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Microarray analysis of CD40-mediated gene expression in Ramos cells

Microarray Platform: Affymetrix® GeneChip® Human Genome U95A array

Reference: Data available from Gene Expression Omnibus (GEO, GSE2350). GEO Summary: Data for this study is a subset of a larger study examining phenotypes representative of normal, transformed and experimentally manipulated human B cells related to the germinal center structure.

Abstract:
Gene expression in Ramos cells stimulated with anti-CD40 was compared to that in untreated cells using the Affymetrix® GeneChip® Human Genome U95A array. Using filtering criteria of a 1.5 or greater fold-change in expression, all present calls in at least one of the groups and a false discovery rate of less than 5%, 598 out of over 12,000 transcripts examined were differentially expressed. The expression of 117 transcripts was increased by anti-CD40 treatment, while 481 showed decreased expression. The Gene Ontology and KEGG pathway terms associated with these genes were examined to identify biological themes associated with each set of genes. The ontology term analysis showed that anti-CD40 treatment regulates the expression of genes involved in the immune response, transcription, cell cycle, apoptosis and cell-matrix adhesion in Ramos cells. The analysis of KEGG pathway terms identified a significant over representation of genes involved in the MAPK signaling pathway, apoptosis and cytokine-cytokine receptor interactions among the up-regulated genes and an over representation of cell cycle genes among the down-regulated genes.

Scientific analysis of the dataset:

Analysis Summary:	[ pdf ]
Step by Step tutorial:	[ pdf ]