Furthermore, this network presents evi dence to the co existence of an up regulation of genes concerned in peptide processing in addition to a down regulation of genes involved in antigen presentation to your cell surface. Right after PMA ionomycin stimulation, 37 KEGG pathways which has a Fisher Precise P Value 0. 05 were recognized. Probably the most represented pathways are cytokine cytokine receptor interaction, oxidative phosphorylation, ribosome, cell adhesion molecules. Jak STAT signaling path way, natural killer cell mediated cytotoxicity and cell cycle. The Toll like receptor signaling pathway occupies the eighth place with 40 genes. Interactions among pathways with their relative importance are presented in Figure 5B.
Globally, PMA ionomycin stimulation mostly modifies pathways linked with all the immune system, signaling molecules and interactions, human ailments dig this and metabolic process like LPS stimulation but it also influences addi tional pathways associated to metabolic process, cell development and death and signal transduction. Expression of probes mapping towards the SLA complex Since sense and antisense probes for all SLA annotated transcripts have been present around the DNA chip. it had been possible to execute an in depth evaluation on the expression profile of all annotated transcripts mapping to your locus. For probes focusing on protein coding genes, only the differential expression was studied. For antisense and non coding transcripts, expression and differential expression between stimulation and mock stimulation had been each analyzed. Every one of the differentially expressed genes belonging to your MHC antigenic processing and presentation pathway are listed in Table six.
Right after LPS stimulation, every one of the genes asso ciated with the MHC class II mediated peptide presenta tion pathway are down regulated. The down regulated genes contain genes concerned in peptide processing from the late endosome. peptide loading and peptide presentation for the CD4 recommended reading T cells. After PMA ionomycin stimulation, a comparable down regulation of MHC class II mediated peptide presentation pathway is observed. In contrast, for your MHC class I mediated peptide presentation pathway, all genes involved in pep tide processing and transport are up regulated whereas probes targeting the classical class I genes SLA 3, the non classical class I genes SLA six and SLA 7 at the same time as pseudogenes SLA four and SLA eleven are down regulated. To be able to analyze anti sense oligonucleotide and non coding RNA probe expression, the A value was employed.