PhyloExpressionSetExample: An Example PhyloExpressionSet Data Set

In myTAI: Evolutionary Transcriptomics

Description

A standard PhyloExpressionSet 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:

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

Details

This 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 evolutionary ages to each gene expression profile.

Value

a standard PhyloExpressionSet object.

Author(s)

Hajk-Georg Drost

Source

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

References

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

See Also

DivergenceExpressionSetExample

myTAI documentation built on Feb. 24, 2021, 9:06 a.m.