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.

PsychENCODE enhancer list and annotations

PsychENCODE enhancer set for the DLPFC: PEC Enhancers (in .bed format) »

QTL Maps

Expression QTLs (eQTLs), chromatin QTLs (cQTLs), isoform expression QTLs (isoQTLs), and cell fraction QTLs (fQTLs).

  1. List of eQTLs (in .txt format) »

  2. List of cQTLs (in .txt format) »

  3. List of isoQTLs (in .txt format) »

  4. List of fQTLs (in .txt format)»

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):

Bulk RNA-seq Decomposition and Deconvolution with Single-cell Data

  1. Brain Cell-type Marker Genes: Marker Genes (in .xlsx format) »

  2. Single-cell Expression Data: Single-Cell Expression (in .tsv format) »

  3. Cell Fractions Derived from Deconvolution:

  4. Decomposition through Non-negative Matrix Factorization (NMF):

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 »

Cortex Transcriptionally Active Regions (TARs)

  1. Genome-wide TARs within each sample: Sample-specific Genome-wide TARs (in .tsv format) »
  2. Genome-wide TARs that are found within at least 70% of the individuals: Consensus Genome-wide TARs (in .bed format) »

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.

Bulk and Single-cell RNA-seq alignment files

  1. PsychENCODE Bulk RNA-seq alignment (.bam) files (link to Synapse; login-secured): RNA-seq files for alignment to both genome and transcriptome »

  2. GTEx Bulk RNA-seq alignment (.bam) files (link to GTEX consortium web portal; login-secured): RNA-seq alignment files »

  3. PsychENCODE Single-cell RNA-seq (.fastq) files (link to Synapse; login-secured): RNA-seq fastq files »

Bulk ChIP-seq alignment files

  1. PsychENCODE Bulk ChIP-seq alignment (.bam) files (link to Synapse; login-secured): ChIP-seq files for alignment to both genome and transcriptome »

  2. Roadmap Epigenomics Consortium (REMC) Bulk ChIP-seq alignment (.tagAlign) files (link to the REMC web portal): ChIP-seq alignment files »

Genotypes

  1. Imputed genotypes and SNP arrays for individuals included in this analysis (link to Synapse; login-secured): Imputed Genotypes »

  2. Metadata for imputed genotypes (link to Synapse; login-secured): Metadata for Imputed Genotypes »

Phenotypes

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