Coexpression cluster:C2567

Full id: C2567_merkel_neuroblastoma_parietal_occipital_duodenum_temporal_brain

Phase1 CAGE Peaks

Hg19::chr1:220701456..220701574,+	p1@MARK1
Hg19::chr2:163645495..163645498,-	p@chr2:163645495..163645498 -
Hg19::chr2:163695238..163695258,-	p2@KCNH7
Hg19::chr2:163695260..163695301,-	p1@KCNH7

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:0004672	protein kinase activity	0.0313840803320159
GO:0000155	two-component sensor activity	0.0313840803320159
GO:0000160	two-component signal transduction system (phosphorelay)	0.0313840803320159
GO:0004673	protein histidine kinase activity	0.0313840803320159
GO:0016773	phosphotransferase activity, alcohol group as acceptor	0.0313840803320159
GO:0016775	phosphotransferase activity, nitrogenous group as acceptor	0.0313840803320159
GO:0016301	kinase activity	0.035627077908378
GO:0016772	transferase activity, transferring phosphorus-containing groups	0.0416307496441538

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
ectodermal cell	4.99e-12	71
neurectodermal cell	2.92e-09	59
epithelial cell	4.90e-08	254
neural cell	6.56e-08	25
ecto-epithelial cell	2.71e-07	33

Uber Anatomy

Ontology term	p-value	n
ectoderm-derived structure	3.38e-38	169
regional part of nervous system	3.51e-37	94
nervous system	3.51e-37	94
ectoderm	3.52e-37	173
presumptive ectoderm	3.52e-37	173
central nervous system	5.12e-35	82
neural tube	9.08e-31	57
neural rod	9.08e-31	57
future spinal cord	9.08e-31	57
neural keel	9.08e-31	57
head	5.46e-30	123
neural plate	2.31e-29	86
presumptive neural plate	2.31e-29	86
anterior region of body	4.48e-29	129
craniocervical region	4.48e-29	129
brain	4.62e-28	69
future brain	4.62e-28	69
neurectoderm	7.62e-28	90
adult organism	4.23e-27	115
regional part of brain	4.63e-26	59
anterior neural tube	1.08e-24	42
regional part of forebrain	2.36e-24	41
forebrain	2.36e-24	41
future forebrain	2.36e-24	41
pre-chordal neural plate	1.50e-23	61
gray matter	1.23e-20	34
brain grey matter	1.23e-20	34
telencephalon	1.56e-20	34
cerebral hemisphere	3.37e-20	32
regional part of telencephalon	7.25e-20	33
organ part	1.46e-18	219
cerebral cortex	1.35e-16	25
pallium	1.35e-16	25
organism subdivision	7.66e-16	365
regional part of cerebral cortex	2.04e-15	22
embryo	1.24e-14	612
neocortex	2.17e-14	20
multi-tissue structure	2.76e-14	347
multi-cellular organism	1.04e-13	659
epithelium	8.47e-13	309
cell layer	1.48e-12	312
embryonic structure	2.15e-12	605
developing anatomical structure	2.15e-12	605
germ layer	3.79e-12	604
embryonic tissue	3.79e-12	604
presumptive structure	3.79e-12	604
epiblast (generic)	3.79e-12	604
anatomical group	1.00e-11	626
anatomical system	1.94e-11	625
anatomical cluster	7.01e-11	286
anatomical conduit	2.25e-10	241
organ	1.46e-08	511
tube	6.18e-08	194
posterior neural tube	2.59e-07	15
chordal neural plate	2.59e-07	15

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.