Coexpression cluster:C3291

Full id: C3291_large_Fibroblast_Mesenchymal_anaplastic_Renal_cervical_Pericytes

Phase1 CAGE Peaks

Hg19::chr12:53343573..53343584,-	p6@KRT8
Hg19::chr12:53343602..53343631,-	p3@KRT8
Hg19::chr12:53343633..53343696,-	p2@KRT8

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>disease_data<br>

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Cell Type

Ontology term	p-value	n
epithelial cell	1.02e-34	254
embryonic cell	4.44e-19	248
mesodermal cell	2.68e-17	119
animal cell	4.11e-12	679
eukaryotic cell	4.11e-12	679
squamous epithelial cell	3.07e-11	62
contractile cell	1.85e-10	59
endothelial cell of vascular tree	3.85e-10	24
lining cell	4.29e-10	57
barrier cell	4.29e-10	57
endothelial cell	8.78e-10	35
blood vessel endothelial cell	7.05e-09	18
embryonic blood vessel endothelial progenitor cell	7.05e-09	18
muscle cell	1.85e-08	54
smooth muscle cell	2.38e-08	42
smooth muscle myoblast	2.38e-08	42
meso-epithelial cell	3.83e-08	44
kidney cell	2.51e-07	18
kidney epithelial cell	2.51e-07	18
muscle precursor cell	3.10e-07	57
myoblast	3.10e-07	57
multi-potent skeletal muscle stem cell	3.10e-07	57
electrically responsive cell	5.15e-07	60
electrically active cell	5.15e-07	60
endodermal cell	5.65e-07	59
non-terminally differentiated cell	6.10e-07	180

Uber Anatomy

Ontology term	p-value	n
epithelial tube	5.10e-23	118
unilaminar epithelium	3.30e-20	138
mesenchyme	2.29e-18	238
entire embryonic mesenchyme	2.29e-18	238
primordium	1.47e-17	168
vasculature	2.37e-17	79
vascular system	2.37e-17	79
trunk	4.70e-16	216
immaterial anatomical entity	5.59e-15	126
multi-tissue structure	8.95e-15	347
endoderm-derived structure	3.15e-14	169
endoderm	3.15e-14	169
presumptive endoderm	3.15e-14	169
splanchnic layer of lateral plate mesoderm	1.81e-13	84
anatomical cluster	6.05e-13	286
vessel	7.93e-13	69
trunk region element	1.22e-12	107
cell layer	1.33e-12	312
cardiovascular system	1.83e-12	110
epithelium	5.78e-12	309
trunk mesenchyme	6.98e-12	143
subdivision of digestive tract	1.13e-11	129
endodermal part of digestive tract	1.13e-11	129
digestive system	1.32e-11	155
digestive tract	1.32e-11	155
primitive gut	1.32e-11	155
circulatory system	2.08e-11	113
blood vessel	3.60e-11	60
epithelial tube open at both ends	3.60e-11	60
blood vasculature	3.60e-11	60
vascular cord	3.60e-11	60
subdivision of trunk	1.12e-10	113
anatomical space	1.30e-10	104
mixed endoderm/mesoderm-derived structure	2.02e-10	130
anatomical conduit	2.16e-10	241
endo-epithelium	2.23e-10	82
simple squamous epithelium	5.82e-10	22
foregut	8.03e-10	98
mesoderm	1.93e-09	448
mesoderm-derived structure	1.93e-09	448
presumptive mesoderm	1.93e-09	448
urinary system structure	6.96e-09	44
endothelium	7.05e-09	18
blood vessel endothelium	7.05e-09	18
cardiovascular system endothelium	7.05e-09	18
organism subdivision	1.07e-08	365
renal system	1.12e-08	45
abdomen element	1.48e-08	55
abdominal segment element	1.48e-08	55
multi-cellular organism	2.52e-08	659
duct	3.60e-08	26
abdominal segment of trunk	4.19e-08	61
abdomen	4.19e-08	61
squamous epithelium	3.16e-07	25
anatomical cavity	3.42e-07	70
artery	3.45e-07	42
arterial blood vessel	3.45e-07	42
arterial system	3.45e-07	42
tube	3.94e-07	194
gut epithelium	5.40e-07	54
anatomical system	6.08e-07	625
body cavity precursor	7.14e-07	63
organ segment	9.57e-07	97

Disease

Ontology term	p-value	n
carcinoma	2.90e-11	106
cell type cancer	1.68e-09	143
disease of cellular proliferation	1.06e-07	239
cancer	1.46e-07	235

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
CCNT2#905	3	6.33620157696263	0.00393075003576489	0.0189443287025957
CHD2#1106	3	10.3440228341169	0.000903370110274688	0.00658986316595503
CTCF#10664	3	5.36025637307503	0.006492509252767	0.0278663203817751
ELF1#1997	3	4.25809795880754	0.0129517987505461	0.0460609837473451
ELK4#2005	3	16.235681658468	0.000233604395574599	0.00255229725592798
EP300#2033	3	6.7739417262232	0.00321688050010379	0.0167031809958407
ETS1#2113	3	9.72876092220234	0.00108584009258484	0.0076064158179266
FOS#2353	3	8.9979553088944	0.00137249927241713	0.00895386666949669
FOSL1#8061	3	39.713579716373	1.59554825631833e-05	0.000370387784711337
FOSL2#2355	3	16.9302006045617	0.000206016205317162	0.00242489873403799
FOXA1#3169	3	11.0814197493855	0.00073475527569867	0.0057993580893813
FOXA2#3170	3	24.6304637526652	6.68983856509345e-05	0.00107077402283494
GABPB1#2553	3	7.06768383618217	0.00283221282541742	0.0153722833007884
GATA2#2624	3	12.744931733554	0.000482952770428379	0.00436248956848032
GTF2F1#2962	3	12.7396608767577	0.000483552504743859	0.00432971022316049
HDAC2#3066	3	13.4156202366263	0.000414076139985721	0.00390163280259552
HNF4A#3172	3	23.1322903629537	8.07584663437677e-05	0.00122556429329799
IRF1#3659	3	7.6371637535639	0.00224469274729724	0.0127749695294522
JUN#3725	3	12.5128291923363	0.000510331399272625	0.00443341382537296
JUNB#3726	3	30.6106326598211	3.4847716247536e-05	0.000679637840742561
JUND#3727	3	6.99466394187103	0.00292184504273499	0.0156313172020387
MAFK#7975	3	27.1007331378299	5.02195559325033e-05	0.00085630697176077
MAX#4149	3	6.45255550900712	0.00372191383426551	0.0186022664116029
MXI1#4601	3	9.9615716287593	0.00101147054125902	0.0071891228976828
MYC#4609	3	5.2222818716094	0.00702084375574015	0.0293523037911111
RAD21#5885	3	10.3550338954563	0.000900491207356542	0.00662438551842712
REST#5978	3	9.65002871612802	0.00111263624711459	0.00765901773084634
RFX5#5993	3	12.0479108271951	0.000571724605031258	0.00483484583197243
RXRA#6256	3	20.0746171391333	0.000123573034843222	0.00164909841374793
SMARCA4#6597	3	156.765903307888	2.58908533335753e-07	1.33928421560439e-05
SMARCB1#6598	3	18.2527157811574	0.00016439776067989	0.00202662154481197
SMC3#9126	3	15.0449328449328	0.000293582542037187	0.00308372393722435
SP1#6667	3	5.6983813781409	0.00540396270171217	0.0245683641217185
SPI1#6688	3	8.20432350852273	0.00181059318941052	0.0108895215726372
TAF7#6879	3	11.4330694049239	0.000669018198194583	0.00541262619887242
TFAP2A#7020	3	16.518634373045	0.000221803388076634	0.00247594314315258
TFAP2C#7022	3	10.8092286098602	0.000791674657575313	0.00613821154881278
TRIM28#10155	3	18.5905250452625	0.000155596929725528	0.00196640703577013
YY1#7528	3	4.91117074985386	0.00844145534180826	0.0328324577105286
ZNF263#10127	3	8.22184163701068	0.00179904392556587	0.0109035717584827

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.