PsychENCODE Adult Integrative Capstone Analysis

Additional details on data generation and analysis can be found in the paper supplement.

Bulk download of all the data on this webpage is available: PEC Adult Integrative Datasets (.tgz format) »

For interactive query and genome browser options: PEC Interactive Portal »

Integrative Analysis

An integration of data across the capstone projects to build a model taking QTLs as inputs and providing both phenotype predictions as well as functional modules involved.

Integrative Analysis for each brain phenotype

  1. Integrative model parameters for all phenotypes:

  2. Multi-level functional enrichment analysis (DSPN-mod) and Weighted Gene Co-Expression Analysis (WGCNA) modules:

  3. Transcription Factor - Target Gene - Enhancer linkages:

  4. HiC-derived Enhancer - Gene linkages: HiC Enhancer - Gene linkages (in .csv format) »

  5. Schizophrenia-associated genes:

Derived Data Types

Enhancer lists, eQTL and cQTL maps, DEX genes, gene co-expression modules, PCA/RCA-based clustering of RNA-seq data and epigenetic data, decomposition and deconvolution of cell-type-specific RNA-seq.

Differentially Expressed (DEX) and Spliced Genes/Transcripts and Gene/Isoform Co-expression modules

This resource provides sets of genes that exhibit significantly different expression levels between different groups of samples.

  1. Brain-specific DEX genes across all PsychENCODE samples relative to the non-brain tissues in GTEx: Brain DEX genes in .tsv format »

  2. Disorder DEX Genes and Transcripts, and Differentially Spliced Genes of PsychENCODE samples (from Capstone #1):

  3. Gene and Isoform Co-Expression Modules calculated using Weighted Gene Co-Expression Analysis (WGCNA) on the PEC RNA-seq samples (from Capstone #1):

Pipeline-Processing Results

RNA-seq quantifications, ChIP-seq signals and peaks, Brain Transcriptionally Active Regions (TARs), Imputed Genotypes (secured),and Phenotypes.

RNA-seq signals and peaks (Synapse access required)

Signal tracks (.bigwig) and peak (.bedgraph) files calculated using PsychENCODE pipeline, available on Synapse: RNA-seq Signal Tracks and Peak Files »

ChIP-seq signals and peaks (Synapse access required)

Signal tracks (.bigwig) and peak (.bed, .narrowPeak, .gappedPeak, and .broadPeak) files calculated using PsychENCODE pipeline, available on Synapse: ChIP-seq Signal Tracks and Peak Files »

Raw Data (Secure Access)

Alignment files for the various experiments, chip arrays for the SNP genotyping assays and phenotype metadata for the different studies under the consortium; external links are provided for the data sources on Synapse, and the GTEx consortium and Roadmap Epigenomics Consortium web portals.

Phenotypes

Demographic and clinical information on individuals included in this analysis (link to Synapse; login-secured): Phenotype information »