Coexpression cluster:C1694

Full id: C1694_squamous_Prostate_Sebocyte_Gingival_Mallassezderived_clear_Urothelial

Phase1 CAGE Peaks

Hg19::chr12:95510642..95510668,-	p@chr12:95510642..95510668 -
Hg19::chr12:95510716..95510730,-	p3@FGD6
Hg19::chr12:95510743..95510753,-	p8@FGD6
Hg19::chr15:71389222..71389244,+	p3@THSD4
Hg19::chr9:114908292..114908313,-	p13@SUSD1

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:0032488	Cdc42 protein signal transduction	0.0219815772092478
GO:0043088	regulation of Cdc42 GTPase activity	0.0219815772092478
GO:0032489	regulation of Cdc42 protein signal transduction	0.0219815772092478
GO:0032319	regulation of Rho GTPase activity	0.0219815772092478
GO:0046847	filopodium formation	0.028616528426325
GO:0030035	microspike biogenesis	0.028616528426325
GO:0030027	lamellipodium	0.028616528426325
GO:0022603	regulation of anatomical structure morphogenesis	0.028616528426325
GO:0008360	regulation of cell shape	0.028616528426325
GO:0022604	regulation of cell morphogenesis	0.028616528426325
GO:0001726	ruffle	0.028616528426325
GO:0030031	cell projection biogenesis	0.0304958262052178
GO:0031252	leading edge	0.0405097317596002
GO:0031267	small GTPase binding	0.0443909858229263
GO:0051020	GTPase binding	0.0472640384308379

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
epithelial cell	4.25e-28	254
endo-epithelial cell	1.32e-17	43
respiratory epithelial cell	3.46e-14	13
endodermal cell	2.21e-11	59
embryonic cell	6.46e-11	248
squamous epithelial cell	3.66e-10	62
epithelial cell of tracheobronchial tree	4.63e-10	9
epithelial cell of lower respiratory tract	4.63e-10	9
general ecto-epithelial cell	1.69e-08	13
ecto-epithelial cell	2.68e-07	33

Uber Anatomy

Ontology term	p-value	n
epithelial bud	1.32e-13	37
epithelial fold	6.75e-12	51
reproductive structure	6.89e-09	59
reproductive system	6.89e-09	59
prostate gland	1.58e-08	11
male accessory sex gland	1.58e-08	11
embryonic cloacal epithelium	1.58e-08	11
epithelium of hindgut	1.58e-08	11
urogenital sinus epithelium	1.58e-08	11
prostate bud	1.58e-08	11
prostate field	1.58e-08	11
endo-epithelium	1.80e-08	82
urinary system structure	4.39e-08	44
tracheobronchial tree	8.91e-08	14
lower respiratory tract	8.91e-08	14
renal system	9.65e-08	45
thoracic segment of trunk	9.68e-08	52
sex gland	1.42e-07	12
male reproductive gland	1.42e-07	12
cloaca	1.45e-07	14
anal region	1.45e-07	14
embryonic cloaca	1.45e-07	14
terminal part of digestive tract	1.45e-07	14
primitive urogenital sinus	1.45e-07	14
proctodeum	1.45e-07	14
male organism	1.55e-07	22
male reproductive system	1.55e-07	22
genitourinary system	7.55e-07	15
urothelium	9.75e-07	5

Disease

Ontology term	p-value	n
carcinoma	4.32e-12	106
squamous cell carcinoma	1.04e-11	14
cell type cancer	1.73e-09	143

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
MEF2A#4205	3	11.2459385457864	0.00139936678741195	0.00910185388992442
RAD21#5885	3	6.2130203372738	0.00775105506881164	0.0318894008403238
RFX5#5993	3	7.22874649631706	0.0050291827895866	0.0234651010258057
STAT3#6774	4	8.41557199772339	0.000377152721159863	0.00374175482523178

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.