Coexpression cluster:C4865

Full id: C4865_Mast_Neutrophils_Dendritic_lymphoma_CD14_CD4_tridermal

Phase1 CAGE Peaks

Hg19::chrX:155110970..155111047,+	p1@VAMP7
Hg19::chrX:1710484..1710537,+	p1@AKAP17A
Hg19::chrX:1710540..1710558,+	p2@AKAP17A

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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No GOStat results

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>

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Cell Type

Ontology term	p-value	n
endocrine cell	7.06e-07	9

Uber Anatomy

Ontology term	p-value	n
female organism	3.12e-11	41
female reproductive organ	6.04e-10	37
female reproductive system	6.04e-10	37
neural tube	1.98e-07	56
neural rod	1.98e-07	56
future spinal cord	1.98e-07	56
neural keel	1.98e-07	56
internal female genitalia	5.11e-07	22
embryonic uterus	6.86e-07	22

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
ATF3#467	2	14.9754496840058	0.00576829454079388	0.0259703803744437
BRCA1#672	2	13.4561537621492	0.00711980771608456	0.0296450025140595
CCNT2#905	3	6.33620157696263	0.00393075003576489	0.019149342428643
CTCFL#140690	2	13.1643162393162	0.00743336703699601	0.0306972487139908
E2F1#1869	3	4.90738921487932	0.00846098534723939	0.0328326093735727
E2F6#1876	3	5.01715573169739	0.0079176980688633	0.0324905295907435
EBF1#1879	3	8.906466846569	0.0014152328356098	0.009198749198298
EGR1#1958	3	4.98817909481014	0.00805648813738344	0.0322998681220802
ELF1#1997	3	4.25809795880754	0.0129517987505461	0.0465507918545076
ELK4#2005	3	16.235681658468	0.000233604395574599	0.0025659875335944
ETS1#2113	3	9.72876092220234	0.00108584009258484	0.00766036567343068
FOS#2353	3	8.9979553088944	0.00137249927241713	0.00902887701637519
GABPB1#2553	3	7.06768383618217	0.00283221282541742	0.0154979291246867
IRF1#3659	3	7.6371637535639	0.00224469274729724	0.012889458205134
NR2C2#7182	2	21.7430739368272	0.00276220797549601	0.0151426297177485
SIN3A#25942	3	5.40888472681514	0.00631896197799152	0.027866990542161
SIX5#147912	3	17.086715355459	0.000200406054632501	0.00240494173730481
SP1#6667	3	5.6983813781409	0.00540396270171217	0.0248233840870917
SP2#6668	2	17.4356869958964	0.00427356848176974	0.0203291832688476
SREBF1#6720	2	31.3372329603255	0.0013381626513618	0.00887962190390592
THAP1#55145	3	31.3691446028513	3.23800758564397e-05	0.000649585620893336
USF1#7391	3	6.36149927720796	0.0038840405729056	0.0191432427274039
YY1#7528	3	4.91117074985386	0.00844145534180826	0.0331634499865751

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.