PsychENCODE Adult Integrative Capstone Analysis

  1. Integrative Model:

    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.

  2. 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.

  3. Pipeline-Processing Results:

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

  4. 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; links provided are for the secured data sources on Synapse.

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

Integrative Analysis

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

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

This resource provides sets of genes that with 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 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)

Bulk and Single-cell RNA-seq alignment files

  1. PsychENCODE Bulk RNA-seq alignment (.bam) files are available on Synapse under condition of secure and approved access: RNA-seq files for alignment to both genome and transcriptome »

  2. GTEx Bulk RNA-seq alignment (.bam) files are available on the GTEX consortium website under condition of secure and approved access: RNA-seq alignment files »

  3. PsychENCODE Single-cell RNA-seq (.fastq) files are available on Synapse under condition of secure and approved access: RNA-seq fastq files »

Genotypes

  1. Imputed genotypes and SNP arrays for individuals included in this analysis are available from Synapse under condition of secure and approved access: Imputed Genotypes »

  2. Metadata for imputed genotypes are available on Synapse under condition of secure and approved access: Metadata for Imputed Genotypes »

Phenotypes

Demographic and clinical information on individuals included in this analysis are available from Synapse under condition of secure and approved access: Phenotype information »