Table 2.
Sp1 motif-regulated modules.
| Module No. | Catergory | Tissue | # of genes in the Module | GO or Pathway Enrichment for the genes within the module | Binding of Sp1 protein to the gene promoters within the module according to ENCODE data | |||||
|---|---|---|---|---|---|---|---|---|---|---|
| GO | GO/Pathway Enrichment pValue | Selected genes in the module with the enriched GO term | Genes with SP1 bound SP1 motif in promoter | Binding Enrichment Fold change | Binding Enrichmentp Value | Binding Depletion pValue | ||||
| 5 | dev | blood vessel | 81 | angiogenesis | 9.91E-15 | NOS3/KDR/FLT1 | 9 | 0.27 | 1.49E-09 | |
| 7 | dev | skin | 73 | skin development | 9.33E-12 | TGM1/KLK7/KLK5 | 8 | 0.26 | 8.15E-09 | |
| 14 | dev | muscle | 69 | muscle system process | 2.26E-36 | NOS1/TNNI3/RYR1 | 14 | 0.49 | 1.42E-04 | |
| 17 | dev | nervous | 61 | synaptic transmission | 5.19E-14 | SLC6A3/TH/GRIN1 | 11 | 0.43 | 7.38E-05 | |
| 33 | dev | nervous | 47 | nervous system development | 4.33E-17 | KCNQ2/DCC/DLL1 | 7 | 0.36 | 7.50E-05 | |
| 42 | dev | reproduction | 40 | spermatogenesis | 2.11E-10 | DDX4/DDX25/SPO11 | 10 | 0.60 | 2.16E-02 | |
| 44 | dev | cartilage | 39 | connective tissue development | 3.59E-10 | COL2A1/COL11A2/COL10A1 | 9 | 0.55 | 1.21E-02 | |
| 46 | dev | liver | 38 | plasma lipoprotein particle assembly | 1.38E-12 | APOA1/APOB/APOA4 | 14 | 0.88 | 3.34E-01 | |
| 57 | dev | extracellular matrix | 33 | extracellular matrix organization | 5.86E-14 | MMP2/COL1A1/TNC | 10 | 0.73 | 1.25E-01 | |
| 60 | dev | extracellular matrix | 32 | extracellular matrix organization | 1.52E-09 | PDGFRA/COL1A2/DCN | 7 | 0.53 | 1.57E-02 | |
| 65 | dev | 31 | tissue morphogenesis | 4.02E-09 | HGF/IGFBP5/SFRP1 | 7 | 0.54 | 2.15E-02 | ||
| 66 | dev | skeletal | 31 | anterior/posterior pattern specification | 6.63E-16 | HOXA10/HOXA1/EN1 | 3 | 0.23 | 1.04E-04 | |
| 70 | dev | nervous | 29 | glial cell differentiation | 4.67E-09 | S100B/ERBB3/RELN | 1 | 0.08 | 3.47E-06 | |
| 78 | dev | liver | 28 | very-low-density lipoprotein particle clearance | 4.40E-08 | APOE/APOC3/APOC1 | 12 | 1.03 | 5.21E-01 | |
| 85 | dev | skin | 25 | skin development | 2.98E-10 | SFN/ITGA3/KRT5 | 6 | 0.58 | 5.29E-02 | |
| 91 | dev | stem cell | 24 | stem cell maintenance | 4.05E-07 | NANOG/NODAL/LIN28A | 10 | 1.00 | 5.77E-01 | |
| 96 | dev | 24 | regionalization | 1.66E-10 | FOXC1/SIX1/TBX3 | 4 | 0.40 | 8.79E-03 | ||
| 110 | dev | 22 | hemopoiesis | 4.16E-07 | SYK/HHEX/GATA2 | 8 | 0.87 | 3.92E-01 | ||
| 111 | dev | 22 | pattern specification process | 1.38E-10 | PAX6/PBX1/NR2F2 | 5 | 0.55 | 5.30E-02 | ||
| 152 | dev | pancreate | 16 | pancreatic A cell differentiation | 8.89E-12 | NEUROD1/INSM1/NKX2-2 | 1 | 0.15 | 2.23E-03 | |
| 212 | dev | thyroid | 12 | cellular modified amino acid metabolic process | 7.22E-08 | DUOX2/AHCY/DUOX1 | 2 | 0.40 | 6.71E-02 | |
| 217 | dev | nervous | 12 | negative regulation of glial cell differentiation | 1.24E-09 | FGFR3/ID2/ID4 | 4 | 0.80 | 3.92E-01 | |
| 255 | dev | reproduction | 10 | cilium assembly | 2.02E-09 | KIF3A/IFT88/FAM161A | 6 | 1.44 | 1.95E-01 | |
| 272 | dev | kidney | 9 | metanephros morphogenesis | 2.47E-07 | SMO/LGR4/FRAS1 | 3 | 0.80 | 4.41E-01 | |
| 2 | house | 134 | cell cycle | 2.85E-69 | BRCA1/BRCA2/BIRC5 | 94 | 1.68 | 1.85E-11 | ||
| 4 | house | 100 | cellular macromolecule metabolic process | 3.44E-07 | APC/ADD1/CSNK2A1 | 57 | 1.37 | 1.35E-03 | ||
| 6 | house | 79 | RNA metabolic process | 5.65E-10 | SP1/MTDH/PDPK1 | 47 | 1.43 | 1.01E-03 | ||
| 9 | house | 72 | pyruvate metabolic process | 1.38E-12 | ENO2/ENO1/DDIT4 | 33 | 1.10 | 2.72E-01 | ||
| 15 | house | 66 | regulation of macromolecule metabolic process | 3.18E-13 | MYC/JUN/EGR1 | 34 | 1.24 | 6.70E-02 | ||
| 16 | house | 65 | response to endoplasmic reticulum stress | 3.73E-20 | HSPA5/HSP90B1/PDIA3 | 51 | 1.88 | 1.43E-09 | 4.41E-01 | |
| 23 | house | 56 | protein folding | 1.30E-22 | HSP90AA1/HSPD1/HSPA8 | 36 | 1.54 | 5.14E-04 | ||
| 26 | house | 55 | translational elongation | 2.74E-38 | RPS19/RPL11/RPL5 | 41 | 1.79 | 7.19E-07 | ||
| 31 | house | 48 | RNA processing | 2.44E-10 | EIF4E/SRSF1/HNRNPD | 32 | 1.60 | 4.00E-04 | ||
| 32 | house | 47 | lipid biosynthetic process | 4.96E-26 | SREBF1/FASN/PNPLA3 | 40 | 2.04 | 9.29E-10 | ||
| 34 | house | 47 | mRNA metabolic process | 6.22E-09 | PRMT5/PSMA6/RPS17 | 28 | 1.43 | 9.87E-03 | ||
| 36 | house | 45 | cellular response to DNA damage stimulus | 4.84E-14 | CDKN1A/MDM2/PCNA | 28 | 1.49 | 4.24E-03 | ||
| 37 | house | 44 | histone modification | 1.79E-13 | MLL/EP300/CREBBP | 27 | 1.47 | 6.48E-03 | ||
| 38 | house | 42 | cellular amino acid metabolic process | 1.64E-17 | ATF4/SLC7A5/ASS1 | 26 | 1.49 | 6.37E-03 | ||
| 43 | house | 39 | organic acid catabolic process | 1.32E-12 | MUT/HMGCL/BCKDHB | 29 | 1.79 | 3.42E-05 | ||
| 45 | house | 39 | regulation of circadian rhythm | 1.58E-08 | PER2/PER3/PER1 | 29 | 1.79 | 3.42E-05 | ||
| 48 | house | 37 | ER to Golgi vesicle-mediated transport | 1.69E-07 | CREB3L2/USO1/SEC31A | 23 | 1.49 | 9.39E-03 | ||
| 67 | house | 31 | fatty acid oxidation | 5.18E-17 | ACADM/HSD17B4/HADHA | 17 | 1.32 | 9.61E-02 | ||
| 79 | house | 28 | pentose biosynthetic process | 4.50E-12 | G6PD/TALDO1/TKT | 18 | 1.54 | 1.31E-02 | ||
| 92 | house | 24 | synapsis | 6.30E-10 | DMC1/STAG3/RNF212 | 9 | 0.90 | 4.23E-01 | ||
| 97 | house | 24 | 'de novo’ posttranslational protein folding | 5.58E-11 | TUBB3/TUBA1A/TUBB2B | 10 | 1.00 | 5.77E-01 | ||
| 105 | house | 22 | ribonucleoprotein complex biogenesis | 3.16E-10 | NOLC1/TFB2M/WDR12 | 10 | 1.09 | 4.38E-01 | ||
| 213 | house | 12 | anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process | 3.13E-07 | MAD2L2/PSMC3/UBE2S | 8 | 1.60 | 7.24E-02 | ||
| 19 | immune | 58 | platelet activation | 9.22E-11 | ITGB3/CLU/F2R | 15 | 0.62 | 9.05E-03 | ||
| 24 | immune | 55 | immune response (TNFalpha)* | 1.85E-17 | TNF/IL1B/NFKB1 | 29 | 1.27 | 6.35E-02 | ||
| 27 | immune | 54 | immune system process (Osteoclast differentiation)* | 2.36E-14 | ITGB2/CD4/FCGR3B | 17 | 0.76 | 8.20E-02 | ||
| 28 | immune | 54 | platelet activation | 3.46E-09 | ILK/RAP1A/CFL1 | 37 | 1.64 | 5.83E-05 | ||
| 62 | immune | 32 | defense response to virus (Interferon alpha/beta signaling)* | 5.24E-16 | PML/EIF2AK2/BST2 | 10 | 0.75 | 1.55E-01 | ||
| 81 | immune | 27 | antigen processing and presentation of peptide antigen via MHC class I | 1.95E-14 | HLA-B/TAP1/PSMB9 | 9 | 0.80 | 2.50E-01 | ||
| 151 | immune | 16 | positive regulation of alpha-beta T cell proliferation | 2.95E-07 | IL12B/IL23A/EBI3 | 10 | 1.50 | 7.61E-02 | ||
| 160 | immune | 16 | chemokine-mediated signaling pathway | 7.80E-08 | CCR5/CCR6/CXCR6 | 2 | 0.30 | 1.32E-02 | ||
| 30 | other | 49 | regulation of transcription, DNA-templated | 9.71E-30 | ZNF267/ZNF420/ZNF92 | 35 | 1.71 | 2.29E-05 | ||
| 73 | other | 29 | cellular lipid metabolic process | 3.70E-09 | ALOX15B/FA2H/CRAT | 7 | 0.58 | 3.91E-02 | ||
| 269 | other | 10 | negative regulation of MAP kinase activity | 1.22E-12 | SPRY2/DUSP6/SPRED1 | 2 | 0.48 | 1.42E-01 | ||
| 287 | other | 9 | JAK-STAT cascade involved in growth hormone signaling pathway | 2.12E-07 | STAT3/STAT5A/STAT5B | 4 | 1.07 | 5.59E-01 | ||
| 349 | other | 6 | regulation of transposition | 5.01E-10 | APOBEC3G/APOBEC3C/APOBEC3B | 3 | 1.20 | 4.90E-01 | ||
Note: * denotes enriched pathways.