Coexpression cluster:C4004

Full id: C4004_Alveolar_Smooth_Renal_Tracheal_Keratinocyte_Bronchial_Esophageal

Phase1 CAGE Peaks

Hg19::chr1:8938709..8938720,-	p3@ENO1
Hg19::chr1:8938736..8938756,-	p1@ENO1
Hg19::chr1:8938766..8938774,-	p2@ENO1

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
animal cell	3.98e-45	679
eukaryotic cell	3.98e-45	679
native cell	2.49e-31	722
somatic cell	3.96e-28	591
non-terminally differentiated cell	2.28e-21	180
embryonic cell	1.63e-17	248
epithelial cell	4.47e-17	254
mesodermal cell	1.14e-14	119
contractile cell	1.17e-11	59
muscle precursor cell	2.88e-11	57
myoblast	2.88e-11	57
multi-potent skeletal muscle stem cell	2.88e-11	57
muscle cell	2.00e-10	54
smooth muscle cell	2.87e-10	42
smooth muscle myoblast	2.87e-10	42
vascular associated smooth muscle cell	5.64e-10	32
electrically responsive cell	1.23e-09	60
electrically active cell	1.23e-09	60
fibroblast	1.27e-07	75
kidney cell	7.15e-07	18
kidney epithelial cell	7.15e-07	18

Uber Anatomy

Ontology term	p-value	n
artery	2.26e-12	42
arterial blood vessel	2.26e-12	42
arterial system	2.26e-12	42
vasculature	1.09e-11	79
vascular system	1.09e-11	79
multilaminar epithelium	2.05e-11	82
epithelial tube	2.63e-11	118
vessel	1.02e-10	69
dermomyotome	1.44e-10	70
blood vessel	1.66e-10	60
epithelial tube open at both ends	1.66e-10	60
blood vasculature	1.66e-10	60
vascular cord	1.66e-10	60
somite	5.17e-10	83
paraxial mesoderm	5.17e-10	83
presomitic mesoderm	5.17e-10	83
presumptive segmental plate	5.17e-10	83
trunk paraxial mesoderm	5.17e-10	83
presumptive paraxial mesoderm	5.17e-10	83
unilaminar epithelium	8.68e-10	138
trunk mesenchyme	9.25e-10	143
trunk	1.73e-09	216
splanchnic layer of lateral plate mesoderm	4.42e-09	84
systemic artery	1.03e-08	33
systemic arterial system	1.03e-08	33
skeletal muscle tissue	1.24e-08	61
striated muscle tissue	1.24e-08	61
myotome	1.24e-08	61
mesenchyme	1.83e-08	238
entire embryonic mesenchyme	1.83e-08	238
muscle tissue	1.37e-07	63
musculature	1.37e-07	63
musculature of body	1.37e-07	63

Disease

Ontology term	p-value	n
disease of cellular proliferation	6.34e-07	239

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
CHD2#1106	3	10.3440228341169	0.000903370110274688	0.00660971493253315
CTCF#10664	3	5.36025637307503	0.006492509252767	0.027979004491427
E2F4#1874	3	12.6680603152844	0.000491798700629898	0.00437653071703187
E2F6#1876	3	5.01715573169739	0.0079176980688633	0.032269910970303
EBF1#1879	3	8.906466846569	0.0014152328356098	0.00915771388588924
EGR1#1958	3	4.98817909481014	0.00805648813738344	0.0321063671759526
ELF1#1997	3	4.25809795880754	0.0129517987505461	0.0462895390359415
ETS1#2113	3	9.72876092220234	0.00108584009258484	0.00763149753899514
FOS#2353	3	8.9979553088944	0.00137249927241713	0.0089841712010011
GABPB1#2553	3	7.06768383618217	0.00283221282541742	0.0154292147135658
GTF2B#2959	3	31.9438299343242	3.06634405746243e-05	0.000628426034178413
GTF2F1#2962	3	12.7396608767577	0.000483552504743859	0.00434498322661481
IRF1#3659	3	7.6371637535639	0.00224469274729724	0.0128231848722775
IRF3#3661	3	46.9819522114896	9.63568551583244e-06	0.000253678184922618
IRF4#3662	3	21.9145126867441	9.49854535978121e-05	0.00136754697936337
MYC#4609	3	5.2222818716094	0.00702084375574015	0.029489237925025
NFKB1#4790	3	5.48806342419384	0.00604938181565543	0.0269846404751735
NFYA#4800	3	18.4255806998305	0.000159813550781416	0.00199865494312781
NFYB#4801	3	16.7597932535365	0.000212364992329618	0.00246134584773199
PBX3#5090	3	21.9145126867441	9.49854535978121e-05	0.0013677355285126
POU2F2#5452	3	9.10612405774252	0.00132416519268213	0.00883050179161796
REST#5978	3	9.65002871612802	0.00111263624711459	0.00768535826801592
RXRA#6256	3	20.0746171391333	0.000123573034843222	0.00165353544983873
SETDB1#9869	3	40.3200261780105	1.52461559299059e-05	0.00035919090439058
SIN3A#25942	3	5.40888472681514	0.00631896197799152	0.0277160165477912
SP1#6667	3	5.6983813781409	0.00540396270171217	0.0246833352549362
SP2#6668	3	26.1535304938446	5.58768218891694e-05	0.000941093275485076
SPI1#6688	3	8.20432350852273	0.00181059318941052	0.010916553637504
SRF#6722	3	13.7971782621678	0.000380661502580019	0.00375409883550091
STAT3#6774	3	10.5194649971542	0.000858918453041531	0.00643228053328585
TAF7#6879	3	11.4330694049239	0.000669018198194583	0.00543790112858931
TCF12#6938	3	10.6344649021864	0.000831352399020207	0.00629764366441368
TFAP2A#7020	3	16.518634373045	0.000221803388076634	0.00248444058851733
TFAP2C#7022	3	10.8092286098602	0.000791674657575313	0.00616383700331803
USF1#7391	3	6.36149927720796	0.0038840405729056	0.0190533261340389
USF2#7392	3	12.9921973850696	0.000455897939342781	0.00422068299681063
YY1#7528	3	4.91117074985386	0.00844145534180826	0.0329786090017249
ZNF143#7702	3	13.5008765522279	0.000406280496299717	0.00389494480934882
ZNF263#10127	3	8.22184163701068	0.00179904392556587	0.0109544279700428

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.