tRanslatomeSampleData: Sample data set for tRanslatome

In tRanslatome: Comparison between multiple levels of gene expression

Description

matrix with data coming from differentiated and undifferentiated human HepaRG cells

Usage

data(tRanslatomeSampleData)

Format

tRanslatomeSampleData is a list that has 7 components :

expressionMatrix is a matrix of 12 columns and 1000 rows containing the microarray signals used as input of the function GetDEGs. Columns are organized in biological triplicates as follows: tot.diff.a, tot.diff.b, tot.diff.c contain the signals coming from the transcriptome of the differentiated cell line.

tot.undiff.a, tot.undiff.b, tot.undiff.c contain the signals coming from the transcriptome of the undifferentiated cell line.

pol.diff.a, pol.diff.b, pol.diff.c contain the signals coming from the translatome of the differentiated cell line.

pol.undiff.a, pol.undiff.b, pol.undiff.c contain the signals coming from the translatome of the undifferentiated cell line.

translatome.analysis is an object of class TranslatomeDataset generated calling newTranslatomeDataset() on expressionMatrix (see the examples section for the exactcall).

limma.DEGs is an object of class DEGs generated calling getDEGs() on expressionMatrix (see the examples section for the exact call).

CCEnrichment is an object of class GOsets generated calling GOEnrichment() on limma.DEGs (see the examples section for the exact call).

CCComparison is an object of class GOsims generated calling GOComparison() on CCEnrichment (see the examples section for the exact call).

regulatory.elements.counts is an object of class data.frame containing the background numbers of regulated and non-regulated genes for each post-transcriptional regulatory factor considered by function RegulatoryEnrichment.

regulatory.elements.regulated is an object of class data.frame containing the list of regulated genes for each post-transcriptional regulatory factor considered by function RegulatoryEnrichment

Source

Parent R, Kolippakkam D, Booth G, Beretta L. Mammalian target of rapamycin activation impairs hepatocytic differentiation and targets genes moderating lipid homeostasis and hepatocellular growth. Cancer Res. 2007;67(9):4337-4345

See Also

TranslatomeDataset computeDEGs DEGs RegulatoryEnrichment EnrichedSets GOEnrichment GOsets GOComparison GOsims

Examples

 ##load the tRanslatome sample data
 data(tRanslatomeSampleData) 

tRanslatome documentation built on Nov. 8, 2020, 6:24 p.m.