Coexpression cluster:C1367

Full id: C1367_optic_extraskeletal_brain_rhabdomyosarcoma_substantia_corpus_thalamus

Phase1 CAGE Peaks

Hg19::chr12:70760058..70760085,+	p1@KCNMB4
Hg19::chr12:70760380..70760395,+	p6@KCNMB4
Hg19::chr12:70760508..70760600,+	p4@KCNMB4
Hg19::chr17:36759531..36759542,+	p@chr17:36759531..36759542 +
Hg19::chr19:1450095..1450102,+	p4@APC2
Hg19::chr19:36370460..36370479,+	p@chr19:36370460..36370479 +

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:0016342	catenin complex	0.00600494524902861
GO:0019228	generation of action potential	0.0108076287272309
GO:0005513	detection of calcium ion	0.0108076287272309
GO:0019229	regulation of vasoconstriction	0.0108076287272309
GO:0008013	beta-catenin binding	0.0108076287272309
GO:0046928	regulation of neurotransmitter secretion	0.0120079460631646
GO:0042310	vasoconstriction	0.0135077461451033
GO:0009593	detection of chemical stimulus	0.0135077461451033
GO:0042391	regulation of membrane potential	0.015179589722366
GO:0015269	calcium-activated potassium channel activity	0.015179589722366
GO:0022839	ion gated channel activity	0.015179589722366
GO:0005227	calcium activated cation channel activity	0.015179589722366
GO:0001508	regulation of action potential	0.015179589722366
GO:0007269	neurotransmitter secretion	0.015179589722366
GO:0035150	regulation of tube size	0.015179589722366
GO:0050880	regulation of blood vessel size	0.015179589722366
GO:0003018	vascular process in circulatory system	0.015179589722366
GO:0008017	microtubule binding	0.0157910906900584
GO:0019897	extrinsic to plasma membrane	0.0157910906900584
GO:0045055	regulated secretory pathway	0.0159009256768253
GO:0051046	regulation of secretion	0.0168566343658797
GO:0015631	tubulin binding	0.0182573598082459
GO:0003001	generation of a signal involved in cell-cell signaling	0.0182573598082459
GO:0044459	plasma membrane part	0.0184552706464487
GO:0001505	regulation of neurotransmitter levels	0.0184552706464487
GO:0051606	detection of stimulus	0.0184552706464487
GO:0035239	tube morphogenesis	0.0186592293268234
GO:0019898	extrinsic to membrane	0.0229116677526957
GO:0035295	tube development	0.0237832898150614
GO:0043234	protein complex	0.0237832898150614
GO:0008076	voltage-gated potassium channel complex	0.0237832898150614
GO:0016055	Wnt receptor signaling pathway	0.027152237988412
GO:0016043	cellular component organization and biogenesis	0.0273869361726116
GO:0008015	blood circulation	0.0273869361726116
GO:0003013	circulatory system process	0.0273869361726116
GO:0005267	potassium channel activity	0.0347753819963962
GO:0005886	plasma membrane	0.0347753819963962
GO:0032991	macromolecular complex	0.0350272484805176
GO:0055082	cellular chemical homeostasis	0.0350272484805176
GO:0006873	cellular ion homeostasis	0.0350272484805176
GO:0045045	secretory pathway	0.0350272484805176
GO:0006813	potassium ion transport	0.0364641979791503
GO:0050801	ion homeostasis	0.0371405398920149
GO:0051239	regulation of multicellular organismal process	0.0376502896809556
GO:0007268	synaptic transmission	0.0384140263190828
GO:0032940	secretion by cell	0.0384140263190828
GO:0048878	chemical homeostasis	0.0384140263190828
GO:0019226	transmission of nerve impulse	0.0410840863746678
GO:0006461	protein complex assembly	0.0414590676224523
GO:0019725	cellular homeostasis	0.0447891739188977
GO:0046903	secretion	0.0449588284627961
GO:0005261	cation channel activity	0.0482023710215125

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
neuronal stem cell	2.29e-09	8
neuron	1.19e-07	6
neuroblast	1.19e-07	6
electrically signaling cell	1.19e-07	6

Uber Anatomy

Ontology term	p-value	n
central nervous system	5.05e-50	81
nervous system	9.66e-48	89
neural tube	6.79e-44	56
neural rod	6.79e-44	56
future spinal cord	6.79e-44	56
neural keel	6.79e-44	56
regional part of nervous system	1.13e-40	53
regional part of brain	1.13e-40	53
neural plate	8.94e-39	82
presumptive neural plate	8.94e-39	82
brain	2.44e-37	68
future brain	2.44e-37	68
neurectoderm	3.70e-37	86
regional part of forebrain	5.27e-33	41
forebrain	5.27e-33	41
anterior neural tube	5.27e-33	41
future forebrain	5.27e-33	41
telencephalon	1.22e-30	34
brain grey matter	1.46e-30	34
gray matter	1.46e-30	34
adult organism	6.03e-30	114
pre-chordal neural plate	9.24e-30	61
regional part of telencephalon	2.16e-28	32
cerebral hemisphere	2.82e-28	32
structure with developmental contribution from neural crest	2.53e-27	132
ectoderm-derived structure	3.16e-27	171
ectoderm	3.16e-27	171
presumptive ectoderm	3.16e-27	171
ecto-epithelium	7.49e-27	104
organ system subdivision	8.45e-26	223
regional part of cerebral cortex	1.18e-25	22
neocortex	1.07e-23	20
cerebral cortex	3.09e-23	25
pallium	3.09e-23	25
anatomical cluster	1.01e-17	373
tube	1.76e-17	192
anatomical conduit	2.22e-12	240
posterior neural tube	9.48e-12	15
chordal neural plate	9.48e-12	15
organ part	4.20e-10	218
multi-tissue structure	6.30e-10	342
segmental subdivision of nervous system	6.53e-10	13
embryo	8.50e-09	592
segmental subdivision of hindbrain	8.71e-09	12
hindbrain	8.71e-09	12
presumptive hindbrain	8.71e-09	12
basal ganglion	9.33e-09	9
nuclear complex of neuraxis	9.33e-09	9
aggregate regional part of brain	9.33e-09	9
collection of basal ganglia	9.33e-09	9
cerebral subcortex	9.33e-09	9
temporal lobe	9.36e-09	6
neural nucleus	1.01e-08	9
nucleus of brain	1.01e-08	9
epithelium	2.81e-08	306
cell layer	5.72e-08	309
brainstem	7.60e-08	6
gyrus	7.87e-08	6
organ	8.22e-08	503
multi-cellular organism	2.18e-07	656
occipital lobe	3.36e-07	5
germ layer	4.31e-07	560
germ layer / neural crest	4.31e-07	560
embryonic tissue	4.31e-07	560
presumptive structure	4.31e-07	560
germ layer / neural crest derived structure	4.31e-07	560
epiblast (generic)	4.31e-07	560
parietal lobe	7.65e-07	5
developing anatomical structure	7.81e-07	581
embryonic structure	8.75e-07	564
anatomical system	8.87e-07	624

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
EGR1#1958	5	4.15681591234178	0.00161796681886444	0.0101312330832414
ZBTB7A#51341	4	4.90127287191726	0.00407962811884375	0.0194847158322551
ZNF263#10127	4	5.48122775800712	0.00267560938060723	0.0147429549488888

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.