Coexpression cluster:C1753
From FANTOM5_SSTAR
Full id: C1753_neuroblastoma_pineal_rectum_retina_merkel_carcinosarcoma_eye
Phase1 CAGE Peaks
| Hg19::chr15:78913289..78913302,- | p4@CHRNA3 |
| Hg19::chr15:78913306..78913349,- | p1@CHRNA3 |
| Hg19::chr15:78913353..78913365,- | p3@CHRNA3 |
| Hg19::chr15:78933542..78933562,- | p2@CHRNB4 |
| Hg19::chr15:78933567..78933604,- | p1@CHRNB4 |
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 |
|---|---|---|---|---|
| 9.04613128104753e-05 | 0.0190873370030103 | 2 | 272 | Neuroactive ligand-receptor interaction (KEGG):04080 |
| 4.73856659734924e-05 | 0.0149975632806103 | 2 | 197 | Synaptic Transmission (Reactome):REACT_13685 |
| 1.91447319275479e-07 | 0.000121186153101378 | 2 | 13 | {CHRNA1,13} (Static Module):NA |
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:0005892 | nicotinic acetylcholine-gated receptor-channel complex | 9.64592211467951e-06 |
| GO:0015464 | acetylcholine receptor activity | 9.64592211467951e-06 |
| GO:0042166 | acetylcholine binding | 9.64592211467951e-06 |
| GO:0004889 | nicotinic acetylcholine-activated cation-selective channel activity | 9.64592211467951e-06 |
| GO:0043176 | amine binding | 2.88538887604326e-05 |
| GO:0005231 | excitatory extracellular ligand-gated ion channel activity | 6.4967001120213e-05 |
| GO:0043235 | receptor complex | 0.000130609380186344 |
| GO:0005230 | extracellular ligand-gated ion channel activity | 0.000145598413308646 |
| GO:0030594 | neurotransmitter receptor activity | 0.000145598413308646 |
| GO:0042165 | neurotransmitter binding | 0.000145598413308646 |
| GO:0045211 | postsynaptic membrane | 0.000145598413308646 |
| GO:0044456 | synapse part | 0.000145598413308646 |
| GO:0015276 | ligand-gated ion channel activity | 0.000145598413308646 |
| GO:0022834 | ligand-gated channel activity | 0.000145598413308646 |
| GO:0035095 | behavioral response to nicotine | 0.00030474923985843 |
| GO:0060073 | micturition | 0.00030474923985843 |
| GO:0060084 | synaptic transmission involved in micturition | 0.00030474923985843 |
| GO:0005261 | cation channel activity | 0.000736886645026226 |
| GO:0030054 | cell junction | 0.000736886645026226 |
| GO:0046873 | metal ion transmembrane transporter activity | 0.000924178466639651 |
| GO:0022836 | gated channel activity | 0.000924178466639651 |
| GO:0035094 | response to nicotine | 0.00117737092459055 |
| GO:0005216 | ion channel activity | 0.00142681635278938 |
| GO:0022838 | substrate specific channel activity | 0.00142681635278938 |
| GO:0022803 | passive transmembrane transporter activity | 0.00142681635278938 |
| GO:0015267 | channel activity | 0.00142681635278938 |
| GO:0043279 | response to alkaloid | 0.00153487505515621 |
| GO:0003014 | renal system process | 0.00160762563893901 |
| GO:0007274 | neuromuscular synaptic transmission | 0.00160762563893901 |
| GO:0014070 | response to organic cyclic substance | 0.00186392717093987 |
| GO:0008324 | cation transmembrane transporter activity | 0.00186392717093987 |
| GO:0046928 | regulation of neurotransmitter secretion | 0.00188359938245719 |
| GO:0007271 | synaptic transmission, cholinergic | 0.00188359938245719 |
| GO:0006940 | regulation of smooth muscle contraction | 0.00304664016645142 |
| GO:0015075 | ion transmembrane transporter activity | 0.00363495337446202 |
| GO:0005887 | integral to plasma membrane | 0.00363495337446202 |
| GO:0031226 | intrinsic to plasma membrane | 0.00363495337446202 |
| GO:0030534 | adult behavior | 0.00363495337446202 |
| GO:0006811 | ion transport | 0.00363495337446202 |
| GO:0022891 | substrate-specific transmembrane transporter activity | 0.00440723325204938 |
| GO:0006939 | smooth muscle contraction | 0.00470705748726614 |
| GO:0006937 | regulation of muscle contraction | 0.00470705748726614 |
| GO:0022857 | transmembrane transporter activity | 0.00470705748726614 |
| GO:0007269 | neurotransmitter secretion | 0.00470705748726614 |
| GO:0022892 | substrate-specific transporter activity | 0.00528172907724811 |
| GO:0045055 | regulated secretory pathway | 0.0059645416008552 |
| GO:0051046 | regulation of secretion | 0.00649792663916262 |
| GO:0004888 | transmembrane receptor activity | 0.00649813937510364 |
| GO:0010033 | response to organic substance | 0.00654933290669141 |
| GO:0003001 | generation of a signal involved in cell-cell signaling | 0.00724566593174309 |
| GO:0044459 | plasma membrane part | 0.00776229847011137 |
| GO:0001505 | regulation of neurotransmitter levels | 0.00776229847011137 |
| GO:0043234 | protein complex | 0.0119540749559224 |
| GO:0004872 | receptor activity | 0.0134608779566729 |
| GO:0003012 | muscle system process | 0.0152278255222535 |
| GO:0006936 | muscle contraction | 0.0152278255222535 |
| GO:0007626 | locomotory behavior | 0.01640752823724 |
| GO:0060089 | molecular transducer activity | 0.0177936923627931 |
| GO:0004871 | signal transducer activity | 0.0177936923627931 |
| GO:0005886 | plasma membrane | 0.0185014123823964 |
| GO:0032991 | macromolecular complex | 0.0188428378990201 |
| GO:0045045 | secretory pathway | 0.0197011740994843 |
| GO:0006810 | transport | 0.0197011740994843 |
| GO:0051234 | establishment of localization | 0.0203666329991751 |
| GO:0051239 | regulation of multicellular organismal process | 0.021988223475816 |
| GO:0007268 | synaptic transmission | 0.0222025422545425 |
| GO:0007610 | behavior | 0.0222025422545425 |
| GO:0051179 | localization | 0.0222025422545425 |
| GO:0032940 | secretion by cell | 0.0222025422545425 |
| GO:0019226 | transmission of nerve impulse | 0.0243052074014842 |
| GO:0046903 | secretion | 0.0278618091882116 |
| GO:0007165 | signal transduction | 0.027996284948599 |
| GO:0007154 | cell communication | 0.0322850773249661 |
| GO:0042221 | response to chemical stimulus | 0.040878993381908 |
| GO:0007267 | cell-cell signaling | 0.0437931675882937 |
| GO:0016021 | integral to membrane | 0.0448731129004987 |
| GO:0031224 | intrinsic to membrane | 0.0448731129004987 |
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 |
|---|---|---|
| neuron | 3.83e-10 | 6 |
| neuroblast | 3.83e-10 | 6 |
| electrically signaling cell | 3.83e-10 | 6 |
| embryonic stem cell | 3.31e-09 | 5 |
| neurectodermal cell | 1.67e-07 | 59 |
| neuronal stem cell | 2.33e-07 | 8 |
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 | 4.96701 |
| MA0004.1 | 0.626788 |
| MA0006.1 | 0.452993 |
| MA0007.1 | 0.606704 |
| MA0009.1 | 1.11255 |
| MA0014.1 | 3.07977 |
| MA0017.1 | 0.496101 |
| MA0019.1 | 0.784036 |
| MA0024.1 | 1.00439 |
| MA0025.1 | 1.24931 |
| MA0027.1 | 2.73598 |
| MA0028.1 | 1.18667 |
| MA0029.1 | 1.02437 |
| MA0030.1 | 1.01252 |
| MA0031.1 | 0.945567 |
| MA0038.1 | 0.736268 |
| MA0040.1 | 1.03042 |
| MA0041.1 | 0.64667 |
| MA0042.1 | 0.612397 |
| MA0043.1 | 1.11288 |
| MA0046.1 | 1.10134 |
| MA0048.1 | 2.41212 |
| MA0050.1 | 0.613347 |
| MA0051.1 | 0.731787 |
| MA0052.1 | 1.03442 |
| MA0055.1 | 1.01397 |
| MA0056.1 | 0 |
| MA0057.1 | 0.554727 |
| MA0058.1 | 0.523638 |
| MA0059.1 | 0.522232 |
| MA0060.1 | 0.321781 |
| MA0061.1 | 0.791444 |
| MA0063.1 | 0 |
| MA0066.1 | 0.736721 |
| MA0067.1 | 1.43651 |
| MA0068.1 | 0.247962 |
| MA0069.1 | 1.09737 |
| MA0070.1 | 1.08584 |
| MA0071.1 | 0.695094 |
| MA0072.1 | 1.0812 |
| MA0073.1 | 0.0140295 |
| MA0074.1 | 1.73427 |
| MA0076.1 | 0.540943 |
| MA0077.1 | 1.07324 |
| MA0078.1 | 0.836493 |
| MA0081.1 | 0.522409 |
| MA0083.1 | 1.12028 |
| MA0084.1 | 1.62584 |
| MA0087.1 | 1.07867 |
| MA0088.1 | 1.3271 |
| MA0089.1 | 0 |
| MA0090.1 | 0.556637 |
| MA0091.1 | 0.629594 |
| MA0092.1 | 0.588959 |
| MA0093.1 | 0.456342 |
| MA0095.1 | 0 |
| MA0098.1 | 0 |
| MA0100.1 | 0.750974 |
| MA0101.1 | 0.459973 |
| MA0103.1 | 1.12656 |
| MA0105.1 | 0.175503 |
| MA0106.1 | 0.779931 |
| MA0107.1 | 0.378225 |
| MA0108.2 | 0.94238 |
| MA0109.1 | 0 |
| MA0111.1 | 0.5713 |
| MA0113.1 | 0.797251 |
| MA0114.1 | 0.973423 |
| MA0115.1 | 1.35895 |
| MA0116.1 | 1.76306 |
| MA0117.1 | 1.1512 |
| MA0119.1 | 0.504689 |
| MA0122.1 | 1.17777 |
| MA0124.1 | 1.31673 |
| MA0125.1 | 1.23103 |
| MA0130.1 | 0 |
| MA0131.1 | 1.99092 |
| MA0132.1 | 0 |
| MA0133.1 | 0 |
| MA0135.1 | 1.14377 |
| MA0136.1 | 0.743749 |
| MA0139.1 | 0.277033 |
| MA0140.1 | 1.65391 |
| MA0141.1 | 0.520334 |
| MA0142.1 | 0.912455 |
| MA0143.1 | 0.797437 |
| MA0144.1 | 0.356507 |
| MA0145.1 | 0.868598 |
| MA0146.1 | 0.143081 |
| MA0147.1 | 0.386018 |
| MA0148.1 | 0.653474 |
| MA0149.1 | 2.7505 |
| MA0062.2 | 0.284987 |
| MA0035.2 | 0.691506 |
| MA0039.2 | 1.50246 |
| MA0138.2 | 0.837782 |
| MA0002.2 | 0.30855 |
| MA0137.2 | 0.47779 |
| MA0104.2 | 0.858845 |
| MA0047.2 | 0.767096 |
| MA0112.2 | 1.35805 |
| MA0065.2 | 2.73531 |
| MA0150.1 | 0.550239 |
| MA0151.1 | 0 |
| MA0152.1 | 0.69926 |
| MA0153.1 | 1.21379 |
| MA0154.1 | 0.514087 |
| MA0155.1 | 0.409315 |
| MA0156.1 | 0.480289 |
| MA0157.1 | 0.883854 |
| MA0158.1 | 0 |
| MA0159.1 | 0.386729 |
| MA0160.1 | 0.669748 |
| MA0161.1 | 0 |
| MA0162.1 | 2.27598 |
| MA0163.1 | 1.05321 |
| MA0164.1 | 0.810347 |
| MA0080.2 | 0.456437 |
| MA0018.2 | 0.781393 |
| MA0099.2 | 0.699641 |
| MA0079.2 | 1.81596 |
| MA0102.2 | 1.66336 |
| MA0258.1 | 0.345771 |
| MA0259.1 | 2.71109 |
| 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 |
|---|---|---|---|---|
| NANOG#79923 | 2 | 11.6979113924051 | 0.0109116495195608 | 0.0402217119321431 |
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.
