Coexpression cluster:C76
From FANTOM5_SSTAR
Full id: C76_argyrophil_gastrointestinal_temporal_duodenum_neuroblastoma_merkel_smallcell
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
| p.value | FDR | nGenes | nPathway | Name |
|---|---|---|---|---|
| 3.1297509870497e-05 | 0.0198113237480246 | 4 | 125 | Integration of energy metabolism (Reactome):REACT_1505 |
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:0030073 | insulin secretion | 0.0207743713648184 |
| GO:0002790 | peptide secretion | 0.0207743713648184 |
| GO:0030072 | peptide hormone secretion | 0.0207743713648184 |
| GO:0005515 | protein binding | 0.036532638926643 |
| GO:0046879 | hormone secretion | 0.036532638926643 |
| GO:0015833 | peptide transport | 0.036532638926643 |
| GO:0060002 | plus-end directed microfilament motor activity | 0.036532638926643 |
| GO:0051594 | detection of glucose | 0.036532638926643 |
| GO:0009730 | detection of carbohydrate stimulus | 0.036532638926643 |
| GO:0005536 | glucose binding | 0.036532638926643 |
| GO:0004340 | glucokinase activity | 0.036532638926643 |
| GO:0046873 | metal ion transmembrane transporter activity | 0.036532638926643 |
| GO:0022836 | gated channel activity | 0.036532638926643 |
| GO:0006112 | energy reserve metabolic process | 0.0379028371044298 |
| GO:0006813 | potassium ion transport | 0.0429179710207958 |
| GO:0003001 | generation of a signal involved in cell-cell signaling | 0.0429179710207958 |
| GO:0009726 | detection of endogenous stimulus | 0.0429179710207958 |
| GO:0045721 | negative regulation of gluconeogenesis | 0.0429179710207958 |
| GO:0032024 | positive regulation of insulin secretion | 0.0429179710207958 |
| GO:0007267 | cell-cell signaling | 0.0429179710207958 |
| GO:0035081 | induction of programmed cell death by hormones | 0.0429179710207958 |
| GO:0008628 | induction of apoptosis by hormones | 0.0429179710207958 |
| GO:0005979 | regulation of glycogen biosynthetic process | 0.0429179710207958 |
| GO:0008140 | cAMP response element binding protein binding | 0.0429179710207958 |
| GO:0045912 | negative regulation of carbohydrate metabolic process | 0.0429179710207958 |
| GO:0004566 | beta-glucuronidase activity | 0.0429179710207958 |
| GO:0045725 | positive regulation of glycogen biosynthetic process | 0.0429179710207958 |
| GO:0008422 | beta-glucosidase activity | 0.0429179710207958 |
| GO:0015079 | potassium ion transmembrane transporter activity | 0.0429179710207958 |
| GO:0030501 | positive regulation of bone mineralization | 0.0429179710207958 |
| GO:0005216 | ion channel activity | 0.0429179710207958 |
| GO:0030001 | metal ion transport | 0.0429179710207958 |
| GO:0007010 | cytoskeleton organization and biogenesis | 0.0429179710207958 |
| GO:0022838 | substrate specific channel activity | 0.0429179710207958 |
| GO:0022803 | passive transmembrane transporter activity | 0.0429179710207958 |
| GO:0015267 | channel activity | 0.0429179710207958 |
| GO:0006111 | regulation of gluconeogenesis | 0.0429179710207958 |
| GO:0005220 | inositol 1,4,5-triphosphate-sensitive calcium-release channel activity | 0.0429179710207958 |
| GO:0008095 | inositol-1,4,5-triphosphate receptor activity | 0.0429179710207958 |
| GO:0030898 | actin-dependent ATPase activity | 0.0429179710207958 |
| GO:0043284 | biopolymer biosynthetic process | 0.0429179710207958 |
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 |
|---|---|---|
| epithelial cell of cervix | 1.55e-98 | 2 |
| Ontology term | p-value | n |
|---|---|---|
| uterine epithelium | 1.55e-98 | 2 |
| cervix epithelium | 1.55e-98 | 2 |
| uterine cervix | 4.27e-34 | 6 |
| neck of organ | 4.27e-34 | 6 |
| uterus | 6.74e-11 | 21 |
| embryonic uterus | 1.80e-10 | 22 |
| internal female genitalia | 1.80e-10 | 22 |
| internal genitalia | 2.15e-09 | 25 |
| female reproductive organ | 8.21e-07 | 37 |
| female reproductive system | 8.21e-07 | 37 |
| Ontology term | p-value | n |
|---|---|---|
| cervical cancer | 1.48e-40 | 5 |
| female reproductive organ cancer | 8.32e-09 | 27 |
| reproductive organ cancer | 2.67e-08 | 29 |
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) |
|---|---|
| MA0003.1 | 0.0617061 |
| MA0004.1 | 1.41945 |
| MA0006.1 | 0.0576547 |
| MA0007.1 | 0.420931 |
| MA0009.1 | 0.0484012 |
| MA0014.1 | 0.0116544 |
| MA0017.1 | 1.902 |
| MA0019.1 | 0.12542 |
| MA0024.1 | 0.423224 |
| MA0025.1 | 0.118087 |
| MA0027.1 | 1.07684 |
| MA0028.1 | 0.0343273 |
| MA0029.1 | 0.158263 |
| MA0030.1 | 0.660812 |
| MA0031.1 | 0.658914 |
| MA0038.1 | 0.036893 |
| MA0040.1 | 1.67636 |
| MA0041.1 | 1.87506 |
| MA0042.1 | 0.892434 |
| MA0043.1 | 0.134137 |
| MA0046.1 | 12.7978 |
| MA0048.1 | 0.100287 |
| MA0050.1 | 0.112241 |
| MA0051.1 | 0.411864 |
| MA0052.1 | 0.1697 |
| MA0055.1 | 0.75625 |
| MA0056.1 | 0 |
| MA0057.1 | 0.044688 |
| MA0058.1 | 1.40505 |
| MA0059.1 | 2.05133 |
| MA0060.1 | 4.35816e-05 |
| MA0061.1 | 0.00154374 |
| MA0063.1 | 0 |
| MA0066.1 | 0.755223 |
| MA0067.1 | 0.580599 |
| MA0068.1 | 0.251413 |
| MA0069.1 | 0.0429721 |
| MA0070.1 | 0.235651 |
| MA0071.1 | 0.294715 |
| MA0072.1 | 0.0376584 |
| MA0073.1 | 0.0518103 |
| MA0074.1 | 0.034207 |
| MA0076.1 | 0.000154555 |
| MA0077.1 | 0.386753 |
| MA0078.1 | 0.471642 |
| MA0081.1 | 0.0630011 |
| MA0083.1 | 0.0103085 |
| MA0084.1 | 0.967398 |
| MA0087.1 | 1.21926 |
| MA0088.1 | 0.706124 |
| MA0089.1 | 0 |
| MA0090.1 | 0.417711 |
| MA0091.1 | 2.51151 |
| MA0092.1 | 0.584957 |
| MA0093.1 | 1.54483 |
| MA0095.1 | 0 |
| MA0098.1 | 0 |
| MA0100.1 | 0.234464 |
| MA0101.1 | 0.00076627 |
| MA0103.1 | 3.71886 |
| MA0105.1 | 0.04882 |
| MA0106.1 | 0.199117 |
| MA0107.1 | 0.0118382 |
| MA0108.2 | 1.16057 |
| MA0109.1 | 0 |
| MA0111.1 | 0.141639 |
| MA0113.1 | 0.14354 |
| MA0114.1 | 1.92495 |
| MA0115.1 | 0.77722 |
| MA0116.1 | 0.312078 |
| MA0117.1 | 0.33712 |
| MA0119.1 | 1.58524 |
| MA0122.1 | 0.076845 |
| MA0124.1 | 1.48285 |
| MA0125.1 | 1.55447 |
| MA0130.1 | 0 |
| MA0131.1 | 0.0756152 |
| MA0132.1 | 0 |
| MA0133.1 | 0 |
| MA0135.1 | 0.324611 |
| MA0136.1 | 0.0409562 |
| MA0139.1 | 0.355469 |
| MA0140.1 | 0.124674 |
| MA0141.1 | 0.565948 |
| MA0142.1 | 0.230897 |
| MA0143.1 | 0.351993 |
| MA0144.1 | 0.648391 |
| MA0145.1 | 0.233663 |
| MA0146.1 | 1.1231 |
| MA0147.1 | 0.967267 |
| MA0148.1 | 2.85308 |
| MA0149.1 | 7.94167e-05 |
| MA0062.2 | 5.71904e-05 |
| MA0035.2 | 0.0390291 |
| MA0039.2 | 0.00181364 |
| MA0138.2 | 0.326671 |
| MA0002.2 | 0.10076 |
| MA0137.2 | 1.44271 |
| MA0104.2 | 1.1833 |
| MA0047.2 | 2.65437 |
| MA0112.2 | 0.201604 |
| MA0065.2 | 1.00057 |
| MA0150.1 | 0.000210939 |
| MA0151.1 | 0 |
| MA0152.1 | 0.306913 |
| MA0153.1 | 7.66008 |
| MA0154.1 | 1.1057 |
| MA0155.1 | 0.0521023 |
| MA0156.1 | 0.00751305 |
| MA0157.1 | 1.71704 |
| MA0158.1 | 0 |
| MA0159.1 | 0.0849684 |
| MA0160.1 | 0.441037 |
| MA0161.1 | 0 |
| MA0162.1 | 0.00539302 |
| MA0163.1 | 0.0977178 |
| MA0164.1 | 0.73419 |
| MA0080.2 | 0.00164457 |
| MA0018.2 | 0.0663448 |
| MA0099.2 | 0.00864036 |
| MA0079.2 | 5.68183e-05 |
| MA0102.2 | 0.551775 |
| MA0258.1 | 0.14961 |
| MA0259.1 | 0.38982 |
| MA0442.1 | 0 |
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 |
|---|---|---|---|---|
| FOXA2#3170 | 23 | 2.38025490046765 | 0.000123961761777975 | 0.00165259668602629 |
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
