Coexpression cluster:C835

Full id: C835_kidney_thyroid_mesothelioma_throat_salivary_seminal_chorionic

Phase1 CAGE Peaks

Hg19::chr15:54051846..54051904,-	p1@WDR72
Hg19::chr16:66731112..66731127,-	p@chr16:66731112..66731127 -
Hg19::chr17:68071389..68071396,+	p7@KCNJ16
Hg19::chr17:68128382..68128407,+	p10@KCNJ16
Hg19::chr17:68130458..68130470,+	p@chr17:68130458..68130470 +
Hg19::chr17:68130693..68130703,+	p@chr17:68130693..68130703 +
Hg19::chr17:68130841..68130856,+	p@chr17:68130841..68130856 +
Hg19::chr17:68131022..68131042,+	p@chr17:68131022..68131042 +
Hg19::chr17:68131163..68131167,+	p@chr17:68131163..68131167 +
Hg19::chr9:132962655..132962688,+	p9@NCS1

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:0005242	inward rectifier potassium channel activity	0.0275521017308371
GO:0030955	potassium ion binding	0.0380313199105145
GO:0005249	voltage-gated potassium channel activity	0.0380313199105145
GO:0005267	potassium channel activity	0.0380313199105145
GO:0031420	alkali metal ion binding	0.0380313199105145
GO:0022843	voltage-gated cation channel activity	0.0380313199105145
GO:0006813	potassium ion transport	0.0380313199105145
GO:0005244	voltage-gated ion channel activity	0.0380313199105145
GO:0022832	voltage-gated channel activity	0.0380313199105145
GO:0005261	cation channel activity	0.0410926645472742
GO:0046873	metal ion transmembrane transporter activity	0.0410926645472742
GO:0022836	gated channel activity	0.0410926645472742
GO:0015672	monovalent inorganic cation transport	0.0410926645472742
GO:0005216	ion channel activity	0.0410926645472742
GO:0030001	metal ion transport	0.0410926645472742
GO:0022838	substrate specific channel activity	0.0410926645472742
GO:0015267	channel activity	0.0410926645472742
GO:0022803	passive transmembrane transporter activity	0.0410926645472742
GO:0006812	cation transport	0.0461497703991522
GO:0008324	cation transmembrane transporter activity	0.0461497703991522

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
chorionic membrane mesenchymal stem cell	1.75e-10	3

Uber Anatomy

Ontology term	p-value	n
adult organism	2.51e-36	114
neural tube	2.22e-35	56
neural rod	2.22e-35	56
future spinal cord	2.22e-35	56
neural keel	2.22e-35	56
regional part of nervous system	2.95e-29	53
regional part of brain	2.95e-29	53
central nervous system	6.60e-24	81
neural plate	5.66e-22	82
presumptive neural plate	5.66e-22	82
brain	4.60e-21	68
future brain	4.60e-21	68
nervous system	7.91e-21	89
neurectoderm	1.25e-20	86
brainstem	6.06e-20	6
posterior neural tube	6.53e-20	15
chordal neural plate	6.53e-20	15
regional part of forebrain	9.14e-19	41
forebrain	9.14e-19	41
anterior neural tube	9.14e-19	41
future forebrain	9.14e-19	41
brain grey matter	1.58e-18	34
gray matter	1.58e-18	34
telencephalon	5.17e-18	34
ecto-epithelium	7.28e-16	104
regional part of telencephalon	1.13e-14	32
structure with developmental contribution from neural crest	1.36e-14	132
cerebral hemisphere	1.61e-14	32
cavitated compound organ	1.89e-14	31
segmental subdivision of hindbrain	1.33e-12	12
hindbrain	1.33e-12	12
presumptive hindbrain	1.33e-12	12
neural nucleus	2.34e-12	9
nucleus of brain	2.34e-12	9
tube	1.17e-11	192
anatomical conduit	1.43e-11	240
segmental subdivision of nervous system	1.51e-11	13
pre-chordal neural plate	2.61e-11	61
male genital duct	2.70e-11	3
internal male genitalia	2.70e-11	3
regional part of cerebral cortex	4.57e-11	22
pons	6.60e-11	3
medulla oblongata	9.15e-11	3
myelencephalon	9.15e-11	3
future myelencephalon	9.15e-11	3
acellular anatomical structure	1.75e-10	3
egg chorion	1.75e-10	3
spinal cord	2.82e-10	3
dorsal region element	2.82e-10	3
dorsum	2.82e-10	3
neocortex	6.78e-10	20
cerebral cortex	1.44e-09	25
pallium	1.44e-09	25
organ system subdivision	2.01e-09	223
anatomical cluster	3.23e-09	373
duct of male reproductive system	1.48e-08	4
ectoderm-derived structure	1.67e-08	171
ectoderm	1.67e-08	171
presumptive ectoderm	1.67e-08	171
kidney	1.90e-08	26
kidney mesenchyme	1.90e-08	26
upper urinary tract	1.90e-08	26
kidney rudiment	1.90e-08	26
kidney field	1.90e-08	26
basal ganglion	2.47e-08	9
nuclear complex of neuraxis	2.47e-08	9
aggregate regional part of brain	2.47e-08	9
collection of basal ganglia	2.47e-08	9
cerebral subcortex	2.47e-08	9
multi-tissue structure	2.64e-08	342
organ	2.92e-08	503
locus ceruleus	7.11e-08	2
brainstem nucleus	7.11e-08	2
hindbrain nucleus	7.11e-08	2
chorion	1.42e-07	7
throat	1.56e-07	2
telencephalic nucleus	2.73e-07	7
organ part	3.64e-07	218
open tracheal system trachea	3.70e-07	2
urinary system structure	4.08e-07	47
compound organ	5.63e-07	68
renal system	6.46e-07	48

Disease

Ontology term	p-value	n
clear cell adenocarcinoma	7.53e-07	2

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.