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ASE Cases

Gene-level Allele Specific Expression Data from Rare Case Cohorts. Briefly for each cohort documented, gene-level haplotype aggregated ASE data has been provided following the best practice protocols. For further information refer to our paper here.

Data Format

Each file is an excel file with the following:

  • Each row corresponds to a gene ID (idenitifed by ENSEMBL ID)
  • Each column is a sample ID with corresponding values being the gene-level (reference count, alternate count, and ANEVA-DOT p-value) for outlier testing.
  • For details on what tissues were used for ANEVA-DOT testing please read our paper here

Datasets

MDM

mdm_cases.xlsx: 46 Muscular Dystrophy Samples from the Genetics of Inherited Muscle Disease Cohort (dbGAP). Phasing of genotypes was performed using EAGLE and the Illumina 30x high coverage genotypes as a reference panel. ASE data was generated using the PAC pipeline.

PCGC

pcgc_cases.xlsx: 257 Pediatric Congential Heart Disease Cases from the CHD Genes. Data produced by @martbro Following a pipeline briefly outlined. Genotypes were merged (WES+WGS) when available and trio-phased using SHAPEIT4. RNA-seq alignments were performed using STAR and WASP filtering to remove any sources of bias. phASER was used to compute the gene level haplotype aggregated counts.

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Gene-level Allele Specific Expression Data from Case Cohorts

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