Post-transcriptional regulation supports the homeostatic expression of mature RNA

Overview

This dataset consists of RNA sequencing data stored in HDF5 files. The data has been processed to quantify gene expression changes at the precursor RNA (preRNA) and mature RNA (matureRNA) levels across various biological conditions, including normal tissues and diseases. The dataset supports the study "Post-transcriptional regulation supports the homeostatic expression of mature RNA," providing insight into the general influence of post-transcriptional regulation (PTR) on gene expression homeostasis.

File Contents

Each HDF5 file contains the following datasets:

logFC_MatureRNA: Represents the log fold change of mature RNA expression levels between different conditions or tissues.

logCPM_MatureRNA: Represents the log counts per million for mature RNA.

PValue_MatureRNA: Represents the p-value for the statistical test performed on mature RNA expression levels.

FDR_MatureRNA: Represents the false discovery rate for the mature RNA expression levels.

logFC_preRNA: Represents the log fold change of precursor RNA expression levels between different conditions or tissues.

logCPM_preRNA: Represents the log counts per million for precursor RNA.

PValue_preRNA: Represents the p-value for the statistical test performed on precursor RNA expression levels.

FDR_preRNA: Represents the false discovery rate for the precursor RNA expression levels.

genes: A list of gene identifiers used in the study.

studies: A list of study or condition names included in the dataset.

File Naming Convention

The HDF5 files are named to reflect the filtering applied to exclude lowly expressed genes (logCPM > 5), and DESeq2 and edgeR refer to the tools used for differential expression analysis:

DESeq2_filtered_exon_intron_abnormal_conditions_all_reads.h5

edgeR_filtered_exon_intron_abnormal_conditions_all_reads.h5

DESeq2_filtered_exon_intron_gtex_tissue_all_reads.h5

edgeR_filtered_exon_intron_gtex_tissue_all_reads.h5

Example Usage

To query the HDF5 files, you can use the provided `parse_h5_file.ipynb` example notebook to parse the HDF5 files.