Coexpression cluster:C2121

Full id: C2121_spinal_epididymis_glioma_thalamus_locus_pineal_medulla

Phase1 CAGE Peaks

Hg19::chr11:24518492..24518510,+	p5@LUZP2
Hg19::chr8:132053091..132053127,-	p1@ADCY8
Hg19::chr8:132053777..132053790,-	p@chr8:132053777..132053790 -
Hg19::chr8:132053800..132053811,-	p@chr8:132053800..132053811 -

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:0008294	calcium- and calmodulin-responsive adenylate cyclase activity	0.00397386082656305
GO:0004016	adenylate cyclase activity	0.00647592134699164
GO:0006171	cAMP biosynthetic process	0.00647592134699164
GO:0046058	cAMP metabolic process	0.00647592134699164
GO:0016849	phosphorus-oxygen lyase activity	0.00647592134699164
GO:0009975	cyclase activity	0.00647592134699164
GO:0004289	subtilase activity	0.00647592134699164
GO:0009190	cyclic nucleotide biosynthetic process	0.00647592134699164
GO:0007611	learning and/or memory	0.00647592134699164
GO:0009187	cyclic nucleotide metabolic process	0.00662310137760509
GO:0009165	nucleotide biosynthetic process	0.0277434357706346
GO:0016829	lyase activity	0.0277434357706346
GO:0007610	behavior	0.0277434357706346
GO:0004252	serine-type endopeptidase activity	0.0277434357706346
GO:0009117	nucleotide metabolic process	0.0277434357706346
GO:0055086	nucleobase, nucleoside and nucleotide metabolic process	0.0277434357706346
GO:0008236	serine-type peptidase activity	0.0277434357706346
GO:0017171	serine hydrolase activity	0.0277434357706346
GO:0000287	magnesium ion binding	0.0311634349030471
GO:0005624	membrane fraction	0.0452357824090427

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
neuronal stem cell	1.22e-07	8

Uber Anatomy

Ontology term	p-value	n
regional part of nervous system	1.29e-51	94
nervous system	1.29e-51	94
central nervous system	1.41e-51	82
neural tube	1.46e-47	57
neural rod	1.46e-47	57
future spinal cord	1.46e-47	57
neural keel	1.46e-47	57
regional part of brain	1.12e-43	59
brain	2.10e-40	69
future brain	2.10e-40	69
neural plate	1.65e-39	86
presumptive neural plate	1.65e-39	86
neurectoderm	1.45e-37	90
regional part of forebrain	2.49e-34	41
forebrain	2.49e-34	41
future forebrain	2.49e-34	41
anterior neural tube	4.11e-33	42
pre-chordal neural plate	3.26e-31	61
adult organism	1.03e-30	115
gray matter	3.44e-30	34
brain grey matter	3.44e-30	34
telencephalon	5.80e-30	34
ectoderm-derived structure	9.21e-30	169
regional part of telencephalon	4.62e-29	33
ectoderm	5.76e-29	173
presumptive ectoderm	5.76e-29	173
anterior region of body	2.37e-28	129
craniocervical region	2.37e-28	129
head	3.09e-28	123
cerebral hemisphere	6.44e-28	32
regional part of cerebral cortex	2.64e-22	22
cerebral cortex	1.57e-21	25
pallium	1.57e-21	25
neocortex	2.92e-20	20
posterior neural tube	2.82e-15	15
chordal neural plate	2.82e-15	15
segmental subdivision of nervous system	1.02e-12	13
organism subdivision	1.84e-12	365
segmental subdivision of hindbrain	4.50e-12	12
hindbrain	4.50e-12	12
presumptive hindbrain	4.50e-12	12
embryo	3.07e-11	612
multi-cellular organism	5.30e-11	659
cell layer	3.16e-10	312
nucleus of brain	4.07e-10	9
neural nucleus	4.07e-10	9
basal ganglion	4.90e-10	9
nuclear complex of neuraxis	4.90e-10	9
aggregate regional part of brain	4.90e-10	9
collection of basal ganglia	4.90e-10	9
cerebral subcortex	4.90e-10	9
epithelium	1.65e-09	309
tube	3.27e-09	194
regional part of metencephalon	5.24e-09	9
metencephalon	5.24e-09	9
future metencephalon	5.24e-09	9
embryonic structure	1.37e-08	605
developing anatomical structure	1.37e-08	605
multi-tissue structure	1.70e-08	347
temporal lobe	1.96e-08	7
organ	2.14e-08	511
germ layer	2.60e-08	604
embryonic tissue	2.60e-08	604
presumptive structure	2.60e-08	604
epiblast (generic)	2.60e-08	604
telencephalic nucleus	5.07e-08	7
anatomical system	1.00e-07	625
anatomical group	1.24e-07	626
organ part	1.90e-07	219
brainstem	1.91e-07	8
gyrus	7.26e-07	6

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	0.0131839026176274

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.