Coexpression cluster:C83
From FANTOM5_SSTAR
Full id: C83_choriocarcinoma_pancreatic_placenta_chorionic_HES3GFP_testicular_amniotic
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:0008523 | sodium-dependent multivitamin transmembrane transporter activity | 0.000169737728278866 |
| GO:0032501 | multicellular organismal process | 0.0274409360695467 |
| GO:0022410 | circadian sleep/wake cycle process | 0.0274409360695467 |
| GO:0045187 | regulation of circadian sleep/wake cycle, sleep | 0.0274409360695467 |
| GO:0042749 | regulation of circadian sleep/wake cycle | 0.0274409360695467 |
| GO:0004230 | glutamyl aminopeptidase activity | 0.0274409360695467 |
| GO:0050802 | circadian sleep/wake cycle, sleep | 0.0274409360695467 |
| GO:0015993 | molecular hydrogen transport | 0.0274409360695467 |
| GO:0005774 | vacuolar membrane | 0.0274409360695467 |
| GO:0044437 | vacuolar part | 0.0274409360695467 |
| GO:0005624 | membrane fraction | 0.0274409360695467 |
| GO:0008283 | cell proliferation | 0.0274409360695467 |
| GO:0005515 | protein binding | 0.0274409360695467 |
| GO:0005011 | macrophage colony stimulating factor receptor activity | 0.0274409360695467 |
| GO:0004667 | prostaglandin-D synthase activity | 0.0274409360695467 |
| GO:0042745 | circadian sleep/wake cycle | 0.0274409360695467 |
| GO:0032090 | Pyrin domain binding | 0.0274409360695467 |
| GO:0001917 | photoreceptor inner segment | 0.0274409360695467 |
| GO:0005887 | integral to plasma membrane | 0.0274409360695467 |
| GO:0016337 | cell-cell adhesion | 0.0274409360695467 |
| GO:0031226 | intrinsic to plasma membrane | 0.0274409360695467 |
| GO:0015370 | solute:sodium symporter activity | 0.0274409360695467 |
| GO:0042802 | identical protein binding | 0.0274409360695467 |
| GO:0046983 | protein dimerization activity | 0.0274409360695467 |
| GO:0031402 | sodium ion binding | 0.0274409360695467 |
| GO:0048512 | circadian behavior | 0.0274409360695467 |
| GO:0019852 | L-ascorbic acid metabolic process | 0.0274409360695467 |
| GO:0042752 | regulation of circadian rhythm | 0.0274409360695467 |
| GO:0047499 | calcium-independent phospholipase A2 activity | 0.0274409360695467 |
| GO:0007622 | rhythmic behavior | 0.0274409360695467 |
| GO:0000267 | cell fraction | 0.0326975459035358 |
| GO:0015294 | solute:cation symporter activity | 0.0326975459035358 |
| GO:0015851 | nucleobase transport | 0.0332514616290853 |
| GO:0044459 | plasma membrane part | 0.0335142285710582 |
| GO:0022610 | biological adhesion | 0.0351589473676664 |
| GO:0007155 | cell adhesion | 0.0351589473676664 |
| GO:0030431 | sleep | 0.0351589473676664 |
| GO:0015205 | nucleobase transmembrane transporter activity | 0.0351589473676664 |
| GO:0030838 | positive regulation of actin filament polymerization | 0.0351589473676664 |
| GO:0001750 | photoreceptor outer segment | 0.0476496838455442 |
| GO:0042803 | protein homodimerization activity | 0.0476496838455442 |
| GO:0050957 | equilibrioception | 0.0476496838455442 |
| GO:0050706 | regulation of interleukin-1 beta secretion | 0.0476496838455442 |
| GO:0008093 | cytoskeletal adaptor activity | 0.0476496838455442 |
| GO:0050718 | positive regulation of interleukin-1 beta secretion | 0.0476496838455442 |
| GO:0007176 | regulation of epidermal growth factor receptor activity | 0.0476496838455442 |
| GO:0006814 | sodium ion transport | 0.0483354787294576 |
| GO:0050716 | positive regulation of interleukin-1 secretion | 0.0483354787294576 |
| GO:0004622 | lysophospholipase activity | 0.0483354787294576 |
| GO:0031513 | nonmotile primary cilium | 0.0483354787294576 |
| GO:0050704 | regulation of interleukin-1 secretion | 0.0483354787294576 |
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>disease_data<br>
| Ontology term | p-value | n |
|---|---|---|
| germ line cell | 4.35e-37 | 7 |
| germ cell | 4.35e-37 | 7 |
| epithelial cell of pancreas | 1.82e-08 | 4 |
| Ontology term | p-value | n |
|---|---|---|
| islet cell tumor | 9.99e-30 | 1 |
| endocrine pancreas cancer | 9.99e-30 | 1 |
| pancreatic endocrine carcinoma | 9.99e-30 | 1 |
| germ cell and embryonal cancer | 2.26e-12 | 22 |
| germ cell cancer | 2.26e-12 | 22 |
| pancreatic cancer | 1.82e-08 | 4 |
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 |
|---|---|---|---|---|
| GATA3#2625 | 20 | 2.46484310924941 | 0.000216141294832004 | 0.00247680279690144 |
| SETDB1#9869 | 25 | 4.56108893416408 | 4.02130008771521e-10 | 3.96208075340461e-08 |
| TRIM28#10155 | 25 | 2.10300057073105 | 0.000396283932276339 | 0.00387414561480937 |
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
