Javascript is disabled/outdated. Please enable Javascript/use updated browser to load site navigation and frame.

Browser needs ECMAScript 6 support.

The aim of science is, on the one hand, as complete a comprehension as possible of the connection between perceptible experiences in their totality, and, on the other hand, the achievement of this aim by employing a minimum of primary concepts and relations.
--- Albert Einstein

Bioinformatics Resources

Gateways to computing facilities

  Globus Online
  Galaxy (public)
   
Databases NIH Commons
  NIH Public Access - manuscript submission (NIHMS)
  dbGaP Authorized Access
  Entrez dbSNP
  dbSNP batch query
  GWAS Central
  EBI Expression Atlas

 

 

Brain QTL Mapping

Pathway & function DAVID
  Gene Ontology
   
Gene expression data repository EBI ArrayExpress
  NCBI GEO
   
   
Databases BrainCloud
  Allen Brain Atlas
   
 

 
eQTL

NCBI GTEx (Genotype-Tissue Expression) eQTL Browser
  seeQTL (UNC)
 

Sanger Genevar (GENe Expression VARiation)
   
  eQTL Browser (U of C)

SNP Functionality

Tools  
  ANNOVAR
  SNPnexus
   
Databases  
   
   

Phenotype genotype epigenotype integration

Tools The Phenotype-Genotype Integrator (NCBI) 
  HuGE Navigator
 

Catalog of Published Genome-Wide Association Studies (GWAS catalog)

   
 

The Pharmacogenomics Knowledge Base [PharmGKB]
   
   
Databases Mouse Phenome Database 
  Mouse GeneNetwork/WebQTL
   
   

 

Genesets and pathways

Tools  
  GSEA
  GSA
   
Major candidate genes Autism from CSHL
  Autism from PKU: AutismKB
  Autism from AutDB
  Autism from AGD
  Autism from SFARIgene
  Schizophrenia Research Forum
  Schizophrenia from Rutgers (candidate regions)
  Schizophrenia from CSHL
  Alzheimer Research Forum
  Bipolar disorder from CSHL
  Bipolar disorder from UIC BDStudies
  Depression from CSHL
   
Databases MSigDB (8513 predefined gene sets, Oct 2012)
  Additiona geneset defined at Stanford for GSA
   
  Our own gene sets (co-expression modules in brain, co-methylation modules, major candidate genes for psychiatric diseases)
   

 

NGS data analysis

Tools  
  RNA-Seq blog
  SEQanswers
  NGS methDB
   
Databases COMPLETE GENOMICS, Public Data
   

 

Human Genomic & Epigenomic Map

GENCODE Human Genome Reference

Encode

  
   
Databases methylomeDB
   

PsychENCODE-related Databases

PsychENCODE Integrative Analysis, by Mark Gerstein Lab @Yale eQTL, coexpression, TFs, DEG and others
by Pinto Lab @ Mt Sinai Query for figures related to Capstone 1 paper
Synapse Synapse data repository for all original documents and data

Association and Causal Analyses

GWAS integrated with tissue expression, by MX Li Lab
  • KGG (Knowledge-based mining system for Genome-wide Genetic studies), including gene-based, gene-set (LDRT), PPI-based gene-pair (HYST), conditional (ECS), driver-tissue (DESE), multivariate analyses (MGAS)
  • KGGSEE, GWAS with eQTL and causal inference
  • PCGA: Phenotype-cell-gene association, with a database to query; AND EMIC for causal genes inference
  • REZ (robust-regression z-score): driver tissue results, calculate tissue selective expression of genes, statics based on GTEx. With a database to query for tissue enrichment for disease-gene relationships.

    • Web site analysis: WSdata