Table 2.
Functional categories (biological process) enriched in genes modulated in MDA MB231 cells co-cultured with fibroblasts from uninvolved lymph nodes [MDA.FN(-)] (A) or involved nodes [MDA.FN(+)] (B)
| (A) | |||
| Biological Process | Genes over-expressed in MDA.FN (-) | Genes under-expressed in MDA.FN (-) | R |
| Humoral immune response | IL6 | RFXANK | 4 |
| Respiratory gaseous exchange | COX5B, HNMT | 4 | |
| Regulation of transcription from RNA polymerase II promoter | TFDP1 | LITAF, SOD2, TEF | 40 |
| SMARCD3, CITED2 | |||
| Brain development | CDK5RAP2, GPR56 | 7 | |
| Positive regulation of I-kappaB kinase/NF-kappaB cascade | SLC20A1 | LITAF, TRADD, RHOC | 28 |
| Positive regulation of cell proliferation | TGFB2, IL6 CUL3 | STIM1 | 29 |
| Generation of precursor metabolites and energy | EHHADH | WFS1 | 11 |
| JNK cascade | DUSP10 | PAK1 | 11 |
| Response to stress | DUSP10, PRKRIR | SNN | 22 |
| Cell cycle | SH3BP4, CTCF, E2F3 | RIF1, SUFU, STIM1 | 127 |
| TFDP1, CUL3 | PARD6A | ||
| Lipid metabolism | SOAT1, HMGCS1, ACSL3 | 51 | |
| Nuclear mRNA splicing, via spliceosome | SF3B4, LSM3, SFRS3 | 32 | |
| Regulation of progression through cell cycle | E2F3, TFDP1, UBE2V2 | PSMD8 | 71 |
| RBBP6 | |||
| Sensory perception of sound | PTPN11 | WFS1 | 22 |
| (B) | |||
| Biological process | Genes over-expressed in MDA.FN (+) | Genes under-expressed in MDA/FN (+) | R |
| Nuclear mRNA splicing, via spliceosome | SF3B4, LSM3, HNRPH3 | 32 | |
| TARDBP, SFRS6, SFRS3 | |||
| SFRS2 | |||
| Regulation of transcription, DNA-dependent | SOX17, TARDBP | ZNF19, IRF7 | 375 |
| Antigen processing, endogenous antigen via MHC class I | TRPC4AP, HLA-F | 4 | |
| Response to stress | DUSP10 | AHSA1, SNN, PTK2B | 22 |
| Brain development | CDK5RAP2, GPR56 | 7 | |
| Response to DNA damage stimulus | RIF1, IRF7 | 7 | |
| Protein targeting | TLOC1 | KATNB1 | 8 |
| Excretion | TACR2, NEDD4L | 9 | |
| RNA splicing | SF3B4, HNRPH3, SFRS2 | 21 | |
| Transcription | SOX17, TARDBP | TEF, ZNF19, SMARCD3 | 315 |
| IRF7 | |||
| Protein ubiquitination | NEDD4L | VCP | 12 |
| Regulation of GTPase activity | GDI2 | CENTG3 | 13 |
Reference (R) stands for the number of genes involved in that specific function that were represented on the cDNA microarray platform (http://vortex.cs.wayne.edu:8080/index.jsp; corrected p value < 0.05). Genes found differentially expressed in MDA.FN co-cultured cells as compared with MDA mono-cultured cells are shown