Coexpression cluster:C398

Full id: C398_neuroepithelioma_neuroectodermal_carcinoid_neuroblastoma_spinal_brain_synovial

Phase1 CAGE Peaks

Hg19::chr10:29717478..29717509,-	p@chr10:29717478..29717509 -
Hg19::chr11:121097296..121097326,+	p@chr11:121097296..121097326 +
Hg19::chr11:68611721..68611749,-	p@chr11:68611721..68611749 -
Hg19::chr13:100953150..100953169,+	p@chr13:100953150..100953169 +
Hg19::chr18:61034757..61034768,-	p5@KDSR
Hg19::chr19:31840130..31840160,-	p2@TSHZ3
Hg19::chr19:49915463..49915468,+	p@chr19:49915463..49915468 +
Hg19::chr19:49950830..49950836,-	p@chr19:49950830..49950836 -
Hg19::chr1:18958059..18958081,+	p6@PAX7
Hg19::chr1:22696471..22696505,-	p@chr1:22696471..22696505 -
Hg19::chr1:37499838..37499850,-	p3@GRIK3
Hg19::chr20:21494684..21494708,-	p1@NKX2-2
Hg19::chr2:162137741..162137745,+	p@chr2:162137741..162137745 +
Hg19::chr5:147011027..147011032,-	p@chr5:147011027..147011032 -
Hg19::chr5:147011039..147011055,-	p@chr5:147011039..147011055 -
Hg19::chr5:147011082..147011102,-	p@chr5:147011082..147011102 -
Hg19::chr6:50786057..50786069,+	p9@TFAP2B
Hg19::chr7:121943677..121943690,+	p1@LOC154860
Hg19::chr8:12808791..12808798,+	p28@KIAA1456
Hg19::chr8:12809246..12809265,+	p6@KIAA1456
Hg19::chr8:1922789..1922822,-	p1@ENST00000521498
Hg19::chr8:37554297..37554313,+	p@chr8:37554297..37554313 +
Hg19::chr8:37824101..37824132,-	p1@ADRB3
Hg19::chr8:37824176..37824185,-	p4@ADRB3
Hg19::chr8:37824442..37824447,-	p9@ADRB3
Hg19::chrX:51361761..51361770,-	p2@ENST00000417339

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

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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

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GO ID	GO name	FDR corrected p-value
GO:0043565	sequence-specific DNA binding	0.00116055591153121
GO:0003700	transcription factor activity	0.00493005322372769
GO:0015052	beta3-adrenergic receptor activity	0.00825679971741433
GO:0021529	spinal cord oligodendrocyte cell differentiation	0.00825679971741433
GO:0045944	positive regulation of transcription from RNA polymerase II promoter	0.00875366199758637
GO:0007275	multicellular organismal development	0.00875366199758637
GO:0051380	norepinephrine binding	0.00880530874965199
GO:0048522	positive regulation of cellular process	0.00880530874965199
GO:0045817	positive regulation of global transcription from RNA polymerase II promoter	0.00880530874965199
GO:0048518	positive regulation of biological process	0.00880530874965199
GO:0045893	positive regulation of transcription, DNA-dependent	0.00880530874965199
GO:0050794	regulation of cellular process	0.00880530874965199
GO:0006358	regulation of global transcription from RNA polymerase II promoter	0.00880530874965199
GO:0048665	neuron fate specification	0.00880530874965199
GO:0004939	beta-adrenergic receptor activity	0.00880530874965199
GO:0050789	regulation of biological process	0.00939786051904262
GO:0045941	positive regulation of transcription	0.00939786051904262
GO:0045935	positive regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process	0.00939786051904262
GO:0021515	cell differentiation in spinal cord	0.00939786051904262
GO:0031018	endocrine pancreas development	0.00939786051904262
GO:0032502	developmental process	0.00939786051904262
GO:0006355	regulation of transcription, DNA-dependent	0.00939786051904262
GO:0006351	transcription, DNA-dependent	0.00939786051904262
GO:0032774	RNA biosynthetic process	0.00939786051904262
GO:0014003	oligodendrocyte development	0.00939786051904262
GO:0015277	kainate selective glutamate receptor activity	0.00939786051904262
GO:0043410	positive regulation of MAPKKK cascade	0.00939786051904262
GO:0003677	DNA binding	0.00939786051904262
GO:0065007	biological regulation	0.00939786051904262
GO:0045449	regulation of transcription	0.00939786051904262
GO:0031325	positive regulation of cellular metabolic process	0.00939786051904262
GO:0046983	protein dimerization activity	0.00939786051904262
GO:0031016	pancreas development	0.00939786051904262
GO:0021510	spinal cord development	0.00939786051904262
GO:0019219	regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process	0.00939786051904262
GO:0009893	positive regulation of metabolic process	0.00939786051904262
GO:0048709	oligodendrocyte differentiation	0.00939786051904262
GO:0006350	transcription	0.00939786051904262
GO:0032501	multicellular organismal process	0.00939786051904262
GO:0010468	regulation of gene expression	0.00939786051904262
GO:0031323	regulation of cellular metabolic process	0.00997615312025724
GO:0006357	regulation of transcription from RNA polymerase II promoter	0.00997615312025724
GO:0021782	glial cell development	0.00997615312025724
GO:0048663	neuron fate commitment	0.0104193052793127
GO:0043408	regulation of MAPKKK cascade	0.0104193052793127
GO:0001708	cell fate specification	0.0104193052793127
GO:0004935	adrenoceptor activity	0.0104193052793127
GO:0019222	regulation of metabolic process	0.0104193052793127
GO:0016070	RNA metabolic process	0.0104193052793127
GO:0048856	anatomical structure development	0.0134138326126212
GO:0007215	glutamate signaling pathway	0.0135794335084424
GO:0007190	adenylate cyclase activation	0.0145845525423315
GO:0045762	positive regulation of adenylate cyclase activity	0.0153058715131997
GO:0031281	positive regulation of cyclase activity	0.0153058715131997
GO:0051349	positive regulation of lyase activity	0.0153058715131997
GO:0042562	hormone binding	0.0153058715131997
GO:0006366	transcription from RNA polymerase II promoter	0.0164796078645652
GO:0010001	glial cell differentiation	0.0164796078645652
GO:0035270	endocrine system development	0.0184293903317657
GO:0007399	nervous system development	0.0190433330980239
GO:0001822	kidney development	0.0190433330980239
GO:0042063	gliogenesis	0.0190433330980239
GO:0004970	ionotropic glutamate receptor activity	0.0190433330980239
GO:0007189	G-protein signaling, adenylate cyclase activating pathway	0.0190433330980239
GO:0005234	extracellular-glutamate-gated ion channel activity	0.0197609833425238
GO:0001655	urogenital system development	0.0199591205669183
GO:0045761	regulation of adenylate cyclase activity	0.0200429495925894
GO:0031279	regulation of cyclase activity	0.0200429495925894
GO:0051339	regulation of lyase activity	0.0200429495925894
GO:0010467	gene expression	0.0202245390867495
GO:0043176	amine binding	0.0204028976861871
GO:0045597	positive regulation of cell differentiation	0.0214865664443413
GO:0006112	energy reserve metabolic process	0.0247581429427409
GO:0006139	nucleobase, nucleoside, nucleotide and nucleic acid metabolic process	0.0247581429427409
GO:0005634	nucleus	0.0278121819963144
GO:0008227	amine receptor activity	0.0289750242419746
GO:0051094	positive regulation of developmental process	0.0290234365138574
GO:0045165	cell fate commitment	0.0299087690292912
GO:0005231	excitatory extracellular ligand-gated ion channel activity	0.029943891968136
GO:0003676	nucleic acid binding	0.0314626919076973
GO:0007188	G-protein signaling, coupled to cAMP nucleotide second messenger	0.0340418938006602
GO:0019933	cAMP-mediated signaling	0.0348107586320543
GO:0048513	organ development	0.0348107586320543
GO:0008066	glutamate receptor activity	0.0364148977951553
GO:0043170	macromolecule metabolic process	0.0364148977951553
GO:0048468	cell development	0.0394914210203462
GO:0043235	receptor complex	0.0414249758746352
GO:0007187	G-protein signaling, coupled to cyclic nucleotide second messenger	0.0429729248948776
GO:0015980	energy derivation by oxidation of organic compounds	0.0429729248948776
GO:0005887	integral to plasma membrane	0.0429729248948776
GO:0031226	intrinsic to plasma membrane	0.0434087731362005
GO:0019935	cyclic-nucleotide-mediated signaling	0.0434087731362005
GO:0005230	extracellular ligand-gated ion channel activity	0.0460793535836692
GO:0007420	brain development	0.0483447649736714
GO:0045595	regulation of cell differentiation	0.0493591462687715
GO:0042165	neurotransmitter binding	0.0493591462687715

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>disease_data<br>

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Uber Anatomy

Ontology term	p-value	n
sympathetic nervous system	1.28e-23	5
autonomic nervous system	1.28e-23	5
neural tissue	1.15e-15	2
peripheral nervous system	1.31e-13	8

Disease

Ontology term	p-value	n
neuroectodermal tumor	1.54e-70	10
germ cell and embryonal cancer	2.03e-32	22
germ cell cancer	2.03e-32	22
neuroendocrine tumor	7.13e-20	6
peripheral nerve sheath neoplasm	1.15e-15	2
neurofibroma	1.15e-15	2
peripheral nervous system neoplasm	6.73e-11	3

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

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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

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(#promoters = Number of promoters in this coexpression cluster that have ChIP signal of the TF)

TF	#promoters	Enrichment	p-value	q-value
MAFF#23764	3	6.49792574883983	0.0107214750985517	0.0395751798196663

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

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This analysis result is provided for C0 - C305 clusters.