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Coexpression cluster:C1753

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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.valueFDRnGenesnPathwayName
9.04613128104753e-050.01908733700301032272Neuroactive ligand-receptor interaction (KEGG):04080
4.73856659734924e-050.01499756328061032197Synaptic Transmission (Reactome):REACT_13685
1.91447319275479e-070.000121186153101378213{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 IDGO nameFDR corrected p-value
GO:0005892nicotinic acetylcholine-gated receptor-channel complex9.64592211467951e-06
GO:0015464acetylcholine receptor activity9.64592211467951e-06
GO:0042166acetylcholine binding9.64592211467951e-06
GO:0004889nicotinic acetylcholine-activated cation-selective channel activity9.64592211467951e-06
GO:0043176amine binding2.88538887604326e-05
GO:0005231excitatory extracellular ligand-gated ion channel activity6.4967001120213e-05
GO:0043235receptor complex0.000130609380186344
GO:0005230extracellular ligand-gated ion channel activity0.000145598413308646
GO:0030594neurotransmitter receptor activity0.000145598413308646
GO:0042165neurotransmitter binding0.000145598413308646
GO:0045211postsynaptic membrane0.000145598413308646
GO:0044456synapse part0.000145598413308646
GO:0015276ligand-gated ion channel activity0.000145598413308646
GO:0022834ligand-gated channel activity0.000145598413308646
GO:0035095behavioral response to nicotine0.00030474923985843
GO:0060073micturition0.00030474923985843
GO:0060084synaptic transmission involved in micturition0.00030474923985843
GO:0005261cation channel activity0.000736886645026226
GO:0030054cell junction0.000736886645026226
GO:0046873metal ion transmembrane transporter activity0.000924178466639651
GO:0022836gated channel activity0.000924178466639651
GO:0035094response to nicotine0.00117737092459055
GO:0005216ion channel activity0.00142681635278938
GO:0022838substrate specific channel activity0.00142681635278938
GO:0022803passive transmembrane transporter activity0.00142681635278938
GO:0015267channel activity0.00142681635278938
GO:0043279response to alkaloid0.00153487505515621
GO:0003014renal system process0.00160762563893901
GO:0007274neuromuscular synaptic transmission0.00160762563893901
GO:0014070response to organic cyclic substance0.00186392717093987
GO:0008324cation transmembrane transporter activity0.00186392717093987
GO:0046928regulation of neurotransmitter secretion0.00188359938245719
GO:0007271synaptic transmission, cholinergic0.00188359938245719
GO:0006940regulation of smooth muscle contraction0.00304664016645142
GO:0015075ion transmembrane transporter activity0.00363495337446202
GO:0005887integral to plasma membrane0.00363495337446202
GO:0031226intrinsic to plasma membrane0.00363495337446202
GO:0030534adult behavior0.00363495337446202
GO:0006811ion transport0.00363495337446202
GO:0022891substrate-specific transmembrane transporter activity0.00440723325204938
GO:0006939smooth muscle contraction0.00470705748726614
GO:0006937regulation of muscle contraction0.00470705748726614
GO:0022857transmembrane transporter activity0.00470705748726614
GO:0007269neurotransmitter secretion0.00470705748726614
GO:0022892substrate-specific transporter activity0.00528172907724811
GO:0045055regulated secretory pathway0.0059645416008552
GO:0051046regulation of secretion0.00649792663916262
GO:0004888transmembrane receptor activity0.00649813937510364
GO:0010033response to organic substance0.00654933290669141
GO:0003001generation of a signal involved in cell-cell signaling0.00724566593174309
GO:0044459plasma membrane part0.00776229847011137
GO:0001505regulation of neurotransmitter levels0.00776229847011137
GO:0043234protein complex0.0119540749559224
GO:0004872receptor activity0.0134608779566729
GO:0003012muscle system process0.0152278255222535
GO:0006936muscle contraction0.0152278255222535
GO:0007626locomotory behavior0.01640752823724
GO:0060089molecular transducer activity0.0177936923627931
GO:0004871signal transducer activity0.0177936923627931
GO:0005886plasma membrane0.0185014123823964
GO:0032991macromolecular complex0.0188428378990201
GO:0045045secretory pathway0.0197011740994843
GO:0006810transport0.0197011740994843
GO:0051234establishment of localization0.0203666329991751
GO:0051239regulation of multicellular organismal process0.021988223475816
GO:0007268synaptic transmission0.0222025422545425
GO:0007610behavior0.0222025422545425
GO:0051179localization0.0222025422545425
GO:0032940secretion by cell0.0222025422545425
GO:0019226transmission of nerve impulse0.0243052074014842
GO:0046903secretion0.0278618091882116
GO:0007165signal transduction0.027996284948599
GO:0007154cell communication0.0322850773249661
GO:0042221response to chemical stimulus0.040878993381908
GO:0007267cell-cell signaling0.0437931675882937
GO:0016021integral to membrane0.0448731129004987
GO:0031224intrinsic to membrane0.0448731129004987



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><br>uberon_data<br><br>


Uber Anatomy
Ontology termp-valuen
regional part of nervous system2.15e-2594
nervous system2.15e-2594
neural plate1.43e-2486
presumptive neural plate1.43e-2486
adult organism2.37e-22115
neurectoderm2.69e-2290
central nervous system3.81e-2282
ectoderm-derived structure4.46e-19169
neural tube3.68e-1857
neural rod3.68e-1857
future spinal cord3.68e-1857
neural keel3.68e-1857
ectoderm7.58e-18173
presumptive ectoderm7.58e-18173
brain4.77e-1669
future brain4.77e-1669
pre-chordal neural plate1.00e-1561
regional part of brain1.65e-1559
anterior region of body2.17e-15129
craniocervical region2.17e-15129
head3.52e-14123
anterior neural tube2.87e-1242
regional part of forebrain6.43e-1241
forebrain6.43e-1241
future forebrain6.43e-1241
organ part1.09e-10219
multi-tissue structure1.58e-08347
cell layer3.02e-08312
embryo3.97e-08612
epithelium5.11e-08309
gray matter6.67e-0834
brain grey matter6.67e-0834
organ segment7.15e-0897
telencephalon9.64e-0834
regional part of telencephalon1.87e-0733
posterior neural tube2.37e-0715
chordal neural plate2.37e-0715
gastrointestinal system3.27e-0735
cerebral hemisphere3.59e-0732
segmental subdivision of hindbrain4.79e-0712
hindbrain4.79e-0712
presumptive hindbrain4.79e-0712
diencephalon8.12e-077
future diencephalon8.12e-077


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#promotersEnrichmentp-valueq-value
NANOG#79923211.69791139240510.01091164951956080.0402217119321431



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.