Coexpression cluster:C1339

Full id: C1339_small_colon_signet_trachea_gall_adenocarcinoma_Renal

Phase1 CAGE Peaks

Hg19::chr11:2925001..2925048,-	p4@SLC22A18AS
Hg19::chr3:168991226..168991244,-	p@chr3:168991226..168991244 -
Hg19::chr6:31846768..31846780,-	p1@SLC44A4
Hg19::chr9:130877529..130877536,-	p@chr9:130877529..130877536 -
Hg19::chr9:130877564..130877577,-	p@chr9:130877564..130877577 -
Hg19::chr9:130877614..130877619,-	p@chr9:130877614..130877619 -

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

---

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

---

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>disease_data<br>

---

Cell Type

Ontology term	p-value	n
endodermal cell	2.05e-09	59
epithelial cell	4.03e-09	254
respiratory epithelial cell	8.57e-09	13
kidney tubule cell	1.05e-07	12
nephron tubule epithelial cell	1.05e-07	12
endo-epithelial cell	3.43e-07	43

Uber Anatomy

Ontology term	p-value	n
endoderm-derived structure	1.54e-23	169
endoderm	1.54e-23	169
presumptive endoderm	1.54e-23	169
subdivision of digestive tract	6.41e-23	129
endodermal part of digestive tract	6.41e-23	129
adult organism	7.42e-23	115
immaterial anatomical entity	2.54e-20	126
digestive system	3.38e-20	155
digestive tract	3.38e-20	155
primitive gut	3.38e-20	155
trunk region element	9.04e-19	107
mixed endoderm/mesoderm-derived structure	2.49e-18	130
endo-epithelium	1.04e-17	82
anatomical space	6.38e-15	104
subdivision of trunk	2.50e-14	113
foregut	2.98e-13	98
renal system	1.60e-12	45
urinary system structure	7.68e-12	44
abdomen element	1.08e-11	55
abdominal segment element	1.08e-11	55
multi-tissue structure	8.94e-11	347
intermediate mesoderm	1.57e-10	37
organ	1.89e-10	511
anatomical conduit	3.02e-10	241
duct	4.01e-10	26
mesenchyme	8.31e-10	238
entire embryonic mesenchyme	8.31e-10	238
abdominal segment of trunk	1.55e-09	61
abdomen	1.55e-09	61
thoracic cavity element	1.77e-09	34
thoracic cavity	1.77e-09	34
thoracic segment organ	5.20e-09	35
gut epithelium	5.54e-09	54
epithelial bud	5.61e-09	37
embryo	7.16e-09	612
respiratory tract	1.26e-08	53
cavitated compound organ	1.49e-08	32
epithelium of foregut-midgut junction	1.88e-08	25
anatomical boundary	1.88e-08	25
hepatobiliary system	1.88e-08	25
foregut-midgut junction	1.88e-08	25
septum transversum	1.88e-08	25
epithelial fold	2.59e-08	51
sac	3.37e-08	26
intraembryonic coelom	3.40e-08	21
urogenital ridge	3.74e-08	20
mesonephros	4.99e-08	18
pronephros	4.99e-08	18
nephrogenic cord	4.99e-08	18
pronephric mesoderm	4.99e-08	18
rostral part of nephrogenic cord	4.99e-08	18
presumptive pronephric mesoderm	4.99e-08	18
lung	7.06e-08	22
respiratory tube	7.06e-08	22
respiration organ	7.06e-08	22
pair of lungs	7.06e-08	22
lung primordium	7.06e-08	22
lung bud	7.06e-08	22
renal tubule	1.05e-07	12
nephron tubule	1.05e-07	12
nephron tubule epithelium	1.05e-07	12
respiratory system	1.05e-07	72
multi-cellular organism	1.25e-07	659
tube	1.41e-07	194
anatomical cluster	2.17e-07	286
epithelial sac	2.22e-07	25
gastrointestinal system	2.62e-07	35
hindgut	2.81e-07	19
digestive tract diverticulum	2.95e-07	23
anatomical cavity	2.96e-07	70
organ part	2.97e-07	219
excretory tube	3.37e-07	17
mesonephric epithelium	3.37e-07	17
mesonephric tubule	3.37e-07	17
nephric duct	3.37e-07	17
kidney epithelium	3.37e-07	17
renal duct	3.37e-07	17
mesonephric duct	3.37e-07	17
pronephric duct	3.37e-07	17
organism subdivision	4.70e-07	365
gland	4.80e-07	59
kidney	5.84e-07	27
kidney mesenchyme	5.84e-07	27
kidney rudiment	5.84e-07	27
kidney field	5.84e-07	27
epithelium	7.98e-07	309
embryonic structure	8.20e-07	605
developing anatomical structure	8.20e-07	605

Disease

Ontology term	p-value	n
carcinoma	7.77e-09	106

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

---

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

---

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

TF	#promoters	Enrichment	p-value	q-value
ATF3#467	3	11.2315872630044	0.00159345997118423	0.0100391727049834
BHLHE40#8553	3	22.4359067734887	0.000210319610478028	0.00244632696277032
FOSL2#2355	3	8.46510030228085	0.00359831563461509	0.0182199401999208
FOXA1#3169	3	5.54070987469273	0.0119217877786028	0.0433757043654241
FOXA2#3170	3	12.3152318763326	0.00121971244012452	0.0082046597664669
GATA1#2623	3	6.78015407190022	0.00676576398334856	0.0287461708090371
GATA2#2624	3	6.372465866777	0.00805882130874255	0.0318832956536012
HDAC2#3066	3	6.70781011831313	0.00697394002796266	0.0294855203052543
HNF4A#3172	3	11.5661451814768	0.00146348715008573	0.0093764268736767
HNF4G#3174	3	14.3767112632234	0.000776977293719738	0.00608981100028486
RXRA#6256	3	10.0373085695666	0.00220541911678922	0.0127051556698301
SMARCA4#6597	2	52.2553011026293	0.000599565921574195	0.00500944522266299
TCF12#6938	3	5.31723245109321	0.01336734573386	0.0472412094307865
TCF7L2#6934	3	5.38508828156867	0.0129048877993104	0.0464013487871712
USF2#7392	3	6.4960986925348	0.00763431981530056	0.0314537349477366

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

---

This analysis result is provided for C0 - C305 clusters.