Coexpression cluster:C186
From FANTOM5_SSTAR
Full id: C186_squamous_papillotubular_large_Tracheal_oral_Small_epidermoid
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:0060166 | olfactory pit development | 0.00603402598852654 |
GO:0002072 | optic cup morphogenesis involved in camera-type eye development | 0.00603402598852654 |
GO:0021768 | nucleus accumbens development | 0.00603402598852654 |
GO:0043584 | nose development | 0.00603402598852654 |
GO:0021756 | striatum development | 0.00603402598852654 |
GO:0048857 | neural nucleus development | 0.00603402598852654 |
GO:0021544 | subpallium development | 0.00775757666933773 |
GO:0048048 | embryonic eye morphogenesis | 0.00904997327703826 |
GO:0042573 | retinoic acid metabolic process | 0.0100549338569124 |
GO:0004028 | 3-chloroallyl aldehyde dehydrogenase activity | 0.0108586892361296 |
GO:0021761 | limbic system development | 0.0115161135774329 |
GO:0048562 | embryonic organ morphogenesis | 0.0150779615211111 |
GO:0021537 | telencephalon development | 0.0153090288070116 |
GO:0048593 | camera-type eye morphogenesis | 0.0167981898572595 |
GO:0004030 | aldehyde dehydrogenase [NAD(P)+] activity | 0.016883340376704 |
GO:0006776 | vitamin A metabolic process | 0.0169577140091317 |
GO:0006775 | fat-soluble vitamin metabolic process | 0.0191488592113784 |
GO:0048568 | embryonic organ development | 0.0200921158836862 |
GO:0016331 | morphogenesis of embryonic epithelium | 0.0209356343747139 |
GO:0048592 | eye morphogenesis | 0.0234994728631865 |
GO:0043010 | camera-type eye development | 0.0292529612633874 |
GO:0030286 | dynein complex | 0.0339912580765414 |
GO:0030900 | forebrain development | 0.0339912580765414 |
GO:0001654 | eye development | 0.0339912580765414 |
GO:0044430 | cytoskeletal part | 0.0339912580765414 |
GO:0016620 | oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor | 0.0347134486806925 |
GO:0002009 | morphogenesis of an epithelium | 0.0420867596980804 |
GO:0016903 | oxidoreductase activity, acting on the aldehyde or oxo group of donors | 0.0463567570676262 |
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 | 2.37e-15 | 2 |
duct epithelial cell | 9.90e-11 | 3 |
branched duct epithelial cell | 9.90e-11 | 3 |
tracheal epithelial cell | 9.90e-11 | 3 |
tracheoblast | 9.90e-11 | 3 |
respiratory epithelial cell | 9.94e-10 | 13 |
squamous epithelial cell | 1.09e-07 | 63 |
endo-epithelial cell | 8.88e-07 | 42 |
Ontology term | p-value | n |
---|---|---|
mammalian vulva | 1.78e-29 | 1 |
external female genitalia | 1.78e-29 | 1 |
uterine epithelium | 2.37e-15 | 2 |
cervix epithelium | 2.37e-15 | 2 |
tongue | 8.17e-11 | 3 |
gustatory system | 8.17e-11 | 3 |
future tongue | 8.17e-11 | 3 |
mucosa of oral region | 1.96e-08 | 4 |
respiratory system mucosa | 1.96e-08 | 4 |
Ontology term | p-value | n |
---|---|---|
squamous cell carcinoma | 9.65e-33 | 14 |
carcinoma | 5.56e-07 | 106 |
cervical cancer | 6.39e-07 | 5 |
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 | 4.99104e-09 |
MA0004.1 | 1.18494 |
MA0006.1 | 0.0457519 |
MA0007.1 | 0.0490025 |
MA0009.1 | 0.112474 |
MA0014.1 | 1.8067e-07 |
MA0017.1 | 0.0353272 |
MA0019.1 | 0.192717 |
MA0024.1 | 0.068993 |
MA0025.1 | 1.63168 |
MA0027.1 | 1.47809 |
MA0028.1 | 0.0247631 |
MA0029.1 | 0.263395 |
MA0030.1 | 0.53603 |
MA0031.1 | 0.736736 |
MA0038.1 | 1.43522 |
MA0040.1 | 0.569275 |
MA0041.1 | 0.295713 |
MA0042.1 | 0.825469 |
MA0043.1 | 0.732147 |
MA0046.1 | 0.348554 |
MA0048.1 | 0.00208597 |
MA0050.1 | 0.122838 |
MA0051.1 | 0.0504177 |
MA0052.1 | 0.0799011 |
MA0055.1 | 0.0025854 |
MA0056.1 | 0 |
MA0057.1 | 0.00359348 |
MA0058.1 | 2.12212 |
MA0059.1 | 1.14824 |
MA0060.1 | 0.825403 |
MA0061.1 | 0.748833 |
MA0063.1 | 0 |
MA0066.1 | 1.43766 |
MA0067.1 | 0.304116 |
MA0068.1 | 0.0140086 |
MA0069.1 | 0.105679 |
MA0070.1 | 0.330546 |
MA0071.1 | 0.0368616 |
MA0072.1 | 0.0986844 |
MA0073.1 | 2.93657e-06 |
MA0074.1 | 0.0500929 |
MA0076.1 | 0.00615153 |
MA0077.1 | 0.316229 |
MA0078.1 | 0.481625 |
MA0081.1 | 0.314544 |
MA0083.1 | 1.2248 |
MA0084.1 | 0.448027 |
MA0087.1 | 0.32237 |
MA0088.1 | 0.787964 |
MA0089.1 | 0 |
MA0090.1 | 0.595868 |
MA0091.1 | 0.0612406 |
MA0092.1 | 0.09894 |
MA0093.1 | 2.12441 |
MA0095.1 | 0 |
MA0098.1 | 0 |
MA0100.1 | 0.315613 |
MA0101.1 | 0.100637 |
MA0103.1 | 0.68197 |
MA0105.1 | 0.141072 |
MA0106.1 | 6.29814 |
MA0107.1 | 0.382797 |
MA0108.2 | 0.0493529 |
MA0109.1 | 0 |
MA0111.1 | 0.892901 |
MA0113.1 | 0.4014 |
MA0114.1 | 0.0558823 |
MA0115.1 | 0.251028 |
MA0116.1 | 0.032712 |
MA0117.1 | 0.409173 |
MA0119.1 | 0.587735 |
MA0122.1 | 0.443081 |
MA0124.1 | 0.636439 |
MA0125.1 | 0.51417 |
MA0130.1 | 0 |
MA0131.1 | 0.0282896 |
MA0132.1 | 0 |
MA0133.1 | 0 |
MA0135.1 | 0.127133 |
MA0136.1 | 0.0554464 |
MA0139.1 | 0.0153393 |
MA0140.1 | 0.614017 |
MA0141.1 | 0.000585776 |
MA0142.1 | 0.654658 |
MA0143.1 | 0.660354 |
MA0144.1 | 0.132301 |
MA0145.1 | 0.197284 |
MA0146.1 | 0.00438042 |
MA0147.1 | 0.292742 |
MA0148.1 | 1.33601 |
MA0149.1 | 0.00598841 |
MA0062.2 | 0.00865138 |
MA0035.2 | 0.389976 |
MA0039.2 | 7.04958e-06 |
MA0138.2 | 0.258548 |
MA0002.2 | 0.156629 |
MA0137.2 | 0.330221 |
MA0104.2 | 0.188886 |
MA0047.2 | 1.21119 |
MA0112.2 | 0.0387444 |
MA0065.2 | 0.0136882 |
MA0150.1 | 3.22736 |
MA0151.1 | 0 |
MA0152.1 | 0.407566 |
MA0153.1 | 0.490722 |
MA0154.1 | 0.023977 |
MA0155.1 | 0.0183044 |
MA0156.1 | 0.126828 |
MA0157.1 | 0.322729 |
MA0158.1 | 0 |
MA0159.1 | 0.0698723 |
MA0160.1 | 0.190068 |
MA0161.1 | 0 |
MA0162.1 | 8.89507e-06 |
MA0163.1 | 3.45651e-08 |
MA0164.1 | 0.223694 |
MA0080.2 | 0.0964526 |
MA0018.2 | 0.18974 |
MA0099.2 | 5.18072 |
MA0079.2 | 0 |
MA0102.2 | 0.478533 |
MA0258.1 | 0.112859 |
MA0259.1 | 0.0409197 |
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 |
---|---|---|---|---|
FOS#2353 | 21 | 2.0538811031172 | 0.00100103000456351 | 0.00717546826675419 |
JUN#3725 | 16 | 2.17614420736284 | 0.00247852644935304 | 0.0139229143633811 |
STAT3#6774 | 22 | 2.51552423844993 | 4.02961446076117e-05 | 0.000738460966252738 |
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