Table 2. Over-represented transcriptional modules in the promoter of the stress-responsive genes in the muscles of cows.
The transcriptional modules were searched with the module inspector function of Genomatix, their occurrence was examined in the promoters of genes of the experimental datasets and the number of target genes was determined in each dataset.
| Muscle | Module | p value | Occurrence of module |
Number of target genes | Gene ID |
|---|---|---|---|---|---|
| LT | ETSF_ETSF_01 | 0.076 | 16 | 15 | IL16 SERPINE1 HES1 HSPBAP1 CDIPT XYLT2 TUBB3 THBS1 MED23 GPAM PIGM CEBPD HEYL HES6 MYOD1 |
| SP1F_CAAT_02 | 0.040 | 10 | 9 | NME6 SDC4 PDPR HES6 PFKFB3 CDIPT PMP22 THBS1 IFRD1 | |
| CAAT_AP1F_01 | 0.035 | 8 | 8 | SLC25A25 SERPINE1 NME6 IMP3 HSPBAP1 SLC2A3 THBS1 ATF3 | |
| SP1F_EBOX_SP1F_01 | 0.024 | 8 | 7 | DFFB GLUL PDK4 IMP3 PMP22 XYLT2 CEBPD | |
| CAAT_SP1F_01 | 0.088 | 5 | 5 | SERPINE1 ATP1B1 GLUL GEM HES6 | |
| GATA_GATA_GATA_01 | 0.037 | 5 | 3 | NME6 SLC16A6 MED23 | |
| YY1F_SRFF_02 | 0.016 | 3 | 3 | SLC2A3 ATF3 FOS | |
| SORY_SORY_EGRF_01 | 0.061 | 3 | 3 | MUSK ATP1B1 RAB3IL1 | |
| NFKB_NFKB_01 | 0.064 | 3 | 3 | SLC25A25 GLUL GEM | |
| HNF1_GATA_01 | 0.098 | 3 | 3 | MED23 PLD1 ATP1B1 | |
| KLFS_NR2F_KLFS_01 | 0.024 | 3 | 2 | SERPINE1 TUBB3 | |
| STAF_SP1F_01 | 0.026 | 2 | 2 | GLUL HEYL | |
| RXRF_EBOX_01 | 0.043 | 2 | 2 | PDPR RAB3IL1 | |
| AP1F_SMAD_01 | 0.055 | 2 | 2 | IL16 THBS1 | |
| ETSF_AP1F_04 | 0.067 | 2 | 2 | ACOT11 HSPBAP1 | |
| CEBP_MYBL_03 | 0.076 | 2 | 2 | ACOT11 HSPBAP1 | |
| AARF_CEBP_01 | 0.091 | 2 | 2 | ABRA NME6 | |
| BRNF_RXRF_02 | 0.066 | 4 | 1 | DLL4 | |
| NFKB_ETSF_01 | 0.007 | 2 | 1 | DLL4 | |
| SRFF_AP1F_01 | 0.047 | 1 | 1 | FOS | |
| ETSF_SP1F_SMAD_01 | 0.062 | 1 | 1 | HEYL | |
| YY1F_SRFF_01 | 0.076 | 1 | 1 | FOS | |
| PAX8_NKXH_01 | 0.076 | 1 | 1 | PMP22 | |
| ETSF_SRFF_01 | 0.091 | 1 | 1 | FOS | |
| ST | SP1F_SP1F_06 | 0.002 | 30 | 14 | PGF GADD45A SLC16A6 ADAMTS9 CYP1A1 SLC2A8 SDC4 PMP22 TUBB3 IFRD1 HYAL2 ATF3 HES6 HEYL |
| NFKB_SP1F_03 | 0.002 | 12 | 8 | SLC2A8 SDC4 MYLK4 PGF LRP4 PMP22 HEYL CEBPD | |
| SP1F_ETSF_04 | 0.087 | 8 | 8 | ABRA SDC4 PGF LCAT PMP22 CYP1A1 SMAD7 HES6 | |
| SMAD_E2FF_01 | 0.088 | 12 | 7 | SLC2A8 SDC4 IFRD1 PDK4 CEBPD HES6 FOS | |
| SP1F_YY1F_01 | 0.044 | 10 | 7 | PGF ABRA GEM SDC4 SLC2A8 ATF3 HES6 | |
| SP1F_CAAT_02 | 0.039 | 6 | 5 | SDC4 PFKFB3 IFRD1 PMP22 HES6 | |
| SP1F_EBOX_SP1F_01 | 0.085 | 4 | 4 | MYLK4 PMP22 PDK4 CEBPD | |
| RUSH_EGRF_01 | 0.049 | 3 | 3 | SDC4 GADD45A SPOCK2 | |
| IRFF_NFAT_01 | 0.084 | 3 | 3 | MYLK4 ADAMTS9 IFRD1 | |
| GATA_GATA_GATA_01 | 0.013 | 4 | 2 | SLC16A6 ADAMTS9 | |
| MYOD_MYOD_03 | 0.066 | 3 | 2 | SPOCK2 HES6 | |
| AP1F_ETSF_04 | 0.013 | 2 | 2 | IFRD1 HYAL2 | |
| YY1F_SRFF_02 | 0.028 | 2 | 2 | ATF3 FOS | |
| ZFHX_ZFHX_NKXH_01 | 0.037 | 2 | 2 | GADD45A ADAMTS9 | |
| SMAD_HIFF_01 | 0.032 | 2 | 1 | PFKFB3 | |
| SP1F_MZF1_01 | 0.035 | 2 | 1 | PMP22 | |
| ETSF_SP1F_SMAD_01 | 0.016 | 1 | 1 | HEYL | |
| SRFF_AP1F_01 | 0.024 | 1 | 1 | FOS | |
| YY1F_SRFF_01 | 0.039 | 1 | 1 | FOS | |
| PAX8_NKXH_01 | 0.039 | 1 | 1 | PMP22 | |
| ETSF_SRFF_01 | 0.047 | 1 | 1 | FOS | |
| MEF2_MYOD_01 | 0.054 | 1 | 1 | SLC16A6 | |
| KLFS_CREB_KLFS_01 | 0.070 | 1 | 1 | SLC2A8 | |
| CAAT_SREB_01 | 0.077 | 1 | 1 | IFRD1 | |
| GATA_HNF1_02 | 0.077 | 1 | 1 | PDK4 |
Notes:
LT: Longissimus thoracis muscle; ST: Semitendinosus muscle.
Modules in bold were in common between muscles.
TFs genes are underlined.