Coexpression cluster:C2076

Full id: C2076_Melanocyte_corpus_brain_occipital_temporal_postcentral_pons

Phase1 CAGE Peaks

Hg19::chr10:83635613..83635633,+	p3@NRG3
Hg19::chr8:22005612..22005623,-	p@chr8:22005612..22005623 -
Hg19::chr8:22014298..22014326,-	p1@LGI3
Hg19::chr8:22014339..22014342,-	p4@LGI3

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:0030297	transmembrane receptor protein tyrosine kinase activator activity	0.00565129725365418
GO:0030971	receptor tyrosine kinase binding	0.00565129725365418
GO:0030296	protein tyrosine kinase activator activity	0.00565129725365418
GO:0030295	protein kinase activator activity	0.00791088449005495
GO:0030879	mammary gland development	0.00791088449005495
GO:0019209	kinase activator activity	0.00847544856163342
GO:0048732	gland development	0.0185576153148636
GO:0019887	protein kinase regulator activity	0.0370325943749413
GO:0019207	kinase regulator activity	0.0382378355329935
GO:0001558	regulation of cell growth	0.0446438476068774
GO:0016049	cell growth	0.0446438476068774
GO:0040008	regulation of growth	0.0446438476068774
GO:0008361	regulation of cell size	0.0446438476068774
GO:0009790	embryonic development	0.0472706531134139
GO:0008083	growth factor activity	0.0474859976685569

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
melanocyte	7.62e-13	10
melanoblast	7.62e-13	10
pigment cell	9.84e-09	14
light melanocyte	4.22e-07	3

Uber Anatomy

Ontology term	p-value	n
neural tube	1.69e-78	56
neural rod	1.69e-78	56
future spinal cord	1.69e-78	56
neural keel	1.69e-78	56
regional part of nervous system	2.32e-72	53
regional part of brain	2.32e-72	53
regional part of forebrain	4.98e-63	41
forebrain	4.98e-63	41
anterior neural tube	4.98e-63	41
future forebrain	4.98e-63	41
adult organism	2.05e-62	114
central nervous system	9.29e-62	81
brain	5.03e-61	68
future brain	5.03e-61	68
neural plate	1.19e-56	82
presumptive neural plate	1.19e-56	82
nervous system	1.38e-56	89
neurectoderm	2.41e-53	86
telencephalon	2.52e-53	34
brain grey matter	5.40e-53	34
gray matter	5.40e-53	34
cerebral hemisphere	6.92e-49	32
regional part of telencephalon	7.06e-49	32
ecto-epithelium	1.27e-45	104
pre-chordal neural plate	5.02e-44	61
regional part of cerebral cortex	9.51e-41	22
structure with developmental contribution from neural crest	3.50e-37	132
neocortex	6.70e-37	20
cerebral cortex	2.89e-35	25
pallium	2.89e-35	25
ectoderm-derived structure	1.12e-28	171
ectoderm	1.12e-28	171
presumptive ectoderm	1.12e-28	171
organ system subdivision	8.65e-23	223
basal ganglion	1.74e-19	9
nuclear complex of neuraxis	1.74e-19	9
aggregate regional part of brain	1.74e-19	9
collection of basal ganglia	1.74e-19	9
cerebral subcortex	1.74e-19	9
neural nucleus	2.46e-19	9
nucleus of brain	2.46e-19	9
tube	1.27e-18	192
posterior neural tube	3.58e-16	15
chordal neural plate	3.58e-16	15
telencephalic nucleus	2.85e-15	7
anatomical conduit	4.95e-15	240
gyrus	1.90e-14	6
brainstem	8.13e-14	6
segmental subdivision of nervous system	1.53e-12	13
epithelium	1.93e-12	306
anatomical cluster	2.88e-12	373
cell layer	3.62e-12	309
parietal lobe	4.15e-12	5
occipital lobe	5.08e-12	5
limbic system	1.23e-11	5
segmental subdivision of hindbrain	6.65e-11	12
hindbrain	6.65e-11	12
presumptive hindbrain	6.65e-11	12
diencephalon	7.76e-11	7
future diencephalon	7.76e-11	7
organ part	1.39e-10	218
multi-tissue structure	2.52e-10	342
corpus striatum	2.15e-09	4
striatum	2.15e-09	4
ventral part of telencephalon	2.15e-09	4
future corpus striatum	2.15e-09	4
regional part of diencephalon	4.38e-09	4
temporal lobe	1.24e-08	6
frontal cortex	7.62e-08	3
pons	8.92e-08	3
medulla oblongata	1.04e-07	3
myelencephalon	1.04e-07	3
future myelencephalon	1.04e-07	3
spinal cord	1.42e-07	3
dorsal region element	1.42e-07	3
dorsum	1.42e-07	3
caudate-putamen	1.94e-07	3
dorsal striatum	1.94e-07	3
organ	2.25e-07	503

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
SUZ12#23512	2	25.0578904555315	0.00232525671652061	0.0131831869180118

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.