Coexpression cluster:C4488

Full id: C4488_Alveolar_Renal_Mesenchymal_leiomyoma_Hepatocyte_tubular_small

Phase1 CAGE Peaks

Hg19::chr5:179233795..179233828,-	p2@MGAT4B
Hg19::chr5:179233829..179233834,-	p6@MGAT4B
Hg19::chr5:179233835..179233873,-	p1@MGAT4B

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><br>

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Cell Type

Ontology term	p-value	n
epithelial cell	3.43e-31	254
embryonic cell	9.83e-31	248
animal cell	1.52e-29	679
eukaryotic cell	1.52e-29	679
mesodermal cell	2.72e-25	119
somatic cell	7.22e-19	591
native cell	5.37e-18	722
lining cell	9.00e-14	57
barrier cell	9.00e-14	57
non-terminally differentiated cell	3.70e-12	180
contractile cell	1.21e-11	59
smooth muscle cell	3.07e-11	42
smooth muscle myoblast	3.07e-11	42
squamous epithelial cell	7.26e-11	62
muscle precursor cell	1.05e-10	57
myoblast	1.05e-10	57
multi-potent skeletal muscle stem cell	1.05e-10	57
vascular associated smooth muscle cell	2.81e-10	32
muscle cell	1.04e-09	54
meso-epithelial cell	2.73e-09	44
endodermal cell	2.86e-09	59
epithelial cell of nephron	4.28e-09	16
endothelial cell	2.45e-08	35
electrically responsive cell	2.47e-08	60
electrically active cell	2.47e-08	60
kidney cell	7.48e-08	18
kidney epithelial cell	7.48e-08	18
kidney tubule cell	7.78e-08	12
nephron tubule epithelial cell	7.78e-08	12
endo-epithelial cell	1.26e-07	43
mesothelial cell	1.36e-07	19
kidney cortical cell	3.42e-07	13
renal cortical epithelial cell	3.42e-07	13
endothelial cell of vascular tree	7.22e-07	24

Uber Anatomy

Ontology term	p-value	n
epithelial tube	1.95e-25	118
trunk	4.66e-16	216
unilaminar epithelium	9.02e-16	138
vasculature	1.12e-15	79
vascular system	1.12e-15	79
vessel	2.04e-15	69
artery	1.07e-14	42
arterial blood vessel	1.07e-14	42
arterial system	1.07e-14	42
trunk mesenchyme	2.78e-14	143
splanchnic layer of lateral plate mesoderm	5.63e-14	84
cardiovascular system	1.17e-13	110
circulatory system	1.47e-13	113
blood vessel	2.44e-13	60
epithelial tube open at both ends	2.44e-13	60
blood vasculature	2.44e-13	60
vascular cord	2.44e-13	60
mesoderm	5.64e-13	448
mesoderm-derived structure	5.64e-13	448
presumptive mesoderm	5.64e-13	448
mesenchyme	2.09e-12	238
entire embryonic mesenchyme	2.09e-12	238
systemic artery	1.42e-11	33
systemic arterial system	1.42e-11	33
subdivision of trunk	2.05e-11	113
multilaminar epithelium	1.23e-09	82
immaterial anatomical entity	2.34e-09	126
nephron epithelium	4.28e-09	16
nephron	4.28e-09	16
uriniferous tubule	4.28e-09	16
metanephric mesenchyme	4.28e-09	16
nephrogenic mesenchyme	4.28e-09	16
skeletal muscle tissue	3.26e-08	61
striated muscle tissue	3.26e-08	61
myotome	3.26e-08	61
endoderm-derived structure	3.56e-08	169
endoderm	3.56e-08	169
presumptive endoderm	3.56e-08	169
muscle tissue	3.99e-08	63
musculature	3.99e-08	63
musculature of body	3.99e-08	63
excretory tube	4.87e-08	17
mesonephric epithelium	4.87e-08	17
mesonephric tubule	4.87e-08	17
nephric duct	4.87e-08	17
kidney epithelium	4.87e-08	17
renal duct	4.87e-08	17
mesonephric duct	4.87e-08	17
pronephric duct	4.87e-08	17
renal tubule	7.78e-08	12
nephron tubule	7.78e-08	12
nephron tubule epithelium	7.78e-08	12
dermomyotome	7.81e-08	70
parenchyma	8.85e-08	17
abdominal segment of trunk	1.49e-07	61
abdomen	1.49e-07	61
urinary system structure	2.31e-07	44
cortex of kidney	3.42e-07	13
renal parenchyma	3.42e-07	13
trunk region element	3.56e-07	107
mesonephros	4.39e-07	18

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	0.0190852442113087
E2F6#1876	3	5.01715573169739	0.0079176980688633	0.0323874537292031
EGR1#1958	3	4.98817909481014	0.00805648813738344	0.0322059084659033
ELF1#1997	3	4.25809795880754	0.0129517987505461	0.0464405160060522
HMGN3#9324	3	8.17854772335059	0.00182776694216421	0.0109048929833013
HNF4G#3174	3	28.7534225264468	4.20470658818262e-05	0.000759486944592191
IRF1#3659	3	7.6371637535639	0.00224469274729724	0.0128597622509587
JUND#3727	3	6.99466394187103	0.00292184504273499	0.0157426008263619
MYC#4609	3	5.2222818716094	0.00702084375574015	0.0295653361157109
NFKB1#4790	3	5.48806342419384	0.00604938181565543	0.0270574469997961
PAX5#5079	3	6.66956553117783	0.00337029099967726	0.0173522219233568
SIN3A#25942	3	5.40888472681514	0.00631896197799152	0.0277918836864927
SP1#6667	3	5.6983813781409	0.00540396270171217	0.0247602202598981
TAF7#6879	3	11.4330694049239	0.000669018198194583	0.00544935202006271
TCF7L2#6934	3	10.7701765631373	0.000800318129839838	0.00616449776254465
YY1#7528	3	4.91117074985386	0.00844145534180826	0.0330850435112062
ZEB1#6935	3	16.8884320175439	0.000207548691732758	0.00243525197347236

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.