Sample overview of A-498
| Sample ID: | Sample_02_268 |
| Biosample type: | Cell line |
| Tissue type: | Kidney |
| Biosample name: | A-498 |
| Data source: | NCBI GEO/SRA |
| GSE ID: | GSE86087 |
| Cancer type: | clear cell renal cell carcinoma |
| CRC number: | 5417 |
| TF number of all CRCs: | 56 |
| TF list of all CRCs: | TCF7L2, RARA, SMAD3, POU3F3, SP3, MAFK, RUNX1, JUNB, ETS1, NFE2L2, HOXA9, GLIS3, HOXA3, SREBF1, NR2F2, NR3C1, KLF4, SP1, RUNX2, TGIF1, TEAD1, RFX2, MYC, PBX1, HOXA10, KLF7, RARB, FOSL2, MEF2D, ETV6, BHLHE40, NR4A2, FOSL1, ELF3, HOXA11, MSC, CREB3, NFIB, RXRA, HES1, CREB3L2, LHX1, BHLHE41, MNT, NR6A1, FOXP1, HOXB4, ETS2, SOX9, CREB5, ZNF217, NFE2L1, HOXB2, BARX2, HOXA7, ZNF628 |
The most representative CRC of A-498
Relationship plot of CRC model
TF number of this CRC: 19
CRC socre: 3258.474
CRC socre: 3258.474
TF list of the most representative CRC
| TF name | TF family | Frequency of TFs |
|---|---|---|
| ETS1 | ETS | 3236 / 5417 |
| HOXA3 | Homeobox | 2738 / 5417 |
| HOXA9 | Homeobox | 2970 / 5417 |
| JUNB | TF_bZIP | 3372 / 5417 |
| KLF4 | zf-C2H2 | 2549 / 5417 |
| KLF7 | zf-C2H2 | 1780 / 5417 |
| MAFK | TF_bZIP | 3905 / 5417 |
| NFE2L2 | TF_bZIP | 3173 / 5417 |
| NR2F2 | RXR-like | 2601 / 5417 |
| NR3C1 | ESR-like | 2573 / 5417 |
| POU3F3 | Pou | 4204 / 5417 |
| RARA | THR-like | 4924 / 5417 |
| RARB | THR-like | 1686 / 5417 |
| RUNX1 | Runt | 3531 / 5417 |
| SMAD3 | MH1 | 4432 / 5417 |
| SP3 | zf-C2H2 | 4131 / 5417 |
| SREBF1 | bHLH | 2699 / 5417 |
| TCF7L2 | HMG | 5127 / 5417 |
| TGIF1 | Homeobox | 2280 / 5417 |
The most representative CRC
Figure legends:
The most representative CRC is generally considered to be the top one ranked CRC.
What is important information?
The TFs of the most representative CRC is outstanding important.
All CRCs of A-498
| CRC rank | TF list of CRCs | CRC score | TF number of CRC | Detail of CRC |
|---|
All CRCs
Figure legends:
All CRCs obtained using the CRC identification software coltron.
What is important information?
According to the scores, the CRCs can be sorted to get the interested CRCs to the users.
Frequency of TFs that appear in CRCs
| TF name | Frequency of TFs | TF family | Ensembl ID |
|---|---|---|---|
| TCF7L2 | 5127 / 5417 | HMG | ENSG00000148737 |
| RARA | 4924 / 5417 | THR-like | ENSG00000131759 |
| SMAD3 | 4432 / 5417 | MH1 | ENSG00000166949 |
| POU3F3 | 4204 / 5417 | Pou | ENSG00000198914 |
| SP3 | 4131 / 5417 | zf-C2H2 | ENSG00000172845 |
| MAFK | 3905 / 5417 | TF_bZIP | ENSG00000198517 |
| RUNX1 | 3531 / 5417 | Runt | ENSG00000159216 |
| JUNB | 3372 / 5417 | TF_bZIP | ENSG00000171223 |
| ETS1 | 3236 / 5417 | ETS | ENSG00000134954 |
| NFE2L2 | 3173 / 5417 | TF_bZIP | ENSG00000116044 |
| HOXA9 | 2970 / 5417 | Homeobox | ENSG00000078399 |
| GLIS3 | 2864 / 5417 | zf-C2H2 | ENSG00000107249 |
| HOXA3 | 2738 / 5417 | Homeobox | ENSG00000105997 |
| SREBF1 | 2699 / 5417 | bHLH | ENSG00000072310 |
| NR2F2 | 2601 / 5417 | RXR-like | ENSG00000185551 |
| NR3C1 | 2573 / 5417 | ESR-like | ENSG00000113580 |
| KLF4 | 2549 / 5417 | zf-C2H2 | ENSG00000136826 |
| SP1 | 2369 / 5417 | zf-C2H2 | ENSG00000185591 |
| RUNX2 | 2367 / 5417 | Runt | ENSG00000124813 |
| TGIF1 | 2280 / 5417 | Homeobox | ENSG00000177426 |
| TEAD1 | 2215 / 5417 | TEA | ENSG00000187079 |
| RFX2 | 2151 / 5417 | RFX | ENSG00000087903 |
| MYC | 1965 / 5417 | bHLH | ENSG00000136997 |
| PBX1 | 1820 / 5417 | Homeobox | ENSG00000185630 |
| HOXA10 | 1790 / 5417 | Homeobox | ENSG00000253293 |
| KLF7 | 1780 / 5417 | zf-C2H2 | ENSG00000118263 |
| RARB | 1686 / 5417 | THR-like | ENSG00000077092 |
| FOSL2 | 1532 / 5417 | TF_bZIP | ENSG00000075426 |
| MEF2D | 1460 / 5417 | SRF | ENSG00000116604 |
| ETV6 | 1353 / 5417 | ETS | ENSG00000139083 |
| BHLHE40 | 1313 / 5417 | bHLH | ENSG00000134107 |
| NR4A2 | 1229 / 5417 | NGFIB-like | ENSG00000153234 |
| FOSL1 | 1143 / 5417 | TF_bZIP | ENSG00000175592 |
| ELF3 | 985 / 5417 | ETS | ENSG00000163435 |
| HOXA11 | 947 / 5417 | Homeobox | ENSG00000005073 |
| MSC | 734 / 5417 | bHLH | ENSG00000178860 |
| CREB3 | 495 / 5417 | TF_bZIP | ENSG00000107175 |
| NFIB | 393 / 5417 | CTF/NFI | ENSG00000147862 |
| RXRA | 370 / 5417 | RXR-like | ENSG00000186350 |
| HES1 | 334 / 5417 | bHLH | ENSG00000114315 |
| CREB3L2 | 331 / 5417 | TF_bZIP | ENSG00000182158 |
| LHX1 | 329 / 5417 | Homeobox | ENSG00000273706 |
| BHLHE41 | 269 / 5417 | bHLH | ENSG00000123095 |
| MNT | 258 / 5417 | bHLH | ENSG00000070444 |
| NR6A1 | 217 / 5417 | GCNF-like | ENSG00000148200 |
| FOXP1 | 169 / 5417 | Fork_head | ENSG00000114861 |
| HOXB4 | 158 / 5417 | Homeobox | ENSG00000182742 |
| ETS2 | 152 / 5417 | ETS | ENSG00000157557 |
| SOX9 | 133 / 5417 | HMG | ENSG00000125398 |
| CREB5 | 112 / 5417 | TF_bZIP | ENSG00000146592 |
| ZNF217 | 109 / 5417 | zf-C2H2 | ENSG00000171940 |
| NFE2L1 | 103 / 5417 | TF_bZIP | ENSG00000082641 |
| HOXB2 | 78 / 5417 | Homeobox | ENSG00000173917 |
| BARX2 | 61 / 5417 | Homeobox | ENSG00000043039 |
| HOXA7 | 46 / 5417 | Homeobox | ENSG00000122592 |
| ZNF628 | 32 / 5417 | zf-C2H2 | ENSG00000197483 |
Frequency of TFs that appear in CRCs
Figure legend:
Frequency of TFs that appear in CRCs: The greater the number of CRCs, the higher the frequency at which the TF is represented in all CRCs. Therefore, this TF may be more important under this sample.
What is important information?
The higher the frequency of TF, the more important TF is under the sample.
Indegree and outdegree of TFs
| TF name | Indegree | Outdegree | Node connections |
|---|---|---|---|
| MAFK | 56 | 91 | 147 |
| RARA | 58 | 90 | 148 |
| LHX1 | 47 | 63 | 110 |
| RARB | 51 | 88 | 139 |
| BHLHE40 | 57 | 71 | 128 |
| NFE2L2 | 58 | 90 | 148 |
| NFE2L1 | 48 | 61 | 109 |
| MYC | 55 | 78 | 133 |
| ETS2 | 57 | 50 | 107 |
| SP1 | 54 | 90 | 144 |
| CREB5 | 54 | 53 | 107 |
| SP3 | 57 | 86 | 143 |
| CREB3 | 50 | 62 | 112 |
| RUNX2 | 52 | 87 | 139 |
| ZNF217 | 57 | 54 | 111 |
| FOXP1 | 36 | 90 | 126 |
| GLIS3 | 58 | 80 | 138 |
| RFX2 | 56 | 80 | 136 |
| ETS1 | 57 | 88 | 145 |
| MNT | 55 | 48 | 103 |
| RUNX1 | 58 | 90 | 148 |
| HOXB2 | 57 | 48 | 105 |
| HOXB4 | 52 | 56 | 108 |
| ETV6 | 56 | 82 | 138 |
| BHLHE41 | 55 | 58 | 113 |
| HES1 | 54 | 65 | 119 |
| SMAD3 | 61 | 88 | 149 |
| NR2F2 | 60 | 76 | 136 |
| ZNF628 | 32 | 62 | 94 |
| NR6A1 | 38 | 79 | 117 |
| HOXA11 | 51 | 77 | 128 |
| HOXA10 | 56 | 85 | 141 |
| FOSL1 | 45 | 86 | 131 |
| FOSL2 | 62 | 79 | 141 |
| RXRA | 48 | 88 | 136 |
| BARX2 | 52 | 55 | 107 |
| HOXA7 | 37 | 72 | 109 |
| SREBF1 | 56 | 82 | 138 |
| HOXA3 | 56 | 79 | 135 |
| HOXA9 | 48 | 89 | 137 |
| JUNB | 54 | 84 | 138 |
| TCF7L2 | 59 | 89 | 148 |
| SOX9 | 37 | 90 | 127 |
| TEAD1 | 55 | 85 | 140 |
| MSC | 55 | 69 | 124 |
| ELF3 | 42 | 89 | 131 |
| KLF7 | 45 | 83 | 128 |
| KLF4 | 52 | 87 | 139 |
| POU3F3 | 61 | 88 | 149 |
| NR3C1 | 53 | 89 | 142 |
| NR4A2 | 50 | 88 | 138 |
| MEF2D | 47 | 79 | 126 |
| PBX1 | 58 | 77 | 135 |
| NFIB | 58 | 67 | 125 |
| CREB3L2 | 60 | 63 | 123 |
| TGIF1 | 57 | 78 | 135 |
Indegree and outdegree of TFs
Figure legend:
In-degrees are assessed by motif analysis within regions of the enhancer. out-degrees are assessed for each TF associated with super-enhancer by
determining all other bound enhancers at TF gene loci; Node connections between TFs are used to discern auto-regulatory cliques that in turn regulate a broader
enhancer network.
What is important information?
TF with high indegree and outdegree values is considered to be an important TF.