Year of Publication

2007

Document Type

Thesis

College

Arts and Sciences

Department

Biology

First Advisor

Jim Lund

Abstract

Forty-six genomic gene expression studies of free living soil nematode C. eleganshave been published. To facilitate exploratory analysis of those studies, we constructed adatabase containing all the published C. elegans expression datasets. A Perl CGIprogram, called Microarray Analysis Display (MAdisplay), allows gene expressionclustergrams of any combination of entered genes and datasets to be viewed(http://elegans.uky.edu/gl/madisplay). Perl programs were used to preprocess the rawdata from different sources into a common format and to transform the data to displaythe expression changes relative to each experiment's controls. Three hundred lists ofgenes from figures and tables were extracted from the publications and made available inthe GeneLists database, which also contains Gene Ontology and KEGG gene lists. Weused these tools to examine in a systematic fashion the mean expression of gene lists inthe set of microarray and SAGE experiments. Seventy-nine percent of publicationderived gene lists show a strong expression change (p-value andlt;0.001) in more than oneexperiment with the median being fourteen out of the 127 experiments that are derivedfrom the forty-six publications. This indicates that groups of genes identified in onepublication typically show an expression effect in many other experiments.

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