Gene Enrichment and Pathway Analysis

MAPPFinder [59 (link)] was used to enrich, rank and classify the differentially expressed genes based on Gene Ontology (GO) [60 ] information of each gene. To visualize the differential expression pattern, before Z value ranking, all gene ontology terms were further filtered manually with the criteria: the number of changed genes: >2; the number of measured genes: >10; the percent of changed genes: >5%; the percent of gene presented on the chip: >20%. If the annotation for interested genes were missed in the gene database of GenMapp, they were examined in Affymetrix NetAffya analysis center [61 ]. The map for heat shock protein (Hsp) was built by MAPPBuilder [59 (link)] based on the information from GO and the Flybase[62 ]. The map for Drosophila immune response pathway was built by GeneMAPP based on the previous reports [63 (link),64 (link)].