Table 2. Gene connections gained by STAT5a from (a) normal prostate to low grade tumor and (b) in low grade to high grade progression.
The p-values shown are from using single gene analysis and the Student’s t-test, with significant p-values (< 0.05) marked in red. Note again that single gene analysis is unable to identify all these associations (some of the p-values are not good). However, the co-regulation analysis and transcription factor filter used in our method readily identified all these links. The functional pathways associated with these genes are shown in Supplementary Table 2.
| Table 2a | |||
|---|---|---|---|
| Gene name | Normal vs. low grade tumor | Normal vs. high grade tumor | Low vs. high grade tumor |
| Student’s t-test p-value | |||
| AKT1 v-akt murine thymoma viral oncogene homolog 1 |
0.001 | 0.001 | 0.770 |
| RAP1GAP RAP1 GTPase activating protein |
0.001 | 0.000 | 0.251 |
| APBA2BP N-terminal EF-hand calcium binding protein 3 |
0.001 | 0.001 | 0.626 |
| ARID1A AT rich interactive domain 1A (SWI-like) |
0.001 | 0.001 | 0.047 |
| CACNA2D2 calcium channel, voltage-dependent, alpha 2/delta subunit 2 |
0.002 | 0.022 | 0.143 |
| ATG4B ATG4 autophagy related 4 homolog B (S. cerevisiae) |
0.002 | 0.001 | 0.638 |
| SPINT1 serine peptidase inhibitor, Kunitz type 1 |
0.002 | 0.001 | 0.465 |
| GMPPA GDP-mannose pyrophosphorylase A |
0.003 | 0.009 | 0.169 |
| CAMK2B calcium/calmodulin-dependent protein kinase II beta |
0.003 | 0.000 | 0.999 |
| AMZ2 archaelysin family metallopeptidase 2 |
0.003 | 0.002 | 0.516 |
| TTLL12 tubulin tyrosine ligase-like family, member 12 |
0.004 | 0.000 | 0.195 |
| MSH5 mutS homolog 5 (E. coli) |
0.005 | 0.001 | 0.169 |
| FGFR2 fibroblast growth factor receptor 2 |
0.008 | 0.114 | 0.161 |
| REPIN1 replication initiator 1 |
0.013 | 0.002 | 0.047 |
| LSS lanosterol synthase (2,3-oxidosqualene-lanosterol cyclase) |
0.014 | 0.159 | 0.023 |
| TSPAN4 tetraspanin 4 |
0.016 | 0.038 | 0.266 |
| KLF10 Kruppel-like factor 10 |
0.020 | 0.011 | 0.371 |
| PYCR1 sirtuin (silent mating type information regulation 2 homolog) 7 (S. cerevisiae) |
0.023 | 0.005 | 0.586 |
| CTSH cathepsin H |
0.039 | 0.007 | 0.526 |
| MGLL monoglyceride lipase |
0.050 | 0.208 | 0.112 |
| CENTG2 ArfGAP with GTPase domain, ankyrin repeat and PH domain 1 |
0.051 | 0.007 | 0.175 |
| TEAD3 TEA domain family member 3 |
0.052 | 0.135 | 0.148 |
| IGF1R insulin-like growth factor 1 receptor |
0.053 | 0.050 | 0.823 |
| MYL9 myosin, light chain 9, regulatory |
0.065 | 0.542 | 0.075 |
| GABRE gamma-aminobutyric acid (GABA) A receptor, epsilon |
0.073 | 0.061 | 0.918 |
| SIM2 single-minded homolog 2 (Drosophila) |
0.083 | 0.001 | 0.186 |
| NRP1 neuropilin 1 |
0.096 | 0.189 | 0.656 |
| PAQR4 progestin and adipoQ receptor family member IV |
0.211 | 0.944 | 0.052 |
| PER2 period homolog 2 (Drosophila) |
0.250 | 0.532 | 0.525 |
| ECGF1 sphingosine-1-phosphate receptor 1 |
0.272 | 0.086 | 0.710 |
| FZD10 frizzled homolog 10 (Drosophila) |
0.310 | 0.049 | 0.404 |
| LMNA lamin A/C |
0.406 | 0.085 | 0.427 |
| PAOX polyamine oxidase (exo-N4-amino) |
0.422 | 0.470 | 0.858 |
| RASSF7 Ras association (RalGDS/AF-6) domain family (N-terminal) member 7 |
0.439 | 0.031 | 0.065 |
| SECTM1secreted and transmembrane 1 | 0.513 | 0.030 | 0.068 |
| DUSP8 dual specificity phosphatase 8 |
0.666 | 0.542 | 0.966 |
| FOSL2 FOS-like antigen 2 |
0.776 | 0.809 | 0.605 |
| CRYBA2 crystallin, beta A2 |
0.787 | 0.934 | 0.663 |
| Table 2b | |||
|---|---|---|---|
| Gene name | Normal vs. low grade tumor | Normal vs. high grade tumor | Low vs. high grade tumor |
| Student’s t-test p-value | |||
| EFS embryonal Fyn-associated substrate |
0.009 | 0.147 | 0.000 |
| NBL1 neuroblastoma, suppression of tumorigenicity 1 |
0.026 | 0.179 | 0.000 |
| GPC1 glypican 1 |
0.028 | 0.868 | 0.003 |
| SCRIB scribbled homolog (Drosophila) | 0.035 | 0.007 | 0.005 |
| EML3 echinoderm microtubule associated protein like 3 |
0.001 | 0.000 | 0.025 |
| IRAK1 interleukin-1 receptor-associated kinase 1 |
0.392 | 0.049 | 0.100 |
| SS18L1 synovial sarcoma translocation gene on chromosome 18-like 1 |
0.010 | 0.003 | 0.130 |
| DLK2 delta-like 2 homolog (Drosophila) |
0.840 | 0.179 | 0.171 |
| BCOR BCL6 co-repressor |
0.089 | 0.018 | 0.209 |
| C20orf149 pancreatic progenitor cell differentiation and proliferation factor homolog (zebrafish) |
0.074 | 0.173 | 0.223 |
| IGF2 insulin-like growth factor 2 (somatomedin A); insulin; INS-IGF2 readthrough transcript |
0.076 | 0.317 | 0.247 |
| CACNA1H calcium channel, voltage-dependent, T type, alpha 1H subunit |
0.037 | 0.172 | 0.249 |
| IRX5 iroquois homeobox 5 |
0.076 | 0.220 | 0.300 |
| MDK Mesomelic dysplasia, Kantaputra type |
0.128 | 0.216 | 0.465 |
| SALL1 sal-like 1 (Drosophila) |
0.697 | 0.623 | 0.511 |
| FGFR3 fibroblast growth factor receptor 3 |
0.047 | 0.103 | 0.548 |
| INHBB inhibin, beta B |
0.938 | 0.588 | 0.585 |
| BCL11A B-cell CLL/lymphoma 11A (zinc finger protein) |
0.791 | 0.618 | 0.796 |
| GATA3 GATA binding protein 3 |
0.617 | 0.468 | 0.801 |
| MFAP2 microfibrillar-associated protein 2 |
0.007 | 0.002 | 0.909 |
| SH3BP4 SH3-domain binding protein 4 |
0.167 | 0.165 | 0.989 |