Coexpression cluster:C2155

Full id: C2155_Alveolar_Mesenchymal_Renal_Hair_Smooth_Fibroblast_Bronchial

Phase1 CAGE Peaks

Hg19::chr11:65625643..65625659,-	p1@CFL1
Hg19::chr11:66036082..66036125,+	p1@RAB1B
Hg19::chr17:79829190..79829260,-	p1@ARHGDIA
Hg19::chr7:5570229..5570234,-	p1@ACTB

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

---

GO ID	GO name	FDR corrected p-value
GO:0007264	small GTPase mediated signal transduction	0.00561280380812922
GO:0006916	anti-apoptosis	0.00561280380812922
GO:0007266	Rho protein signal transduction	0.00561280380812922
GO:0043066	negative regulation of apoptosis	0.00561280380812922
GO:0043069	negative regulation of programmed cell death	0.00561280380812922
GO:0005856	cytoskeleton	0.00561280380812922
GO:0035267	NuA4 histone acetyltransferase complex	0.00898898000577465
GO:0007242	intracellular signaling cascade	0.00898898000577465
GO:0051674	localization of cell	0.00898898000577465
GO:0006928	cell motility	0.00898898000577465
GO:0043189	H4/H2A histone acetyltransferase complex	0.00898898000577465
GO:0007265	Ras protein signal transduction	0.00951756176553976
GO:0000123	histone acetyltransferase complex	0.0134669426856117
GO:0042981	regulation of apoptosis	0.0134669426856117
GO:0043067	regulation of programmed cell death	0.0134669426856117
GO:0005094	Rho GDP-dissociation inhibitor activity	0.0144325718247894
GO:0005737	cytoplasm	0.0144325718247894
GO:0043232	intracellular non-membrane-bound organelle	0.0144325718247894
GO:0043228	non-membrane-bound organelle	0.0144325718247894
GO:0031981	nuclear lumen	0.0144325718247894
GO:0007162	negative regulation of cell adhesion	0.017474096358452
GO:0005092	GDP-dissociation inhibitor activity	0.0179612957941699
GO:0006915	apoptosis	0.0186480408191993
GO:0012501	programmed cell death	0.0186480408191993
GO:0016265	death	0.0190659149538056
GO:0008219	cell death	0.0190659149538056
GO:0031974	membrane-enclosed lumen	0.0201966507970214
GO:0043233	organelle lumen	0.0201966507970214
GO:0005515	protein binding	0.0204183646101707
GO:0016363	nuclear matrix	0.0220909551404238
GO:0044428	nuclear part	0.0236262360421581
GO:0048523	negative regulation of cellular process	0.0240742996074799
GO:0048519	negative regulation of biological process	0.0251846368767134
GO:0048468	cell development	0.0265674164750137
GO:0030155	regulation of cell adhesion	0.0265674164750137
GO:0051179	localization	0.0275572213624321
GO:0005200	structural constituent of cytoskeleton	0.0310461000661591
GO:0043229	intracellular organelle	0.0310461000661591
GO:0043226	organelle	0.0310461000661591
GO:0007165	signal transduction	0.0368719025886468
GO:0007154	cell communication	0.0422377920115624
GO:0050954	sensory perception of mechanical stimulus	0.0422377920115624
GO:0007605	sensory perception of sound	0.0422377920115624
GO:0048869	cellular developmental process	0.0422377920115624
GO:0030154	cell differentiation	0.0422377920115624
GO:0050794	regulation of cellular process	0.0431562287345324

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>

---

Cell Type

Ontology term	p-value	n
somatic cell	8.80e-48	588
animal cell	7.68e-36	679
eukaryotic cell	7.68e-36	679
native cell	1.17e-29	722
mesodermal cell	1.92e-24	121
embryonic cell	6.29e-20	250
somatic stem cell	2.09e-17	433
contractile cell	4.24e-17	59
multi fate stem cell	6.71e-17	427
smooth muscle cell	9.99e-17	43
smooth muscle myoblast	9.99e-17	43
stem cell	8.98e-16	441
muscle precursor cell	9.96e-16	58
myoblast	9.96e-16	58
multi-potent skeletal muscle stem cell	9.96e-16	58
muscle cell	3.26e-15	55
vascular associated smooth muscle cell	4.60e-15	32
electrically responsive cell	2.34e-13	61
electrically active cell	2.34e-13	61
endothelial cell	1.28e-12	36
non-terminally differentiated cell	2.75e-12	106
meso-epithelial cell	5.74e-11	45
endothelial cell of vascular tree	1.80e-09	24
lining cell	8.04e-09	58
barrier cell	8.04e-09	58
blood vessel endothelial cell	1.13e-08	18
embryonic blood vessel endothelial progenitor cell	1.13e-08	18
fibroblast	1.37e-08	76
epithelial cell of nephron	2.14e-08	15
kidney cortical cell	4.04e-07	12
renal cortical epithelial cell	4.04e-07	12

Uber Anatomy

Ontology term	p-value	n
vasculature	2.61e-23	78
vascular system	2.61e-23	78
vessel	2.42e-20	68
cardiovascular system	5.12e-19	109
epithelial tube open at both ends	8.53e-19	59
blood vessel	8.53e-19	59
blood vasculature	8.53e-19	59
vascular cord	8.53e-19	59
mesoderm	2.77e-18	315
mesoderm-derived structure	2.77e-18	315
presumptive mesoderm	2.77e-18	315
splanchnic layer of lateral plate mesoderm	2.88e-18	83
artery	1.08e-17	42
arterial blood vessel	1.08e-17	42
arterial system	1.08e-17	42
epithelial vesicle	1.24e-17	78
circulatory system	1.75e-17	112
lateral plate mesoderm	1.82e-17	203
epithelial tube	4.86e-16	117
multilaminar epithelium	1.13e-14	83
somite	2.35e-14	71
presomitic mesoderm	2.35e-14	71
presumptive segmental plate	2.35e-14	71
dermomyotome	2.35e-14	71
trunk paraxial mesoderm	2.35e-14	71
unilaminar epithelium	7.77e-14	148
paraxial mesoderm	8.92e-14	72
presumptive paraxial mesoderm	8.92e-14	72
dense mesenchyme tissue	9.75e-14	73
systemic artery	9.12e-13	33
systemic arterial system	9.12e-13	33
skeletal muscle tissue	1.07e-12	62
striated muscle tissue	1.07e-12	62
myotome	1.07e-12	62
muscle tissue	2.00e-12	64
musculature	2.00e-12	64
musculature of body	2.00e-12	64
musculoskeletal system	6.93e-12	167
trunk mesenchyme	7.51e-10	122
blood vessel endothelium	1.13e-08	18
endothelium	1.13e-08	18
cardiovascular system endothelium	1.13e-08	18
nephron epithelium	2.14e-08	15
renal tubule	2.14e-08	15
nephron tubule	2.14e-08	15
nephron	2.14e-08	15
uriniferous tubule	2.14e-08	15
nephrogenic mesenchyme	2.14e-08	15
simple squamous epithelium	2.18e-08	22
excretory tube	1.83e-07	16
kidney epithelium	1.83e-07	16
aorta	1.93e-07	21
aortic system	1.93e-07	21
mesenchyme	1.93e-07	160
entire embryonic mesenchyme	1.93e-07	160
parenchyma	2.13e-07	15
trunk	3.97e-07	199
cortex of kidney	4.04e-07	12
renal parenchyma	4.04e-07	12
squamous epithelium	6.64e-07	25
organism subdivision	8.97e-07	264

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
BCLAF1#9774	2	10.8263238050609	0.0120220381643258	0.0436431451855824
CCNT2#905	4	6.33620157696263	0.000620310058721564	0.00511362871756425
CHD2#1106	3	7.75801712558764	0.00335152246453634	0.0172896841034187
E2F1#1869	4	4.90738921487932	0.00172402235736179	0.0106277399941275
E2F4#1874	3	9.50104523646333	0.00185075103472827	0.0109240752410978
ELF1#1997	4	4.25809795880754	0.00304152556578124	0.0160585353907602
ETS1#2113	4	9.72876092220234	0.000111595531741814	0.0015434943371187
GABPB1#2553	3	5.30076287713663	0.0101267882423427	0.0378387763315099
GTF2B#2959	2	15.9719149671621	0.00563658572353722	0.0254663166802433
GTF2F1#2962	3	9.55474565756824	0.00182036231930478	0.0108968200989208
HEY1#23462	4	4.04011104310571	0.0037530463691798	0.0185597996946243
IRF1#3659	3	5.72787281517293	0.00809711479033333	0.0319875391151652
MYC#4609	4	5.2222818716094	0.00134430939527274	0.0088573799087054
NRF1#4899	3	9.15770958578318	0.00206195379173342	0.0119591487785221
PAX5#5079	4	6.66956553117783	0.000505277416948326	0.00443190292673773
PBX3#5090	2	10.9572563433721	0.0117453018068803	0.0428201059590455
RDBP#7936	2	76.8192019950125	0.000251781005061704	0.00271062327467677
SP1#6667	4	5.6983813781409	0.000948260606533398	0.00683049792990838
TAF1#6872	4	3.34304628574529	0.00800566489870165	0.032131879495619
TBP#6908	4	3.70677068709639	0.00529637781478435	0.0243538239157426
YY1#7528	4	4.91117074985386	0.0017187183805544	0.0106636505047657
ZBTB7A#51341	3	5.51393198090692	0.00903835282108109	0.0342261251008299
ZNF143#7702	3	10.1256574141709	0.00153486161068818	0.00976126000235436

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.