Coexpression cluster:C4555

Full id: C4555_neuroblastoma_occipital_parietal_carcinoid_brain_Neural_mesothelioma

Phase1 CAGE Peaks

Hg19::chr6:127840021..127840047,-	p4@C6orf174
Hg19::chr6:127840048..127840074,-	p5@C6orf174
Hg19::chr6:127840089..127840099,-	p16@C6orf174

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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No GOStat results

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
non-terminally differentiated cell	2.07e-21	180
neurectodermal cell	5.70e-16	59
neural cell	3.31e-14	25
migratory neural crest cell	1.26e-12	41
electrically responsive cell	4.34e-12	60
electrically active cell	4.34e-12	60
ectodermal cell	8.23e-12	71
contractile cell	3.51e-09	59
muscle precursor cell	8.03e-09	57
myoblast	8.03e-09	57
multi-potent skeletal muscle stem cell	8.03e-09	57
muscle cell	1.05e-08	54
neuron associated cell	3.52e-08	17
neuron associated cell (sensu Vertebrata)	3.52e-08	17
neuronal stem cell	4.05e-08	8
columnar/cuboidal epithelial cell	7.16e-07	27

Uber Anatomy

Ontology term	p-value	n
regional part of nervous system	4.55e-33	94
nervous system	4.55e-33	94
central nervous system	1.97e-32	82
brain	1.97e-24	69
future brain	1.97e-24	69
neural tube	5.59e-23	57
neural rod	5.59e-23	57
future spinal cord	5.59e-23	57
neural keel	5.59e-23	57
regional part of brain	1.02e-21	59
neural plate	1.05e-21	86
presumptive neural plate	1.05e-21	86
neurectoderm	2.61e-21	90
ectoderm-derived structure	3.70e-21	169
ectoderm	4.09e-21	173
presumptive ectoderm	4.09e-21	173
head	2.16e-18	123
pre-chordal neural plate	2.08e-17	61
organism subdivision	2.43e-17	365
anterior region of body	2.94e-16	129
craniocervical region	2.94e-16	129
cell layer	9.31e-16	312
regional part of forebrain	9.74e-16	41
forebrain	9.74e-16	41
future forebrain	9.74e-16	41
anterior neural tube	4.85e-15	42
epithelium	6.16e-15	309
tube	1.23e-13	194
gray matter	1.67e-13	34
brain grey matter	1.67e-13	34
telencephalon	5.08e-13	34
regional part of telencephalon	1.31e-12	33
cerebral hemisphere	1.51e-12	32
multi-tissue structure	4.55e-12	347
cerebral cortex	1.14e-11	25
pallium	1.14e-11	25
somite	7.03e-10	83
paraxial mesoderm	7.03e-10	83
presomitic mesoderm	7.03e-10	83
presumptive segmental plate	7.03e-10	83
trunk paraxial mesoderm	7.03e-10	83
presumptive paraxial mesoderm	7.03e-10	83
regional part of cerebral cortex	1.45e-09	22
posterior neural tube	1.90e-09	15
chordal neural plate	1.90e-09	15
dermomyotome	2.97e-09	70
neocortex	4.40e-09	20
segmental subdivision of nervous system	8.17e-09	13
segmental subdivision of hindbrain	2.13e-08	12
hindbrain	2.13e-08	12
presumptive hindbrain	2.13e-08	12
anatomical conduit	3.35e-08	241
anatomical cluster	6.78e-08	286
skeletal muscle tissue	1.78e-07	61
striated muscle tissue	1.78e-07	61
myotome	1.78e-07	61
muscle tissue	2.74e-07	63
musculature	2.74e-07	63
musculature of body	2.74e-07	63
regional part of metencephalon	6.19e-07	9
metencephalon	6.19e-07	9
future metencephalon	6.19e-07	9
organ part	7.79e-07	219

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
REST#5978	3	9.65002871612802	0.00111263624711459	0.00770727711165355
RXRA#6256	3	20.0746171391333	0.000123573034843222	0.001658848867094
SIN3A#25942	3	5.40888472681514	0.00631896197799152	0.0278047638516729
YY1#7528	3	4.91117074985386	0.00844145534180826	0.0330987068044418

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.