Coexpression cluster:C1334

Full id: C1334_Alveolar_gall_Renal_nasal_Prostate_signet_colon

Phase1 CAGE Peaks

Hg19::chr11:130029635..130029654,+	p3@ST14
Hg19::chr11:130029668..130029690,+	p1@ST14
Hg19::chr15:41136360..41136365,+	p8@SPINT1
Hg19::chr15:41136369..41136420,+	p3@SPINT1
Hg19::chr17:7165787..7165807,-	p1@CLDN7
Hg19::chr19:6464243..6464325,+	p1@CRB3

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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p.value	FDR	nGenes	nPathway	Name
0.000128481434866115	0.0406643741351255	2	133	Tight junction (KEGG):04530
6.82636944046713e-05	0.0406643741351255	2	97	Cell junction organization (Reactome):REACT_20676

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:0005923	tight junction	0.00109318546569462
GO:0043296	apical junction complex	0.00109318546569462
GO:0016327	apicolateral plasma membrane	0.00109318546569462
GO:0005911	intercellular junction	0.00222815365861779
GO:0001892	embryonic placenta development	0.00546259906066675
GO:0030054	cell junction	0.00907390042342841
GO:0044459	plasma membrane part	0.00956535539574324
GO:0001890	placenta development	0.0127967491689525
GO:0016338	calcium-independent cell-cell adhesion	0.0166780129869154
GO:0001763	morphogenesis of a branching structure	0.0218233954500037
GO:0005886	plasma membrane	0.0262091988801033
GO:0019897	extrinsic to plasma membrane	0.0262091988801033
GO:0001701	in utero embryonic development	0.0262091988801033
GO:0016324	apical plasma membrane	0.0330721699696492
GO:0045177	apical part of cell	0.0380048061144456
GO:0009792	embryonic development ending in birth or egg hatching	0.0380048061144456
GO:0043009	chordate embryonic development	0.0380048061144456
GO:0019898	extrinsic to membrane	0.0404059085111664

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	3.56e-30	253
endo-epithelial cell	8.35e-21	42
endodermal cell	3.50e-18	58
respiratory epithelial cell	2.38e-10	13
epithelial cell of alimentary canal	6.73e-10	20
general ecto-epithelial cell	4.15e-08	14
kidney tubule cell	6.93e-08	10
nephron tubule epithelial cell	6.93e-08	10
epithelial cell of tracheobronchial tree	3.14e-07	9
epithelial cell of lower respiratory tract	3.14e-07	9
germ line cell	6.71e-07	7
germ cell	6.71e-07	7

Uber Anatomy

Ontology term	p-value	n
endoderm-derived structure	6.11e-25	160
endoderm	6.11e-25	160
presumptive endoderm	6.11e-25	160
digestive system	1.92e-19	145
digestive tract	1.92e-19	145
primitive gut	1.92e-19	145
subdivision of digestive tract	2.22e-18	118
respiratory system	1.11e-12	74
anatomical space	1.44e-12	95
immaterial anatomical entity	2.01e-12	117
endo-epithelium	5.67e-12	82
foregut	2.29e-11	87
renal system	2.70e-11	48
trunk region element	3.00e-11	101
urinary system structure	7.70e-11	47
epithelial bud	1.15e-09	37
respiratory tract	5.16e-09	54
orifice	5.87e-09	36
organ	2.59e-08	503
thoracic cavity element	2.61e-08	34
thoracic cavity	2.61e-08	34
reproductive structure	2.85e-08	59
reproductive system	2.85e-08	59
subdivision of trunk	3.35e-08	112
nephron tubule epithelium	6.93e-08	10
thoracic segment organ	7.17e-08	35
epithelial fold	9.77e-08	47
male organism	3.03e-07	22
male reproductive system	3.03e-07	22
organism subdivision	3.57e-07	264
reproductive organ	5.88e-07	48

Disease

Ontology term	p-value	n
carcinoma	1.63e-17	106
squamous cell carcinoma	1.67e-10	14
cell type cancer	1.73e-10	143
adenocarcinoma	9.09e-08	25

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
E2F1#1869	5	4.08949101239944	0.00174981759776199	0.0107556471127458
POLR2A#5430	6	2.14745317655807	0.0101957067681878	0.0379943416528497
SUZ12#23512	2	16.7052603036876	0.00566023468207957	0.0255576848232472
TAF1#6872	6	3.34304628574529	0.000716247428463562	0.00572641546209186
ZEB1#6935	6	16.8884320175439	4.30431371220266e-08	2.827284401187e-06

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.