase (ref)

 miRBase   miRDB   mrSNP   TargetScan   miRWalk 2.0 (ref)  StarBase (tutorial / ref)   miRNA SNiPer (ref)   microSNiPer (ref

DIANA-TarBase (ref)    miRTarBase (ref-2014 / 2016)   miRmap (ref)   miRNAmap (tutorial/ref)   Human miRNA Tissue Atlas (ref)   miRFocus   

 Human miRNA Disease Database (HMDD)   miRCancer   OncomiRDB (ref)   HOCTAR (refFAME (ref)   IntaRNA (ref / help)

RegNetwork (TF and miRNA networks) (ref)    Genome-wide Predictions of miRNA Regulation by Transcription Factors Database  (ref)

miRNA-SNP db (ref)   AVIA miR SNP Analysis Tool   miTranscriptome (ref

FANTOM CAT/lncRNA Atlas (ref)    MNDR (Mammal ncRNA-Disease Repository) (ref)

lncRNA and Disease Database   Human lincRNA catalog (Broad)    lncRNA2Target (ref)   lncReg (ref)   lncTar for Target Prediction (ref)

 lncRNome (ref / user guide)   LNCiPedia (ref)  lncRBase (ref)   DIANA-lncBase (ref / v2.0)   lncRNAtor (ref)   lncRNAdb    LncRNADisease (ref)

EVLncRNAs (database for long non-coding RNAs) (ref)    ncRNA (Functional RNA Analysis)

Lnc2Meth (database of regulatory relationships between long non-coding RNAs and DNA methylation)  (ref)

Database of CpG Islands

lnCaNet Database (lncRNA-Cancer co-expression database) (ref)   co-lncRNA (ref

 lncRNA-SNP db (ref)   LincSNP v2.0 (ref)   LncVar (ref)

lncScape (Hematopoietic lineage and leukemia lncRNA expression atlas) (ref)

IntaRNA (ncRNA-mRNA interaction prediction) (ref)   decodeRNA (ref)

Database of small human noncoding RNAs (DASHR) (ref)    miRVaS (miRNA search within sequences) (ref / manual)

 PseudoMap (ref / tutorial)    RNASNP (Predicting SNP effects on local RNA secondary structure)  RBP-Var2 (ref)

 

Gene expression (incl. cancer) & Cancer Informatics

Cancer Cell Line Encyclopedia / CCLE (ref)   Human Protein Atlas: Cancer

   RNA-seq Atlas (ref)   Expression Atlas (ref)   lnCaNet Database (ref)

TSEA (Tissue Specific Expression Analysis) (ref)

PancanQTL (ref)

ORGANize (linking genes to the organs they affect) (ref / help)

Gene Enrichment Profiler (ref)

Brain: Cortecon (ref)   BrainSpan (ref / help)

 & 

Cancer Genomics and Epidemiology Navigator (CGEN)

(KM Plotter)  Human Protein Atlas KM Plotter (ref)

BloodSpot (AML) (ref)

Databases for Cancer Genomics (Table 2 in Chin, 2011)

UCSC Xena Browser    ActiveDriverDB (variation in post-translational modification sites) (ref)

 

Transcription Factor Binding Site Search

TransFac  TFBS Search (Qiagen)  TFBS Mapper (refTFBIND  MFold   JasPar  PAZAR  SNP@llincRNA TFBS (ref)

 Swiss Regulon (by TF Name)   AR Target Gene Dbase   TESS-discontinued  

CTCFBSDB v2 (ref)

 

Cancer Somatic Mutations

 COSMIC (somatic mutations in cancer) .. COSMIC Browser .. ICGC Data Portal .. NCBI Cancer Genome Anatomy Project .. cBioPortal 

Integrative OncoGenomics Database (intOgen) (ref)   DriverDBv2 (ref, help)   OncodriveFML (ref)

 CRAVAT (ref / help)    CIViC (ref)    TCGA Clinical Explorer

TransFIC    PRISMAD (ref)   BRCA1 Circos (ref)    Cancer cell line encyclopedia (CCLE) (ref)

(See also Yang, 2015 & Raphael, 2015)

 

Gene Set Enrichment and Pathway Analysis

ENRICHR (ref / help)    GSEA/MSigDB    ConsensusPath (CPdB) (ref / protocol)   Pathway Commons (Guide / Primer)

  DAVID (ref / tutorial / wizard) .. IPAD (ref) .. SSEA (ref) .. See also Huang, 2009

 Cytoscape    Disease Connect    ToppGene (ref)    Panda (ref / video tutorial)   WebGestalt (ref)

UniHi   Reactome (user guide)   BioSystems   Pathway Searcher   KEGG   PDB: Biological Process Browser

Gene Ontology    GeneSigDB    GeneSetDB    GeneFamilies            

GSEA & GSEA-SNP   GIANT (Gene Networks in Tissues; Ref)   Onto-Tools (user guide)

Comparative Toxicogenomics Database (CTD) 

 

GWAS SNP Set Analysis

i-Gsea4Gwas Web Server (ref / tutorial)    GSEA & GSEA-SNP    VSEAMS (ref)-for local use    MAGENTA (ref)-requires MatLab

 

Gene Network Analysis

The Genome Network Project (GNP)   Genetic Network Analysis Tool (GNAT) (ref)

GeneNetwork-UT / GN2 (co-expression) (ref)    Human Gene Correlation Analysis (co-expression) (ref)   CORD (ref) (co-regulation) 

GLITTER (tissue-specific coexpression) (ref)

GIANT (Gene Networks in Tissues; ref)    BioGrid    String  

RegNetwork (TF and miRNA networks) (ref)   ChIPBase (ref)

 Genome-wide Predictions of miRNA Regulation by Transcription Factors Database  (ref)

Ingenuity Target Analysis  

 

Gene Ontology

QuickGO (ontology) .. Gene Ontology (AmiGO browser)

GeneNetwork-UCMG (function, expression and co-expression) .. GeneNetwork-UT

Harmonizome (ref)

 

Immunoinformatics

 MHC Haplotype Project   dbMHC (search)

IPD-IMGT/HLA (ref)    MHCcluster (ref)   Immune Epitope Database (IEDB) (video tutorials/ref)

Registry of Antibody-Defined HLA Epitopes (ref)    HLA Epitopes @ Allele Frequencies.Net (ref)

IMGT/HLA Allele Query    IGDAWG (Global Frequency Map Browser)   PyPop Population Data

 ImmPort (tutorial)   ImmVar   ImmunoBase (browser)   ImmuNet (ref)   ImmuneCellScience (ref)   ImmGene-Mouse (ref / video)

FineMapping / PICS (ref)    SNP2HLA (Imputation of Amino Acid Polymorphisms in HLA) (ref / manual)

BIGDAWG Case-Control HLA Data Analysis (ref)   HLA-NET GENE[RATE] Tools (publications)

HLA-NET: Charts & Maps

The SysteMHC Atlas project: MS-generated immunopeptidomic data (ref)

HLA-MA (ref)

 

 Proteins

Human Protein Atlas (ref) .. ProteomicsDB .. Protein Data Bank .. MOPED .. SWISS-MODEL .. SwissVar .. AS-ALPS (ref)

Structure PPi (ref)   Phyre 2 (ref; tutorial; tutorial notes)   Phyre 2 Investigator   ConsensusPath (CPdB)  (ref)

SusPect (ref)   UniProt (query)   SwissProt   Protein-Protein Interaction Mining Tool   MINT (interactions)

BioPlex (ref)   Genome3D   SMART   STRING  Jet2Viewer (PPI) (ref)

Structural Biology Knowledgebase (SBKB)  MEME Suite   iHOP

Protein Sequence Analysis     Protein Functional Analysis (PFA) @ EMBL

ExPasy: Proteomics Tools    Tools for Protein Analysis    GenomeNet Chemical Analysis Tools

 Post-translational Modifications

GPS    PhosSNP (ref)    Functional Glycomics   ActiveDriverDB (variation in post-translational modification sites) (ref)

Protein-related Bioinformatics Resources

 

Human Metabolome Database (HMDB)   Metabolomics GWAS   HumanMine (ref)

 ANNOVAR (ref / quick startup guide / protocol)  wANNOVAR (tutorial)   AVIA

AURA: Atlas of UTR Regulatory Activity (ref)

 

Disease Databases

dSysMap (ref / tutorial)   Disease Connect   CoreMine   GWASdb v2   Phenolyzer (ref / tutorial)   PhenoPred   SNPs3D  DisGeNET (ref)

FANTOM CAT Traits Database    3Disease Browser (ref / tutorial

Comparative Toxicogenomics Database (CTD) 

SZGR (ref)    SZDB Database (refxQTL Serve (ref)

 

Various Other Resources

Gene Prediction Tools

GeneMark   AUGUSTUS Gene Prediction Tool (tutorial)  GenScan (info)   Gene Prediction   Melina II (promoter)

Rfam (RNA sequence families of structural RNAs) Prediction Tool   moses (ncRNA) 

 

STR Database

 TaqMan SNP Genotyping Assays (1)  (2)  

Chang Bioscience Tools    VISTA Tools

ThermoFisher Learning Center .. Access Biotech

Restriction Enzyme Database .. NEBCutter .. GenScript Tools

Primer Design Resources .. SNP-RFLPing (PCR-RFLP Design)

Primer Design Software Primer3 (help) .. Primer3Plus .. BatchPrimer3 (help / ref) .. Viz-Primer

 Oligo Analyser and PrimerQuest (IDT)

FastPCR .. FastPCR Online Tools .. In Silico PCR .. OEGE Sequence Tools 

Multiple Sequence Alignment: Clustal (help) .. BioEdit .. Topali v2 .. Jabaws   

Expasy Translate Tool .. ORF Finder (NCBI) .. JustBio Bioinformatics Tools  

JJ Wang Lab

 

Search Templates

(use these static URLs for quick searches by changing the indicated identifier to yours in the address line)

Gene (Gene Name1/Human)  Gene (Gene Name2)  Gene (GeneID)

dbSNP (GeneID)  dbSNP (rs#)   RefSNP (rs#)  Ensembl (rs#)  SNiPA (rs#)

GWAS Cat (NIH) (rs#)   GWAS Cat (EBI) (rs#)  PhenoScanner (rs#)   GeneAtlas-PheWAS (UK Biobank) (rs#)

 PheGenI (rs#)  dbGAP (rs#)   GWAS Central (rs#)   ImmunoBase (rs#)

eQTL-Chicago (rs#)   GTEx (rs#)  

GTeX (Gene Name)  GTEx Visualizer (Gene Name)  GTEx (your own SNP)  GTEX (alt. splicing variants for a gene)

GWAS Central (Gene Name)    Ingenuity Target Explorer (Gene Name)

Variation Viewer (geneName)   Broad Institute (rs#)   rVarBase (rs#)   HaploReg v4 (rs#)   HSM (rs#)

Vega / Ensembl (Gene Name)  Ensembl (rs#)   SNPedia (rs#)

RegulomeDB (chr#/nt#)   OpenSNP (rs#)  MSV3d (missense rs#)   SNPDelScore: Restful (API)

ENCODE Regulatory Elements DB (Gene Name)    GenCode - Alternative Splicing Variants (Gene Name)

 Expression Atlas (Gene Name)   Protein Atlas (Gene Name)   

Virtual 4C (rsID and GM12878)

LDAssoc / LDPair (LD between two SNPs in EUR populations)  

COSMIC Gene Analysis Search (Gene Name)

LnCaNet search: general info by Gene ID; expression by Gene ID; PTM by Gene ID

mirBase microRNA search (Chr coordinates)

 HGMD (Gene Name)   PPI Mining Tool (Gene Name)    GeneCards    Entrez Structure   RVIS (GeneName)  

Amino Acids   Genetic Code   Ambiguity (Mixed Base) Codes

 BioCompare

 

ONLINE TUTORIALS / TRAINING

EMBER - A Practical Guide to Bioinformatics

GOBLET - the Global Organisation for Bioinformatics Learning, Education & Training

Applied Bioinformatics Course (ABC) (ref)

Bioinformatics Training and Services (BITS) - Exercises

Tutorials: NCBI  Ensembl  UCSC  Haploview  Galaxy  GoldenHelix  ImmPort  Omixon

EMBL-EBI Training

Tutorials @ Open Helix    Open Helix Blog    Mayo Bioinfo YouTube Channel

Online Lectures on Bioinformatics

Getting Genetics Done   BioStars   Swedish Bioinformatics Support (SBS)

Genome Biology & Applied Bioinformatics Course Notes

Melbourne Bioinformatics (formerly VLSCI)   Genomics Virtual Laboratory (GVL) (tutorial)  

 

LINKS

Links to Bioinformatics Tools @ ABC

Bioinformatics.ca

OMICSTools     Dataset2Tools (Tools) (ref)

Online Bioinformatics Resources Collection

 

Mehmet Tevfik DORAK, MD, PhD

 

Genome Biology     Genetics     Biostatistics     Population Genetics    Genetic Epidemiology     HLA     MHC     Homepage

 

2 June 2018