Coexpression cluster:C3189

Full id: C3189_Renal_Alveolar_Astrocyte_Hepatic_Smooth_Mesenchymal_Preadipocyte

Phase1 CAGE Peaks

Hg19::chr11:65625678..65625687,-	p2@CFL1
Hg19::chr5:176900590..176900601,-	p2@DBN1
Hg19::chr5:176900610..176900662,-	p1@DBN1

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:0030036	actin cytoskeleton organization and biogenesis	0.00172691235919777
GO:0030029	actin filament-based process	0.00172691235919777
GO:0042641	actomyosin	0.00172691235919777
GO:0003779	actin binding	0.00364878926538013
GO:0050773	regulation of dendrite development	0.00395429430057747
GO:0005522	profilin binding	0.00395429430057747
GO:0008092	cytoskeletal protein binding	0.00395429430057747
GO:0007010	cytoskeleton organization and biogenesis	0.00447896764911961
GO:0048168	regulation of neuronal synaptic plasticity	0.00518012705880347
GO:0016358	dendrite development	0.00621587796210872
GO:0048167	regulation of synaptic plasticity	0.00753395387979974
GO:0050803	regulation of synapse structure and activity	0.0077691611814973
GO:0048468	cell development	0.00904072481948437
GO:0005856	cytoskeleton	0.0109284430475919
GO:0006996	organelle organization and biogenesis	0.0115741645968369
GO:0050767	regulation of neurogenesis	0.0115741645968369
GO:0030425	dendrite	0.0115741645968369
GO:0007015	actin filament organization	0.0117936203516336
GO:0016363	nuclear matrix	0.0118891572824671
GO:0048869	cellular developmental process	0.0118891572824671
GO:0030154	cell differentiation	0.0118891572824671
GO:0043005	neuron projection	0.0190520721847851
GO:0043232	intracellular non-membrane-bound organelle	0.027080640390655
GO:0043228	non-membrane-bound organelle	0.027080640390655
GO:0031175	neurite development	0.0279208040194611
GO:0048666	neuron development	0.0302942956279923
GO:0016043	cellular component organization and biogenesis	0.0302942956279923
GO:0032502	developmental process	0.0302942956279923
GO:0006916	anti-apoptosis	0.0302942956279923
GO:0007266	Rho protein signal transduction	0.0319002373737859
GO:0032990	cell part morphogenesis	0.0319002373737859
GO:0030030	cell projection organization and biogenesis	0.0319002373737859
GO:0048858	cell projection morphogenesis	0.0319002373737859
GO:0030182	neuron differentiation	0.0319002373737859
GO:0043066	negative regulation of apoptosis	0.0325078441224394
GO:0043069	negative regulation of programmed cell death	0.0325078441224394
GO:0050793	regulation of developmental process	0.0325078441224394
GO:0048699	generation of neurons	0.0325078441224394
GO:0044446	intracellular organelle part	0.0325078441224394
GO:0044422	organelle part	0.0325078441224394
GO:0022008	neurogenesis	0.0329789957614248
GO:0007268	synaptic transmission	0.0355079027878207
GO:0015629	actin cytoskeleton	0.0355079027878207
GO:0042995	cell projection	0.0366846410436107
GO:0019226	transmission of nerve impulse	0.0378081004023087
GO:0007265	Ras protein signal transduction	0.0483452356566323

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>

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Cell Type

Ontology term	p-value	n
non-terminally differentiated cell	2.18e-39	180
embryonic cell	7.70e-33	248
mesodermal cell	6.54e-30	119
contractile cell	5.79e-21	59
electrically responsive cell	2.08e-19	60
electrically active cell	2.08e-19	60
muscle precursor cell	1.35e-18	57
myoblast	1.35e-18	57
multi-potent skeletal muscle stem cell	1.35e-18	57
muscle cell	4.46e-18	54
smooth muscle cell	2.38e-16	42
smooth muscle myoblast	2.38e-16	42
fibroblast	3.62e-15	75
animal cell	1.34e-14	679
eukaryotic cell	1.34e-14	679
vascular associated smooth muscle cell	2.17e-13	32
somatic cell	8.16e-13	591
meso-epithelial cell	1.22e-10	44
lining cell	1.43e-10	57
barrier cell	1.43e-10	57
endothelial cell	9.50e-10	35
ectodermal cell	4.19e-09	71
epithelial cell of nephron	6.84e-09	16
endothelial cell of vascular tree	1.27e-08	24
blood vessel endothelial cell	1.74e-08	18
embryonic blood vessel endothelial progenitor cell	1.74e-08	18
neurectodermal cell	1.80e-08	59
epithelial cell	1.20e-07	254
kidney cell	2.07e-07	18
kidney epithelial cell	2.07e-07	18
kidney cortical cell	3.03e-07	13
renal cortical epithelial cell	3.03e-07	13
kidney tubule cell	6.59e-07	12
nephron tubule epithelial cell	6.59e-07	12

Uber Anatomy

Ontology term	p-value	n
vasculature	1.63e-24	79
vascular system	1.63e-24	79
cell layer	9.91e-24	312
epithelium	1.77e-22	309
somite	1.91e-20	83
paraxial mesoderm	1.91e-20	83
presomitic mesoderm	1.91e-20	83
presumptive segmental plate	1.91e-20	83
trunk paraxial mesoderm	1.91e-20	83
presumptive paraxial mesoderm	1.91e-20	83
multilaminar epithelium	5.83e-20	82
organism subdivision	6.66e-20	365
dermomyotome	1.10e-19	70
trunk mesenchyme	1.48e-19	143
vessel	1.70e-19	69
epithelial tube	3.48e-19	118
blood vessel	6.43e-19	60
epithelial tube open at both ends	6.43e-19	60
blood vasculature	6.43e-19	60
vascular cord	6.43e-19	60
splanchnic layer of lateral plate mesoderm	2.48e-18	84
skeletal muscle tissue	3.64e-17	61
striated muscle tissue	3.64e-17	61
myotome	3.64e-17	61
artery	7.57e-17	42
arterial blood vessel	7.57e-17	42
arterial system	7.57e-17	42
unilaminar epithelium	2.49e-16	138
muscle tissue	2.71e-16	63
musculature	2.71e-16	63
musculature of body	2.71e-16	63
trunk	4.52e-16	216
cardiovascular system	5.02e-15	110
circulatory system	5.62e-14	113
multi-tissue structure	6.22e-13	347
systemic artery	8.34e-13	33
systemic arterial system	8.34e-13	33
multi-cellular organism	7.26e-12	659
tube	1.68e-10	194
anatomical cluster	1.80e-10	286
mesenchyme	6.18e-10	238
entire embryonic mesenchyme	6.18e-10	238
anatomical conduit	1.81e-09	241
nephron epithelium	6.84e-09	16
nephron	6.84e-09	16
uriniferous tubule	6.84e-09	16
metanephric mesenchyme	6.84e-09	16
nephrogenic mesenchyme	6.84e-09	16
endothelium	1.74e-08	18
blood vessel endothelium	1.74e-08	18
cardiovascular system endothelium	1.74e-08	18
simple squamous epithelium	2.14e-08	22
aorta	2.57e-08	21
aortic system	2.57e-08	21
excretory tube	2.70e-08	17
mesonephric epithelium	2.70e-08	17
mesonephric tubule	2.70e-08	17
nephric duct	2.70e-08	17
kidney epithelium	2.70e-08	17
renal duct	2.70e-08	17
mesonephric duct	2.70e-08	17

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
E2F6#1876	3	5.01715573169739	0.0079176980688633	0.0320634536104697
FOSL1#8061	2	26.4757198109153	0.00186983370259098	0.0110230053096014
TAF7#6879	3	11.4330694049239	0.000669018198194583	0.00540801792579288
ZNF143#7702	3	13.5008765522279	0.000406280496299717	0.00387856752770074

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.