DivergenceExpressionSetExample: An Example DivergenceExpressionSet Data Set
In YTLogos/myTAI: Evolutionary Transcriptomics

Description Details Value Author(s) Source References See Also

A standard DivergenceExpressionSet is a data.frame consisting of a standardized sequence of columns to store the age information for each gene and its corresponding gene expression profile.

The standard is defined as follows:

Divergencestratum | GeneID | Expression-level 1 | ... | Expression-level N

This example DivergenceExpressionSet dataset covers 7 developmental stages of Arabidopsis thaliana embryo development. The initial gene expression dataset was published by Xiang et al., 2011 (see references section) and was then used by Quint et al., 2012 (see references section) to assign sequence divergence values (divergence strata) to each gene expression profile.

a standard DivergenceExpressionSet object.

Hajk-Georg Drost

http://www.plantphysiol.org/content/156/1/346/suppl/DC1

Quint M et al. 2012. "A transcriptomic hourglass in plant embryogenesis". Nature (490): 98-101. Supplementary Table 2 : http://www.nature.com/nature/journal/v490/n7418/full/nature11394.html

Xiang D et al. 2011. "Genome-Wide Analysis Reveals Gene Expression and Metabolic Network Dynamics during Embryo Development in Arabidopsis". Plant Physiology (156): 346-356. Supplemental Table 1 : http://www.plantphysiol.org/content/156/1/346/suppl/DC1

PhyloExpressionSetExample

YTLogos/myTAI documentation built on May 19, 2019, 1:46 a.m.