Coexpression cluster:C133
From FANTOM5_SSTAR
Full id: C133_signet_gall_small_kidney_colon_ductal_adenocarcinoma
Phase1 CAGE Peaks
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:0005912 | adherens junction | 0.00215716088844199 |
| GO:0001936 | regulation of endothelial cell proliferation | 0.00898727966365281 |
| GO:0001935 | endothelial cell proliferation | 0.00898727966365281 |
| GO:0042127 | regulation of cell proliferation | 0.0194174866352181 |
| GO:0030324 | lung development | 0.021744029977528 |
| GO:0030323 | respiratory tube development | 0.021744029977528 |
| GO:0008285 | negative regulation of cell proliferation | 0.021744029977528 |
| GO:0008092 | cytoskeletal protein binding | 0.0245014610963039 |
| GO:0005515 | protein binding | 0.0245014610963039 |
| GO:0005224 | ATP-binding and phosphorylation-dependent chloride channel activity | 0.0245014610963039 |
| GO:0005260 | channel-conductance-controlling ATPase activity | 0.0245014610963039 |
| GO:0005624 | membrane fraction | 0.0255493356009633 |
| GO:0016324 | apical plasma membrane | 0.0255493356009633 |
| GO:0006820 | anion transport | 0.0255493356009633 |
| GO:0008283 | cell proliferation | 0.0255493356009633 |
| GO:0042975 | peroxisome proliferator activated receptor binding | 0.0255493356009633 |
| GO:0043482 | cellular pigment accumulation | 0.0255493356009633 |
| GO:0004240 | mitochondrial processing peptidase activity | 0.0255493356009633 |
| GO:0043476 | pigment accumulation | 0.0255493356009633 |
| GO:0006345 | loss of chromatin silencing | 0.0255493356009633 |
| GO:0003680 | AT DNA binding | 0.0255493356009633 |
| GO:0045177 | apical part of cell | 0.0255493356009633 |
| GO:0051128 | regulation of cellular component organization and biogenesis | 0.0310797031657759 |
| GO:0016020 | membrane | 0.0310797031657759 |
| GO:0016322 | neuron remodeling | 0.0310797031657759 |
| GO:0033059 | cellular pigmentation | 0.0310797031657759 |
| GO:0000267 | cell fraction | 0.0332688085403726 |
| GO:0030054 | cell junction | 0.0347455676759035 |
| GO:0035295 | tube development | 0.0347455676759035 |
| GO:0003891 | delta DNA polymerase activity | 0.0347455676759035 |
| GO:0046965 | retinoid X receptor binding | 0.0347455676759035 |
| GO:0017110 | nucleoside-diphosphatase activity | 0.0384569858713336 |
| GO:0005916 | fascia adherens | 0.0384569858713336 |
| GO:0006337 | nucleosome disassembly | 0.0384569858713336 |
| GO:0031498 | chromatin disassembly | 0.0384569858713336 |
| GO:0001938 | positive regulation of endothelial cell proliferation | 0.042492581409193 |
| GO:0015355 | secondary active monocarboxylate transmembrane transporter activity | 0.042492581409193 |
| GO:0009898 | internal side of plasma membrane | 0.042492581409193 |
| GO:0045815 | positive regulation of gene expression, epigenetic | 0.0459337426993214 |
| GO:0031116 | positive regulation of microtubule polymerization | 0.0459337426993214 |
| GO:0050998 | nitric-oxide synthase binding | 0.0459337426993214 |
| GO:0048523 | negative regulation of cellular process | 0.04677588402999 |
| GO:0030321 | transepithelial chloride transport | 0.04677588402999 |
| GO:0031112 | positive regulation of microtubule polymerization or depolymerization | 0.04677588402999 |
| GO:0031113 | regulation of microtubule polymerization | 0.04677588402999 |
| GO:0045176 | apical protein localization | 0.04677588402999 |
| GO:0048519 | negative regulation of biological process | 0.0493865270640579 |
| GO:0016601 | Rac protein signal transduction | 0.0493865270640579 |
| GO:0042974 | retinoic acid receptor binding | 0.0493865270640579 |
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><br><br>disease_data<br>
| Ontology term | p-value | n |
|---|---|---|
| signet ring cell adenocarcinoma | 1.55e-98 | 2 |
| adenocarcinoma | 2.15e-09 | 25 |
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) |
|---|---|
|
{{{tfbs_overrepresentation_jaspar}}} |
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 |
|---|---|---|---|---|
| PRDM1#639 | 5 | 4.84672631534782 | 0.00396228780051937 | 0.0190182166275308 |
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
