Transcriptomics,Genomics

Dataset Information

40

Identification of gene expression logical invariants in Arabidopsis


ABSTRACT: Numerous gene expression datasets from diverse tissue samples from the plant variety Arabidopsis thaliana have been already deposited in the public domain. There have been several attempts to do large scale meta-analyses of all of these datasets. Most of these analyses summarize pairwise gene expression relationships using correlation, or identify differentially expressed genes in two conditions. We propose here a new large scale meta-analysis of all of the publicly available Arabidopsis datasets to identify Boolean logical relationships between genes. Boolean logic is a branch of mathematics that deals with two possible values. In the context of gene expression datasets we use qualitative high and low expression values. A strong logical relationship between genes emerges if at least one of the quadrants is sparsely populated. We put together a web resource where gene expression relationships can be explored online which helps visualize the logical relationships between genes. We believe that this website will be useful in identifying important genes in different biological context. The web link is http://hegemon.ucsd.edu/plant/. Overall design: 5972 published Arabidopsis microarray samples from about 300 series assayed on the GPL198 were re-analyzed. Metadata were derived from GSE69995 and RMA was used to normalize the CEL files.

SUBMITTER: Debashis Sahoo  

PROVIDER: GSE118579 | GEO | 2018-10-31

REPOSITORIES: GEO