Coexpression cluster:C1884

Full id: C1884_small_parietal_temporal_duodenum_occipital_rhabdomyosarcoma_acute

Phase1 CAGE Peaks

Hg19::chr2:172949484..172949522,+	p1@DLX1
Hg19::chr2:172949532..172949541,+	p6@DLX1
Hg19::chr2:172950053..172950081,-	p@chr2:172950053..172950081 -
Hg19::chr2:172950227..172950249,+	p2@DLX1
Hg19::chr2:172967621..172967637,-	p1@DLX2

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	0.0329591072552472
GO:0003727	single-stranded RNA binding	0.0329591072552472
GO:0003700	transcription factor activity	0.0363204124571804
GO:0007275	multicellular organismal development	0.0380691710092592
GO:0003682	chromatin binding	0.0380691710092592
GO:0007420	brain development	0.0380691710092592
GO:0045944	positive regulation of transcription from RNA polymerase II promoter	0.0380691710092592
GO:0032502	developmental process	0.0380691710092592
GO:0006355	regulation of transcription, DNA-dependent	0.0380691710092592
GO:0006351	transcription, DNA-dependent	0.0380691710092592
GO:0032774	RNA biosynthetic process	0.0380691710092592
GO:0003677	DNA binding	0.0380691710092592
GO:0045449	regulation of transcription	0.0380691710092592
GO:0019219	regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process	0.0380691710092592
GO:0006350	transcription	0.0380691710092592
GO:0032501	multicellular organismal process	0.0380691710092592
GO:0010468	regulation of gene expression	0.0380691710092592
GO:0045893	positive regulation of transcription, DNA-dependent	0.0380691710092592
GO:0031323	regulation of cellular metabolic process	0.0380691710092592
GO:0007417	central nervous system development	0.0380691710092592
GO:0019222	regulation of metabolic process	0.0380691710092592
GO:0016070	RNA metabolic process	0.0380691710092592
GO:0045941	positive regulation of transcription	0.0395310782558458
GO:0045935	positive regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process	0.0395310782558458
GO:0031325	positive regulation of cellular metabolic process	0.0478758800868458
GO:0009893	positive regulation of metabolic process	0.0492946969816967

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>

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Cell Type

Ontology term	p-value	n
neural cell	6.13e-08	25
skin fibroblast	1.11e-07	23

Uber Anatomy

Ontology term	p-value	n
cerebral hemisphere	7.35e-16	32
regional part of telencephalon	1.83e-14	32
telencephalon	2.81e-14	34
cerebral cortex	1.21e-13	25
pallium	1.21e-13	25
regional part of cerebral cortex	1.88e-13	22
nervous system	4.39e-13	89
brain grey matter	5.35e-13	34
gray matter	5.35e-13	34
neocortex	2.05e-12	20
regional part of forebrain	1.47e-11	41
forebrain	1.47e-11	41
anterior neural tube	1.47e-11	41
future forebrain	1.47e-11	41
ectoderm-derived structure	2.34e-11	171
ectoderm	2.34e-11	171
presumptive ectoderm	2.34e-11	171
central nervous system	3.53e-11	81
brain	2.16e-10	68
future brain	2.16e-10	68
skin of body	3.03e-08	41
regional part of nervous system	3.29e-08	53
regional part of brain	3.29e-08	53
organ system subdivision	3.58e-08	223
neural tube	3.16e-07	56
neural rod	3.16e-07	56
future spinal cord	3.16e-07	56
neural keel	3.16e-07	56

Disease

Ontology term	p-value	n
disease of cellular proliferation	5.29e-20	239
cancer	8.74e-20	235
cell type cancer	6.71e-17	143
carcinoma	1.80e-08	106
sarcoma	2.01e-07	20
disease of anatomical entity	7.19e-07	39

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
CHD2#1106	5	10.3440228341169	8.43981772346334e-06	0.000230262832607311
CTBP2#1488	2	25.0868001357313	0.00246143859967838	0.0138515106369853
E2F1#1869	5	4.90738921487932	0.000351281809925646	0.00353138135978675
E2F4#1874	3	7.60083618917066	0.00435414736037571	0.0206504153385531
E2F6#1876	5	5.01715573169739	0.000314497859929779	0.00322999724586549
ETS1#2113	5	9.72876092220234	1.14685159850452e-05	0.000292279243768212
FOS#2353	3	5.39877318533664	0.0115389531727874	0.0421944865520377
HEY1#23462	5	4.04011104310571	0.000928885220517799	0.00674677262296811
HMGN3#9324	5	8.17854772335059	2.73180911341838e-05	0.000582378877314354
MAFK#7975	2	10.840293255132	0.0126368327733788	0.045689198158932
NFYA#4800	3	11.0553484198983	0.00147089290764443	0.00941290345474732
NFYB#4801	3	10.0558759521219	0.00193816560672546	0.0113885494430517
REST#5978	4	7.72002297290242	0.000528636377365057	0.00457379294305602
SUZ12#23512	2	20.0463123644252	0.00382407565415475	0.0188744157487839
TAL1#6886	2	11.9474466709761	0.010475778180992	0.0388081653463614
TBP#6908	5	3.70677068709639	0.00142875510672112	0.00919677994396594
TFAP2C#7022	3	6.48553716591613	0.00685895151794	0.0290628869515635
THAP1#55145	3	18.8214867617108	0.000308522194815001	0.00317549517140868
ZBTB33#10009	2	12.6658900119925	0.00935701605965159	0.035341846597011
ZBTB7A#51341	4	5.88152744630072	0.00152494756104223	0.0097159589023725

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.