Coexpression cluster:C2199

Full id: C2199_caudate_parietal_occipital_middle_medial_globus_thalamus

Phase1 CAGE Peaks

Hg19::chr12:19358228..19358248,+	p7@PLEKHA5
Hg19::chr2:152527863..152527893,-	p4@NEB
Hg19::chr2:3050387..3050399,-	p@chr2:3050387..3050399 -
Hg19::chr9:138594018..138594036,+	p4@KCNT1

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:0007525	somatic muscle development	0.027319432152077
GO:0030018	Z disc	0.027319432152077
GO:0031674	I band	0.027319432152077
GO:0005545	phosphatidylinositol binding	0.027319432152077
GO:0015269	calcium-activated potassium channel activity	0.027319432152077
GO:0022839	ion gated channel activity	0.027319432152077
GO:0005227	calcium activated cation channel activity	0.027319432152077
GO:0008307	structural constituent of muscle	0.027319432152077
GO:0030832	regulation of actin filament length	0.027319432152077
GO:0032535	regulation of cellular component size	0.027319432152077
GO:0032956	regulation of actin cytoskeleton organization and biogenesis	0.027319432152077
GO:0030017	sarcomere	0.027319432152077
GO:0030016	myofibril	0.027319432152077
GO:0051493	regulation of cytoskeleton organization and biogenesis	0.027319432152077
GO:0033043	regulation of organelle organization and biogenesis	0.027319432152077
GO:0044449	contractile fiber part	0.027438161099036
GO:0043292	contractile fiber	0.0275425165044705
GO:0051128	regulation of cellular component organization and biogenesis	0.0406012548667762

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><br>

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Uber Anatomy

Ontology term	p-value	n
neural tube	6.99e-42	57
neural rod	6.99e-42	57
future spinal cord	6.99e-42	57
neural keel	6.99e-42	57
regional part of forebrain	3.79e-38	41
forebrain	3.79e-38	41
future forebrain	3.79e-38	41
regional part of brain	1.20e-37	59
anterior neural tube	6.57e-37	42
brain	8.71e-36	69
future brain	8.71e-36	69
central nervous system	3.44e-33	82
adult organism	4.43e-32	115
gray matter	5.74e-31	34
brain grey matter	5.74e-31	34
telencephalon	1.91e-30	34
regional part of nervous system	9.49e-30	94
nervous system	9.49e-30	94
neurectoderm	2.08e-29	90
regional part of telencephalon	3.39e-29	33
cerebral hemisphere	4.17e-29	32
neural plate	6.52e-29	86
presumptive neural plate	6.52e-29	86
pre-chordal neural plate	7.46e-25	61
regional part of cerebral cortex	3.82e-24	22
neocortex	8.51e-22	20
cerebral cortex	2.12e-20	25
pallium	2.12e-20	25
head	1.35e-18	123
anterior region of body	6.94e-17	129
craniocervical region	6.94e-17	129
ectoderm	4.55e-15	173
presumptive ectoderm	4.55e-15	173
ectoderm-derived structure	1.83e-14	169
basal ganglion	1.30e-12	9
nuclear complex of neuraxis	1.30e-12	9
aggregate regional part of brain	1.30e-12	9
collection of basal ganglia	1.30e-12	9
cerebral subcortex	1.30e-12	9
nucleus of brain	2.45e-12	9
neural nucleus	2.45e-12	9
tube	5.29e-12	194
organism subdivision	7.28e-11	365
telencephalic nucleus	3.60e-10	7
anatomical conduit	1.16e-09	241
organ	1.93e-09	511
gyrus	3.47e-09	6
diencephalon	4.04e-09	7
future diencephalon	4.04e-09	7
epithelium	4.40e-09	309
cell layer	8.89e-09	312
temporal lobe	1.14e-08	7
anatomical cluster	5.06e-08	286
limbic system	1.14e-07	5
occipital lobe	1.41e-07	5
organ part	2.70e-07	219
brainstem	3.16e-07	8
anatomical system	5.18e-07	625
anatomical group	6.09e-07	626
multi-cellular organism	6.09e-07	659
posterior neural tube	6.21e-07	15
chordal neural plate	6.21e-07	15
corpus striatum	8.29e-07	4
striatum	8.29e-07	4
ventral part of telencephalon	8.29e-07	4
future corpus striatum	8.29e-07	4

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.