Coexpression cluster:C4420

Full id: C4420_colon_Hepatocyte_placenta_mesothelioma_liver_lung_amniotic

Phase1 CAGE Peaks

Hg19::chr4:48018580..48018602,-	p5@CNGA1
Hg19::chr4:48018616..48018632,-	p3@CNGA1
Hg19::chr4:48018648..48018676,-	p1@CNGA1

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	8.04e-10	254
endodermal cell	4.97e-09	59
endo-epithelial cell	2.38e-07	43

Uber Anatomy

Ontology term	p-value	n
endoderm-derived structure	9.43e-14	169
endoderm	9.43e-14	169
presumptive endoderm	9.43e-14	169
digestive system	7.73e-12	155
digestive tract	7.73e-12	155
primitive gut	7.73e-12	155
embryo	1.38e-11	612
organ	5.87e-11	511
subdivision of digestive tract	7.73e-11	129
endodermal part of digestive tract	7.73e-11	129
multi-cellular organism	1.31e-09	659
embryonic structure	3.89e-09	605
developing anatomical structure	3.89e-09	605
immaterial anatomical entity	4.61e-09	126
germ layer	7.42e-09	604
embryonic tissue	7.42e-09	604
presumptive structure	7.42e-09	604
epiblast (generic)	7.42e-09	604
multi-tissue structure	2.04e-08	347
mixed endoderm/mesoderm-derived structure	2.40e-08	130
orifice	8.40e-08	35
anatomical system	1.14e-07	625
anatomical group	1.51e-07	626
anatomical space	3.29e-07	104
anatomical conduit	7.64e-07	241
mesenchyme	8.31e-07	238
entire embryonic mesenchyme	8.31e-07	238
anatomical cavity	8.46e-07	70
renal system	9.80e-07	45

Disease

Ontology term	p-value	n
carcinoma	5.78e-08	106
squamous cell carcinoma	6.07e-08	14

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
CTCF#10664	3	5.36025637307503	0.006492509252767	0.0280705072797538
CTCFL#140690	2	13.1643162393162	0.00743336703699601	0.0306911808648676
E2F1#1869	3	4.90738921487932	0.00846098534723939	0.0326953360965085
E2F6#1876	3	5.01715573169739	0.0079176980688633	0.0323722388276704
EBF1#1879	3	8.906466846569	0.0014152328356098	0.009182176934724
EGR1#1958	3	4.98817909481014	0.00805648813738344	0.0321911226788656
ELF1#1997	3	4.25809795880754	0.0129517987505461	0.0464213909093752
HMGN3#9324	3	8.17854772335059	0.00182776694216421	0.0109005340151147
IRF1#3659	3	7.6371637535639	0.00224469274729724	0.0128555311381321
NFYB#4801	3	16.7597932535365	0.000212364992329618	0.00246490191530484
RAD21#5885	3	10.3550338954563	0.000900491207356542	0.0066690115731889
SMC3#9126	3	15.0449328449328	0.000293582542037187	0.00310275927017018
STAT1#6772	3	20.7065874971992	0.000112599244104667	0.00155223765246136
TFAP2A#7020	3	16.518634373045	0.000221803388076634	0.00249111991045656
TFAP2C#7022	3	10.8092286098602	0.000791674657575313	0.00617949996730255
TRIM28#10155	3	18.5905250452625	0.000155596929725528	0.00197645192697694
ZEB1#6935	3	16.8884320175439	0.000207548691732758	0.0024349784111298

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.