Coexpression cluster:C2825

Full id: C2825_cervical_gall_bile_rectal_epitheloid_large_umbilical

Phase1 CAGE Peaks

Hg19::chr5:58571724..58571727,-	p8@uc003jsd.1
Hg19::chr5:58571770..58571781,-	p7@uc003jsd.1
Hg19::chr5:58571807..58571821,-	p24@PDE4D
Hg19::chr5:58571829..58571862,-	p9@PDE4D

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:0004115	3',5'-cyclic-AMP phosphodiesterase activity	0.00638761332862357
GO:0005626	insoluble fraction	0.00912516189803367
GO:0004114	3',5'-cyclic-nucleotide phosphodiesterase activity	0.0107220652301896
GO:0004112	cyclic-nucleotide phosphodiesterase activity	0.0107220652301896
GO:0005813	centrosome	0.0191628399858707
GO:0008081	phosphoric diester hydrolase activity	0.0191628399858707
GO:0005815	microtubule organizing center	0.0191628399858707
GO:0005625	soluble fraction	0.0266910985517485

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><br>uberon_data<br>disease_data<br>

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Uber Anatomy

Ontology term	p-value	n
adult organism	2.76e-26	114
larynx	1.85e-17	9
upper respiratory tract	5.56e-14	19
organ part	8.34e-13	218
organ system subdivision	1.58e-12	223
respiratory primordium	2.68e-12	38
endoderm of foregut	2.68e-12	38
respiratory tract	4.78e-11	54
subdivision of digestive tract	1.14e-10	118
digestive system	2.71e-10	145
digestive tract	2.71e-10	145
primitive gut	2.71e-10	145
segment of respiratory tract	1.67e-09	47
anatomical cluster	2.18e-09	373
organ	4.20e-09	503
endoderm-derived structure	5.71e-09	160
endoderm	5.71e-09	160
presumptive endoderm	5.71e-09	160
organ segment	6.48e-09	98
multi-tissue structure	7.51e-09	342
neocortex	1.17e-08	20
telencephalon	8.24e-08	34
regional part of cerebral cortex	1.14e-07	22
cerebral hemisphere	2.08e-07	32
foregut	2.32e-07	87
respiratory system	3.48e-07	74
large intestine	5.01e-07	11
neural tube	5.93e-07	56
neural rod	5.93e-07	56
future spinal cord	5.93e-07	56
neural keel	5.93e-07	56
regional part of forebrain	6.22e-07	41
forebrain	6.22e-07	41
anterior neural tube	6.22e-07	41
future forebrain	6.22e-07	41

Disease

Ontology term	p-value	n
carcinoma	7.78e-07	106

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
GATA3#2625	4	27.236516357206	1.81561517799785e-06	6.78672274784957e-05
NR3C1#2908	4	14.973023331173	1.98868032687801e-05	0.000444079077739603
TBP#6908	4	3.70677068709639	0.00529637781478435	0.024490764305245
TFAP2C#7022	4	10.8092286098602	7.32289634782688e-05	0.00114765301871352

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.