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Stimulation of mature B lymphocytes by extracellular ligands induces phenotypic changes through complex signal transduction pathways . Gene expression is altered as a result of these changes and re -programs the cell to undergo differentiation , activation , effecter function , anergy , and /or apoptosis . Gene expression microarrays are used to determine expression levels of a large number (tens of thousands ) of genes simultaneously , resulting in a gene expression profile of the experimental sample . Microarray data must be appended with biological information in order to be interesting , and this field of microarray bioinformatics is rapidly expanding . These studies prompted the development of a bioinformatics tool termed CLASSIFI (Cluster Assignment for Biological Inference ) , which identifies statistically significant co -clustering of genes with similar Gene Ontology annotation within microarray gene clusters . CLASSIFI was used to analyze microarray results from two B cell projects from the Alliance for Cellular Signaling (AfCS ) : 1 ) the BAFF /CD40L project , which evaluates the effects of BAFF and CD40L on primary mouse B cells in long -term cultures , and 2 ) the B cell single ligand screen project , which evaluates the effects of 32 single ligands on primary mouse B cells in short -term cultures . CLASSIFI was able to identify significant overrepresentation of related genes within gene clusters for both of these data sets and facilitates hypothesis generation as to the biological process affected by a specific ligand . As CLASSIFI is strictly a statistical tool that aids in hypothesis generation , experimental validation of hypotheses was performed . The B cell single ligand screen microarray and CLASSIFI analysis followed by experimental validation revealed a biological process specific to B cell antigen receptor stimulation but not LPS or CD40L stimulation - antigen processing and presentation - and provides the groundwork for new discoveries in this field . As a result , several putative components were identified that are not currently known to play a role in antigen processing and presentation in B cells . |
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