Coexpression cluster:C2327

Full id: C2327_Hepatocyte_spinal_liver_normal_optic_tubular_corpus

Phase1 CAGE Peaks

Hg19::chr15:102029900..102029917,-	p1@PCSK6
Hg19::chr1:155099927..155099964,+	p4@EFNA1
Hg19::chr3:133493719..133493723,+	p11@TF
Hg19::chr3:133497553..133497587,+	p@chr3:133497553..133497587 +

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:0007267	cell-cell signaling	0.000805307766608751
GO:0015682	ferric iron transport	0.00267131755563405
GO:0015091	ferric iron transmembrane transporter activity	0.00267131755563405
GO:0031643	positive regulation of myelination	0.00267131755563405
GO:0031641	regulation of myelination	0.00854746129459153
GO:0005381	iron ion transmembrane transporter activity	0.00915745506820525
GO:0046875	ephrin receptor binding	0.00915745506820525
GO:0031646	positive regulation of neurological process	0.0106830685655978
GO:0014070	response to organic cyclic substance	0.0130559306666949
GO:0030139	endocytic vesicle	0.021351044647696
GO:0031644	regulation of neurological process	0.021351044647696
GO:0042552	myelination	0.021351044647696
GO:0046915	transition metal ion transmembrane transporter activity	0.021351044647696
GO:0007272	ensheathment of neurons	0.021351044647696
GO:0006953	acute-phase response	0.021351044647696
GO:0008366	axon ensheathment	0.021351044647696
GO:0004289	subtilase activity	0.0219408985330224
GO:0008199	ferric iron binding	0.0219408985330224
GO:0001508	regulation of action potential	0.0224694898948729
GO:0001666	response to hypoxia	0.024322277194695
GO:0007154	cell communication	0.024322277194695
GO:0015082	di-, tri-valent inorganic cation transmembrane transporter activity	0.024322277194695
GO:0055072	iron ion homeostasis	0.024322277194695
GO:0006879	cellular iron ion homeostasis	0.024322277194695
GO:0006826	iron ion transport	0.024322277194695
GO:0010033	response to organic substance	0.0254345330902621
GO:0002526	acute inflammatory response	0.0311925781763437
GO:0000041	transition metal ion transport	0.0388092979149681
GO:0048503	GPI anchor binding	0.0462550364175995

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
endodermal cell	2.08e-11	58
epithelial cell	3.71e-07	253
epithelial cell of alimentary canal	4.52e-07	20

Uber Anatomy

Ontology term	p-value	n
adult organism	8.51e-46	114
neural tube	4.74e-37	56
neural rod	4.74e-37	56
future spinal cord	4.74e-37	56
neural keel	4.74e-37	56
regional part of nervous system	7.92e-34	53
regional part of brain	7.92e-34	53
organ system subdivision	2.78e-33	223
regional part of forebrain	5.18e-30	41
forebrain	5.18e-30	41
anterior neural tube	5.18e-30	41
future forebrain	5.18e-30	41
brain grey matter	1.42e-26	34
gray matter	1.42e-26	34
telencephalon	3.41e-26	34
brain	7.01e-26	68
future brain	7.01e-26	68
anatomical cluster	3.59e-25	373
central nervous system	7.21e-25	81
regional part of telencephalon	2.18e-24	32
cerebral hemisphere	4.71e-24	32
neural plate	6.95e-24	82
presumptive neural plate	6.95e-24	82
anatomical conduit	1.79e-23	240
multi-tissue structure	9.98e-23	342
neurectoderm	7.13e-22	86
nervous system	9.61e-22	89
ecto-epithelium	9.69e-22	104
tube	1.00e-19	192
pre-chordal neural plate	3.47e-19	61
structure with developmental contribution from neural crest	1.85e-18	132
regional part of cerebral cortex	1.45e-17	22
cerebral cortex	1.55e-17	25
pallium	1.55e-17	25
neocortex	1.17e-15	20
organ part	7.86e-15	218
organ	8.86e-15	503
endoderm-derived structure	1.65e-13	160
endoderm	1.65e-13	160
presumptive endoderm	1.65e-13	160
epithelium	1.77e-13	306
cell layer	4.88e-13	309
subdivision of digestive tract	7.90e-13	118
digestive system	8.85e-13	145
digestive tract	8.85e-13	145
primitive gut	8.85e-13	145
ectoderm-derived structure	1.83e-12	171
ectoderm	1.83e-12	171
presumptive ectoderm	1.83e-12	171
multi-cellular organism	3.70e-12	656
anatomical system	6.99e-11	624
neural nucleus	8.29e-11	9
nucleus of brain	8.29e-11	9
anatomical group	8.81e-11	625
embryo	1.45e-10	592
foregut	2.28e-10	87
basal ganglion	2.71e-10	9
nuclear complex of neuraxis	2.71e-10	9
aggregate regional part of brain	2.71e-10	9
collection of basal ganglia	2.71e-10	9
cerebral subcortex	2.71e-10	9
developing anatomical structure	6.04e-10	581
embryonic structure	1.35e-08	564
telencephalic nucleus	1.37e-08	7
posterior neural tube	2.74e-08	15
chordal neural plate	2.74e-08	15
germ layer	2.91e-08	560
germ layer / neural crest	2.91e-08	560
embryonic tissue	2.91e-08	560
presumptive structure	2.91e-08	560
germ layer / neural crest derived structure	2.91e-08	560
epiblast (generic)	2.91e-08	560
brainstem	7.44e-08	6
temporal lobe	2.14e-07	6
gyrus	3.67e-07	6
epithelium of foregut-midgut junction	4.57e-07	25
anatomical boundary	4.57e-07	25
hepatobiliary system	4.57e-07	25
foregut-midgut junction	4.57e-07	25
septum transversum	4.57e-07	25
digestive tract diverticulum	8.00e-07	23
endo-epithelium	9.70e-07	82

Disease

Ontology term	p-value	n
carcinoma	9.66e-09	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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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.