Coexpression cluster:C1297

Full id: C1297_trachea_salivary_seminal_ductus_eye_submaxillary_throat

Phase1 CAGE Peaks

Hg19::chr10:115511386..115511397,+	p4@C10orf81
Hg19::chr10:115511412..115511428,+	p3@C10orf81
Hg19::chr10:115511434..115511454,+	p1@C10orf81
Hg19::chr11:34909948..34909959,-	p@chr11:34909948..34909959 -
Hg19::chr13:24144796..24144809,+	p6@TNFRSF19
Hg19::chr3:46506387..46506404,-	p1@LTF

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:0005031	tumor necrosis factor receptor activity	0.0166781938844186
GO:0043120	tumor necrosis factor binding	0.0166781938844186
GO:0005035	death receptor activity	0.0166781938844186
GO:0008199	ferric iron binding	0.0374900304819804
GO:0055072	iron ion homeostasis	0.0374900304819804
GO:0006879	cellular iron ion homeostasis	0.0374900304819804
GO:0006826	iron ion transport	0.0374900304819804
GO:0007254	JNK cascade	0.0374900304819804
GO:0031098	stress-activated protein kinase signaling pathway	0.0374900304819804
GO:0006959	humoral immune response	0.0374900304819804
GO:0042742	defense response to bacterium	0.037829791018342
GO:0019955	cytokine binding	0.037829791018342
GO:0000041	transition metal ion transport	0.037829791018342
GO:0009617	response to bacterium	0.037829791018342
GO:0000165	MAPKKK cascade	0.0475310480760905
GO:0030005	cellular di-, tri-valent inorganic cation homeostasis	0.0475310480760905
GO:0055066	di-, tri-valent inorganic cation homeostasis	0.0475310480760905
GO:0030003	cellular cation homeostasis	0.0475310480760905
GO:0055080	cation homeostasis	0.0475310480760905
GO:0051707	response to other organism	0.0475310480760905
GO:0006917	induction of apoptosis	0.0475310480760905
GO:0012502	induction of programmed cell death	0.0475310480760905
GO:0055082	cellular chemical homeostasis	0.0475310480760905
GO:0006873	cellular ion homeostasis	0.0475310480760905
GO:0015674	di-, tri-valent inorganic cation transport	0.0475310480760905
GO:0043065	positive regulation of apoptosis	0.0475310480760905
GO:0043068	positive regulation of programmed cell death	0.0475310480760905
GO:0050801	ion homeostasis	0.0475310480760905
GO:0009607	response to biotic stimulus	0.0496572657893629

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
granulocyte	4.87e-07	8

Uber Anatomy

Ontology term	p-value	n
adult organism	1.38e-40	115
neural tube	1.07e-14	57
neural rod	1.07e-14	57
future spinal cord	1.07e-14	57
neural keel	1.07e-14	57
central nervous system	1.54e-13	82
brain	3.72e-12	69
future brain	3.72e-12	69
regional part of brain	3.40e-11	59
regional part of nervous system	1.54e-10	94
nervous system	1.54e-10	94
anterior neural tube	2.39e-10	42
regional part of forebrain	1.02e-09	41
forebrain	1.02e-09	41
future forebrain	1.02e-09	41
organ	1.23e-09	511
neural plate	4.62e-08	86
presumptive neural plate	4.62e-08	86
anterior region of body	5.40e-08	129
craniocervical region	5.40e-08	129
neurectoderm	5.56e-08	90
multi-cellular organism	1.03e-07	659
anatomical system	4.56e-07	625
telencephalon	5.00e-07	34
head	5.54e-07	123
anatomical group	5.93e-07	626
gray matter	7.25e-07	34
brain grey matter	7.25e-07	34
regional part of telencephalon	9.11e-07	33

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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No analysis results for this cluster

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.