Coexpression cluster:C2157
From FANTOM5_SSTAR
Full id: C2157_Mallassezderived_Smooth_Alveolar_Bronchial_Keratocytes_Tracheal_mesothelioma
Phase1 CAGE Peaks
| Hg19::chr11:6704513..6704578,- | p1@MRPL17 |
| Hg19::chr12:120720030..120720046,+ | p1@NME2P1 |
| Hg19::chr16:67880820..67880844,+ | p1@NUTF2 |
| Hg19::chr17:49243792..49243828,+ | p2@NME1-NME2 p2@NME2 |
Enriched pathways on this co-expression cluster<b>Summary:</b><br>Canonical pathway gene sets were compiled from Reactome, Wikipathways and KEGG. For the major signaling pathways, the transcriptionally-regulated genes (downstream targets) were obtained from Netpath. Combined, the canonical pathways and downstream targets totaled 489 human gene sets. The corresponding M. musculus gene sets were inferred by homology using the HomoloGene database. Enrichment for each of the canonical 489 pathways and gene sets included in the co-expression cluster was assessed by the hypergeometric probability. The resulting P values were also then adjusted by the Benjamini-Hochberg method for multiple comparisons.<br><b>Analyst: </b>Emmanuel Dimont<br><br>link to source dataset<br>data
No results for this coexpression
Enriched Gene Ontology terms on this co-expression cluster<b>Summary:</b> Results for GOStat analysis on co-expressed clusters. Each cluster with promoters mapping to at least two different genes was analysed with GOStat (PMID: 14962934) with default parameter. <br><b>Analyst:</b> Erik Arner<br><br>link to source dataset<br>data
| GO ID | GO name | FDR corrected p-value |
|---|---|---|
| GO:0031967 | organelle envelope | 0.0286527553894789 |
| GO:0031975 | envelope | 0.0286527553894789 |
| GO:0006228 | UTP biosynthetic process | 0.0286527553894789 |
| GO:0046051 | UTP metabolic process | 0.0286527553894789 |
| GO:0004550 | nucleoside diphosphate kinase activity | 0.0286527553894789 |
| GO:0046036 | CTP metabolic process | 0.0286527553894789 |
| GO:0009209 | pyrimidine ribonucleoside triphosphate biosynthetic process | 0.0286527553894789 |
| GO:0009208 | pyrimidine ribonucleoside triphosphate metabolic process | 0.0286527553894789 |
| GO:0006241 | CTP biosynthetic process | 0.0286527553894789 |
| GO:0006183 | GTP biosynthetic process | 0.0286527553894789 |
| GO:0046039 | GTP metabolic process | 0.0286527553894789 |
| GO:0009220 | pyrimidine ribonucleotide biosynthetic process | 0.0286527553894789 |
| GO:0009218 | pyrimidine ribonucleotide metabolic process | 0.0286527553894789 |
| GO:0009147 | pyrimidine nucleoside triphosphate metabolic process | 0.032089061554363 |
| GO:0006221 | pyrimidine nucleotide biosynthetic process | 0.032089061554363 |
| GO:0031090 | organelle membrane | 0.0353004691211007 |
| GO:0006220 | pyrimidine nucleotide metabolic process | 0.0353004691211007 |
| GO:0016776 | phosphotransferase activity, phosphate group as acceptor | 0.0353004691211007 |
| GO:0005643 | nuclear pore | 0.0393385481596267 |
| GO:0019205 | nucleobase, nucleoside, nucleotide kinase activity | 0.0393385481596267 |
| GO:0046930 | pore complex | 0.0393385481596267 |
| GO:0044249 | cellular biosynthetic process | 0.0393385481596267 |
| GO:0044453 | nuclear membrane part | 0.0393385481596267 |
| GO:0009206 | purine ribonucleoside triphosphate biosynthetic process | 0.0393385481596267 |
| GO:0009145 | purine nucleoside triphosphate biosynthetic process | 0.0393385481596267 |
| GO:0009201 | ribonucleoside triphosphate biosynthetic process | 0.0393385481596267 |
| GO:0009142 | nucleoside triphosphate biosynthetic process | 0.0393385481596267 |
| GO:0009205 | purine ribonucleoside triphosphate metabolic process | 0.0393385481596267 |
| GO:0009144 | purine nucleoside triphosphate metabolic process | 0.0393385481596267 |
| GO:0009199 | ribonucleoside triphosphate metabolic process | 0.0393385481596267 |
| GO:0009152 | purine ribonucleotide biosynthetic process | 0.0393385481596267 |
| GO:0009141 | nucleoside triphosphate metabolic process | 0.0393385481596267 |
| GO:0031965 | nuclear membrane | 0.0393385481596267 |
| GO:0009150 | purine ribonucleotide metabolic process | 0.0393385481596267 |
| GO:0009260 | ribonucleotide biosynthetic process | 0.0393385481596267 |
| GO:0006164 | purine nucleotide biosynthetic process | 0.0393385481596267 |
| GO:0006163 | purine nucleotide metabolic process | 0.0393385481596267 |
| GO:0009259 | ribonucleotide metabolic process | 0.0393385481596267 |
| GO:0009058 | biosynthetic process | 0.0393385481596267 |
| GO:0005635 | nuclear envelope | 0.0438641156314734 |
Enriched sample ontology terms on this co-expression cluster<b>Summary:</b>To summarize promoter activities (expression profile of a TSS region) across ~1000 samples, we performed enrichment analysis based on FANTOM5 Sample Ontology (FF ontology). The question here is “in which type of samples the promoter is more active”. To answer this question, we compared expressions (TPMs) in the samples associated with a sample ontology term and the rest of the samples by using the Mann-Whitney rank sum test. To summarize ontologies enriched in this co-expression cluster, we ran the same analysis on an averaged expression profile of all promoters that make up. <b>Analyst:</b> Hideya Kawaji <br><br>links to source dataset<br><br>cell_data<br>uberon_data<br><br>
| Ontology term | p-value | n |
|---|---|---|
| embryonic cell | 7.92e-39 | 250 |
| animal cell | 9.47e-31 | 679 |
| eukaryotic cell | 9.47e-31 | 679 |
| mesodermal cell | 1.83e-29 | 121 |
| epithelial cell | 2.84e-26 | 253 |
| contractile cell | 1.30e-19 | 59 |
| electrically responsive cell | 4.34e-19 | 61 |
| electrically active cell | 4.34e-19 | 61 |
| muscle precursor cell | 9.80e-19 | 58 |
| myoblast | 9.80e-19 | 58 |
| multi-potent skeletal muscle stem cell | 9.80e-19 | 58 |
| non-terminally differentiated cell | 1.80e-18 | 106 |
| muscle cell | 2.90e-18 | 55 |
| native cell | 2.79e-16 | 722 |
| smooth muscle cell | 9.74e-16 | 43 |
| smooth muscle myoblast | 9.74e-16 | 43 |
| somatic cell | 4.91e-14 | 588 |
| vascular associated smooth muscle cell | 9.59e-14 | 32 |
| lining cell | 2.23e-10 | 58 |
| barrier cell | 2.23e-10 | 58 |
| squamous epithelial cell | 1.85e-09 | 63 |
| meso-epithelial cell | 5.25e-09 | 45 |
| endothelial cell | 1.38e-08 | 36 |
| epithelial cell of nephron | 3.19e-08 | 15 |
| ectodermal cell | 1.39e-07 | 72 |
| kidney cortical cell | 3.52e-07 | 12 |
| renal cortical epithelial cell | 3.52e-07 | 12 |
| blood vessel endothelial cell | 3.97e-07 | 18 |
| embryonic blood vessel endothelial progenitor cell | 3.97e-07 | 18 |
| endothelial cell of vascular tree | 6.24e-07 | 24 |
Overrepresented TFBS (DNA) motifs on this co-expression cluster<b>Summary:</b>The values shown are the p-values for overrepresentation of the motif in this coexpression cluster. So a small p-value means a strong overrepresentation. <b>Analyst:</b> Michiel de Hoon <br><br>link to source data <br> Novel motifs <br>data <br><br> Jaspar motifs <br>data
Novel motifs
JASPAR motifs
| Motifs | -log10(p-value) |
|---|---|
|
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ENCODE TF ChIP-seq peak enrichment analysis<b>Summary:</b> For each TF and each co-expression cluster, the number of promoters with ENCODE TF ChIP signal was compared with the rest of promoters from the robust set using Fisher's exact test. Clusters with significant ChIP enrichment (q <= 0.05) after Benjamini-Hochberg correction were retained. <br><b>Analyst:</b> Erik Arner<br><br>link to source dataset<br><br>data
(#promoters = Number of promoters in this coexpression cluster that have ChIP signal of the TF)
| TF | #promoters | Enrichment | p-value | q-value |
|---|---|---|---|---|
| CCNT2#905 | 3 | 4.75215118272197 | 0.0138620699668949 | 0.0487044819267463 |
| GABPB1#2553 | 3 | 5.30076287713663 | 0.0101267882423427 | 0.0378414840331329 |
| IRF1#3659 | 3 | 5.72787281517293 | 0.00809711479033333 | 0.0319887491143752 |
| JUND#3727 | 3 | 5.24599795640327 | 0.0104343275174842 | 0.0386710692547386 |
| NR2C2#7182 | 2 | 16.3073054526204 | 0.00541182534464822 | 0.0245506744492101 |
| RXRA#6256 | 2 | 10.0373085695666 | 0.0139170380592011 | 0.048871306878212 |
Relative expression of the co-expression cluster<b>Summary:</b>Co-expression clusters are compared against FANTOM5 samples to obtain relative expression. <br><b>Analyst:</b>NA<br><br>link to data source<br> data
This analysis result is provided for C0 - C305 clusters.
