Framework for reanalysis of publicly available Affymetrix® GeneChip® data sets based on functional regions of interest.

ABSTRACT:

Background

Since the introduction of microarrays in 1995, researchers world-wide have used both commercial and custom-designed microarrays for understanding differential expression of transcribed genes. Public databases such as ArrayExpress and the Gene Expression Omnibus (GEO) have made millions of samples readily available. One main drawback to microarray data analysis involves the selection of probes to represent a specific transcript of interest, particularly in light of the fact that transcript-specific knowledge (notably alternative splicing) is dynamic in nature.

Results

We therefore developed a framework for reannotating and reassigning probe groups for Affymetrix® GeneChip® technology based on functional regions of interest. This framework addresses three issues of

SUBMITTER: Saka E 

PROVIDER: S-EPMC5731501 | biostudies-literature | 2017 Dec

REPOSITORIES: biostudies-literature