Coexpression cluster:C327

Full id: C327_Melanocyte_corpus_thalamus_substantia_melanoma_globus_optic

Phase1 CAGE Peaks

Hg19::chr10:128358928..128358933,-	p15@C10orf90
Hg19::chr10:128358986..128359007,-	p2@C10orf90
Hg19::chr10:128359008..128359022,-	p4@C10orf90
Hg19::chr10:128359027..128359032,-	p13@C10orf90
Hg19::chr10:128359039..128359050,-	p5@C10orf90
Hg19::chr10:14066761..14066793,-	p@chr10:14066761..14066793 -
Hg19::chr11:73363887..73363920,+	p13@PLEKHB1
Hg19::chr12:40704263..40704279,+	p@chr12:40704263..40704279 +
Hg19::chr12:53438222..53438234,+	p@chr12:53438222..53438234 +
Hg19::chr12:53438236..53438270,+	p@chr12:53438236..53438270 +
Hg19::chr15:42696929..42696951,+	p5@CAPN3
Hg19::chr15:42696954..42696986,+	p1@CAPN3
Hg19::chr15:42696992..42697017,+	p3@CAPN3
Hg19::chr15:42697018..42697035,+	p6@CAPN3
Hg19::chr15:42697040..42697052,+	p4@CAPN3
Hg19::chr16:19777384..19777399,-	p@chr16:19777384..19777399 -
Hg19::chr16:48307127..48307152,+	p@chr16:48307127..48307152 +
Hg19::chr17:76870126..76870201,-	p10@TIMP2
Hg19::chr17:76870222..76870242,-	p15@TIMP2
Hg19::chr17:79358943..79358954,-	p@chr17:79358943..79358954 -
Hg19::chr17:79358956..79358981,-	p@chr17:79358956..79358981 -
Hg19::chr17:79359021..79359029,-	p@chr17:79359021..79359029 -
Hg19::chr17:79359048..79359058,-	p@chr17:79359048..79359058 -
Hg19::chr17:79359154..79359164,-	p@chr17:79359154..79359164 -
Hg19::chr17:79359173..79359188,-	p@chr17:79359173..79359188 -
Hg19::chr17:79359195..79359212,-	p@chr17:79359195..79359212 -
Hg19::chr19:3544836..3544874,-	p@chr19:3544836..3544874 -
Hg19::chr22:38368890..38368901,-	p@chr22:38368890..38368901 -
Hg19::chr22:38369134..38369144,-	p@chr22:38369134..38369144 -
Hg19::chr22:38369664..38369689,+	p2@CU678225
Hg19::chr22:38369881..38369891,-	p@chr22:38369881..38369891 -
Hg19::chr22:38370098..38370111,-	p@chr22:38370098..38370111 -
Hg19::chr22:38370123..38370134,-	p@chr22:38370123..38370134 -
Hg19::chr22:38374029..38374049,+	p@chr22:38374029..38374049 +
Hg19::chr22:38380543..38380569,-	p1@SOX10

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:0032501	multicellular organismal process	0.0227175415179066
GO:0030814	regulation of cAMP metabolic process	0.029251639102125
GO:0048856	anatomical structure development	0.029251639102125
GO:0030799	regulation of cyclic nucleotide metabolic process	0.029251639102125
GO:0006140	regulation of nucleotide metabolic process	0.0333906082972598
GO:0043408	regulation of MAPKKK cascade	0.0333906082972598
GO:0008191	metalloendopeptidase inhibitor activity	0.0333906082972598
GO:0046058	cAMP metabolic process	0.0333906082972598
GO:0045664	regulation of neuron differentiation	0.0333906082972598
GO:0003705	RNA polymerase II transcription factor activity, enhancer binding	0.0333906082972598
GO:0004198	calcium-dependent cysteine-type endopeptidase activity	0.0333906082972598
GO:0007602	phototransduction	0.0333906082972598
GO:0032502	developmental process	0.0333906082972598
GO:0050962	detection of light stimulus during sensory perception	0.0333906082972598
GO:0050908	detection of light stimulus during visual perception	0.0333906082972598
GO:0009584	detection of visible light	0.0333906082972598
GO:0009583	detection of light stimulus	0.0333906082972598
GO:0007600	sensory perception	0.034757314032091
GO:0005178	integrin binding	0.034757314032091
GO:0048469	cell maturation	0.034757314032091
GO:0009582	detection of abiotic stimulus	0.034757314032091
GO:0050906	detection of stimulus during sensory perception	0.034757314032091
GO:0009187	cyclic nucleotide metabolic process	0.034757314032091
GO:0009581	detection of external stimulus	0.034757314032091
GO:0021700	developmental maturation	0.0353643566264006
GO:0048468	cell development	0.0416643861860936
GO:0050877	neurological system process	0.0418400056854547
GO:0005604	basement membrane	0.0440454197736863
GO:0051606	detection of stimulus	0.0449838416222539
GO:0009416	response to light stimulus	0.0449838416222539

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
melanocyte	2.45e-22	10
melanoblast	2.45e-22	10
pigment cell	1.57e-15	14
light melanocyte	4.78e-12	3
neurecto-epithelial cell	1.98e-10	20
columnar/cuboidal epithelial cell	2.35e-07	27

Uber Anatomy

Ontology term	p-value	n
neural tube	2.00e-86	56
neural rod	2.00e-86	56
future spinal cord	2.00e-86	56
neural keel	2.00e-86	56
regional part of nervous system	1.51e-77	53
regional part of brain	1.51e-77	53
central nervous system	4.25e-69	81
brain	1.02e-64	68
future brain	1.02e-64	68
nervous system	2.08e-64	89
neural plate	1.34e-62	82
presumptive neural plate	1.34e-62	82
regional part of forebrain	3.68e-61	41
forebrain	3.68e-61	41
anterior neural tube	3.68e-61	41
future forebrain	3.68e-61	41
neurectoderm	3.01e-59	86
telencephalon	5.33e-59	34
brain grey matter	5.60e-59	34
gray matter	5.60e-59	34
regional part of telencephalon	6.10e-53	32
ecto-epithelium	6.21e-53	104
cerebral hemisphere	1.39e-52	32
adult organism	4.46e-50	114
pre-chordal neural plate	4.99e-45	61
structure with developmental contribution from neural crest	3.11e-39	132
regional part of cerebral cortex	7.09e-38	22
ectoderm-derived structure	2.72e-34	171
ectoderm	2.72e-34	171
presumptive ectoderm	2.72e-34	171
cerebral cortex	5.25e-33	25
pallium	5.25e-33	25
neocortex	2.84e-32	20
neural nucleus	4.78e-30	9
nucleus of brain	4.78e-30	9
basal ganglion	9.47e-30	9
nuclear complex of neuraxis	9.47e-30	9
aggregate regional part of brain	9.47e-30	9
collection of basal ganglia	9.47e-30	9
cerebral subcortex	9.47e-30	9
posterior neural tube	3.64e-25	15
chordal neural plate	3.64e-25	15
telencephalic nucleus	1.20e-23	7
organ system subdivision	5.40e-21	223
brainstem	1.70e-20	6
segmental subdivision of nervous system	2.01e-19	13
tube	1.46e-18	192
limbic system	6.40e-17	5
segmental subdivision of hindbrain	8.12e-17	12
hindbrain	8.12e-17	12
presumptive hindbrain	8.12e-17	12
gyrus	7.55e-14	6
corpus striatum	1.71e-13	4
striatum	1.71e-13	4
ventral part of telencephalon	1.71e-13	4
future corpus striatum	1.71e-13	4
anatomical conduit	5.84e-13	240
temporal lobe	5.83e-12	6
epithelium	3.17e-11	306
pons	3.21e-11	3
parietal lobe	5.09e-11	5
cell layer	5.09e-11	309
medulla oblongata	5.20e-11	3
myelencephalon	5.20e-11	3
future myelencephalon	5.20e-11	3
spinal cord	5.39e-11	3
dorsal region element	5.39e-11	3
dorsum	5.39e-11	3
caudate-putamen	2.00e-10	3
dorsal striatum	2.00e-10	3
organ part	3.10e-10	218
anatomical cluster	4.12e-09	373
regional part of metencephalon	4.15e-09	9
metencephalon	4.15e-09	9
future metencephalon	4.15e-09	9
globus pallidus	2.12e-08	2
pallidum	2.12e-08	2
dorsal plus ventral thalamus	2.20e-08	2
thalamic complex	2.20e-08	2
locus ceruleus	4.16e-08	2
brainstem nucleus	4.16e-08	2
hindbrain nucleus	4.16e-08	2
multi cell component structure	4.79e-08	2
neuron projection bundle	4.79e-08	2
middle temporal gyrus	8.05e-08	2
amygdala	8.33e-08	2
Ammon's horn	9.88e-08	2
lobe parts of cerebral cortex	9.88e-08	2
hippocampal formation	9.88e-08	2
limbic lobe	9.88e-08	2
caudate nucleus	1.30e-07	2
future caudate nucleus	1.30e-07	2
meninx	4.27e-07	2
membrane organ	4.27e-07	2

Disease

Ontology term	p-value	n

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.