featureBasedData: featureBasedData

In SCCC-BBC/PathwaySplice: An R Package for Unbiased Splicing Pathway Analysis in RNAseq data

Description

This dataset includes analysis results of RNA-seq data in Dolatshad et al. (2015), which compared transcriptome of CD34+ cells from myelodysplastic syndrome (MDS) patients with SF3B1 mutations vs. healthy controls using RNA sequencing. The JunctionSeq package was used to assess differential usage of counting bins, which are non-overlapping segments of the exons or splicing junctions (see Fig 1 in Anders et al. (2012)). Because of the size limit, only counting bins associated with a subset of genes were included here for demonstration.

Usage

data(featureBasedData)

Format

A data frame with variables for gene identifier (geneID), gene feature identifier (countbinID), and p-value for gene feature (pvalue). Here we used "gene feature" and "counting bin" interchangeably

References

H Dolatshad, A Pellagatti, M Fernandez-Mercado1, B H Yip, L Malcovati, M Attwood, B Przychodzen N Sahgal, A A Kanapin, H Lockstone, L Scifo, P Vandenberghe, E Papaemmanuil, C W J Smith, P J Campbell, S Ogawa1, J P Maciejewski, M Cazzola, K I Savage1 and J Boultwood1 (2015) Disruption of SF3B1 results in deregulated expression and splicing of key genes and pathways in myelodysplastic syndrome hematopoietic stem and progenitor cells. Leukemia (2015) 29, 1092-1103

Anders S, Reyes A, Huber W (2012) Dececting differential usage of exons from RNA-seq data. Genome Research 22(10): 2008-2017

SCCC-BBC/PathwaySplice documentation built on May 9, 2019, 11:07 a.m.