Results The Bioconductor and IPA programs identified 356 genes that changed with a positive or negative S score of 2.5 or greater (maximum 13.54). Three hundred were Selleckchem CA4P up-regulated and 56 were down-regulated (Additional file 1). Up-regulated genes Table 2 shows 48 genes that were up-regulated with an S score of 5 or greater. These were grouped by class and ordered by the highest S score in each class. Chemokines dominate the most highly up-regulated genes with six of the ten highest S scores. Members of the TNFα-NF-κB super family were also highly up-regulated (Table 2). Other highly up-regulated genes were those involved in apoptosis and ubiquitination,

extra-cellular matrix proteins, the folate receptor, superoxide dismutase, thioredoxin reductase, Intercellular Adhesion Molecule Temsirolimus (ICAM) 1 and cytokines or their receptors (Colony Stimulating Factor [CSF]

2 and interferon-γ receptor 1). Down-regulated genes Fewer genes were down-regulated than those that were up-regulated and negative S scores were less pronounced than those for the up-regulated genes. For comparative purposes Table 3 shows down-regulated genes that were selected on the basis of a more permissive S score of -2.6 or less to yield a similar number (46). These genes were grouped by class and ordered by the highest negatively regulated (lowest value) S score in each class. The pattern of down-regulated gene classes differ markedly to those that were up-regulated. Most prominent were genes concerned with the maintenance of normal cell cycle, DNA see more replication and cell structure. The down-regulated group feature specific 3-mercaptopyruvate sulfurtransferase genes encoding components involved in membrane transport, mitosis, nucleotide synthesis, transcription, protein synthesis and export, membrane transport and energy metabolism. Table 3 Down-regulated genes Functional classes of genes shown are ordered by the S score of the most highly regulated examples in the class with S score ≤ -2.6. Function Symbol Name S Score Cell cycle, DNA replication and Mitosis ID1 Inhibitor Of DNA Binding 1 -4.416

  ID3 Inhibitor Of DNA Binding 3 -4.304   ID2 Inhibitor Of DNA Binding 2 -4.054   LHX3 LIM Homeobox 3 -3.181   KLF1 Kruppel-Like Factor 1 -2.97   FOXF2 Forkhead Box F2 -2.684   SFN Stratifin -4.086   FGFBP1 Fibroblast Growth Factor Binding Protein 1 -3.922   SKP2 S-Phase Kinase-Associated Protein 2 (P45) -3.035   RPA3 Replication Protein A3 -2.975   RFC4 Replication Factor C 4 -2.845   SPBC25 Spindle Pole Body Component 25 Homolog -2.688 Structural REG1A Regenerating Islet-Derived 1 Alpha -4.213   CX36 Connexin-36 -3.79   COL4A5 Collagen, Type IV, Alpha 5 -3.69   ODF1 Outer Dense Fiber Of Sperm Tails 1 -3.511   CD248 CD248 Molecule, Endosialin -2.965 Membrane transport SLC2A1 Solute Carrier Family 2, Member 1 -3.912   CRIP1 Cysteine-Rich Protein 1 (Intestinal) -3.079   SCNN1A Sodium Channel, Nonvoltage-Gated 1 Alpha -2.