Coexpression cluster:C2709

Full id: C2709_pituitary_pineal_retinoblastoma_argyrophil_carcinoid_cerebellum_iPS

Phase1 CAGE Peaks

Hg19::chr2:98962946..98962963,+	p1@CNGA3
Hg19::chr3:19189589..19189626,+	p5@KCNH8
Hg19::chr5:89854580..89854593,+	p4@GPR98
Hg19::chr5:89854867..89854899,+	p@chr5:89854867..89854899 +

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:0005249	voltage-gated potassium channel activity	0.00354585496442826
GO:0005267	potassium channel activity	0.00354585496442826
GO:0007601	visual perception	0.00354585496442826
GO:0050953	sensory perception of light stimulus	0.00354585496442826
GO:0022843	voltage-gated cation channel activity	0.00354585496442826
GO:0006813	potassium ion transport	0.00354585496442826
GO:0022832	voltage-gated channel activity	0.00423142055570313
GO:0005244	voltage-gated ion channel activity	0.00423142055570313
GO:0048496	maintenance of organ identity	0.00494481231918518
GO:0005261	cation channel activity	0.00571673838554059
GO:0046873	metal ion transmembrane transporter activity	0.00687851363887805
GO:0022836	gated channel activity	0.00687851363887805
GO:0015672	monovalent inorganic cation transport	0.00693836414094316
GO:0019002	GMP binding	0.00785864363720596
GO:0030553	cGMP binding	0.00785864363720596
GO:0005216	ion channel activity	0.00785864363720596
GO:0030001	metal ion transport	0.00785864363720596
GO:0022838	substrate specific channel activity	0.00785864363720596
GO:0022803	passive transmembrane transporter activity	0.00785864363720596
GO:0015267	channel activity	0.00785864363720596
GO:0045494	photoreceptor cell maintenance	0.00794444668596613
GO:0000155	two-component sensor activity	0.00978554135310251
GO:0006812	cation transport	0.00978554135310251
GO:0008324	cation transmembrane transporter activity	0.00978554135310251
GO:0000160	two-component signal transduction system (phosphorelay)	0.00978554135310251
GO:0030551	cyclic nucleotide binding	0.0106912991966847
GO:0007600	sensory perception	0.0107332785924815
GO:0004673	protein histidine kinase activity	0.0111179690311578
GO:0016775	phosphotransferase activity, nitrogenous group as acceptor	0.012266658879953
GO:0007165	signal transduction	0.0145568394445184
GO:0050877	neurological system process	0.0165785386159458
GO:0007154	cell communication	0.0168591289326561
GO:0015075	ion transmembrane transporter activity	0.0168591289326561
GO:0006811	ion transport	0.0174311980338561
GO:0045596	negative regulation of cell differentiation	0.0203214149269298
GO:0022891	substrate-specific transmembrane transporter activity	0.0203214149269298
GO:0003008	system process	0.0203214149269298
GO:0022857	transmembrane transporter activity	0.0219192063984734
GO:0051093	negative regulation of developmental process	0.0219192063984734
GO:0016021	integral to membrane	0.023466445814658
GO:0031224	intrinsic to membrane	0.023466445814658
GO:0022892	substrate-specific transporter activity	0.023466445814658
GO:0050954	sensory perception of mechanical stimulus	0.032925205536912
GO:0007605	sensory perception of sound	0.032925205536912
GO:0044425	membrane part	0.032925205536912
GO:0030955	potassium ion binding	0.0339473491586143
GO:0045595	regulation of cell differentiation	0.0339473491586143
GO:0009986	cell surface	0.0341594209964774
GO:0015276	ligand-gated ion channel activity	0.0363211010183369
GO:0022834	ligand-gated channel activity	0.0363211010183369
GO:0007218	neuropeptide signaling pathway	0.0364731310049928
GO:0031420	alkali metal ion binding	0.0471945555141875
GO:0050793	regulation of developmental process	0.0492038426264123

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
neural cell	4.48e-12	25
neuronal stem cell	1.67e-09	8
neurectodermal cell	1.25e-07	59
neuron	2.24e-07	6
neuroblast	2.24e-07	6
electrically signaling cell	2.24e-07	6

Uber Anatomy

Ontology term	p-value	n
regional part of nervous system	5.89e-49	94
nervous system	5.89e-49	94
central nervous system	2.21e-44	82
neural tube	7.91e-39	57
neural rod	7.91e-39	57
future spinal cord	7.91e-39	57
neural keel	7.91e-39	57
brain	4.42e-34	69
future brain	4.42e-34	69
regional part of brain	1.46e-31	59
adult organism	8.24e-31	115
neural plate	7.77e-30	86
presumptive neural plate	7.77e-30	86
anterior neural tube	1.12e-29	42
regional part of forebrain	6.86e-29	41
forebrain	6.86e-29	41
future forebrain	6.86e-29	41
neurectoderm	1.40e-28	90
pre-chordal neural plate	3.99e-26	61
ectoderm-derived structure	4.25e-23	169
ectoderm	1.27e-22	173
presumptive ectoderm	1.27e-22	173
telencephalon	1.68e-22	34
gray matter	4.07e-22	34
brain grey matter	4.07e-22	34
regional part of telencephalon	8.71e-22	33
cerebral hemisphere	3.83e-21	32
anterior region of body	2.54e-20	129
craniocervical region	2.54e-20	129
head	4.53e-19	123
cerebral cortex	4.45e-18	25
pallium	4.45e-18	25
regional part of cerebral cortex	2.23e-15	22
neocortex	7.41e-14	20
posterior neural tube	4.06e-10	15
chordal neural plate	4.06e-10	15
segmental subdivision of nervous system	2.22e-08	13
diencephalon	5.63e-08	7
future diencephalon	5.63e-08	7
segmental subdivision of hindbrain	1.07e-07	12
hindbrain	1.07e-07	12
presumptive hindbrain	1.07e-07	12
brainstem	1.67e-07	8
epithelium	2.66e-07	309
organism subdivision	3.71e-07	365
tube	4.87e-07	194
cell layer	5.22e-07	312
male reproductive organ	9.06e-07	11
organ part	9.29e-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	7.23752153709602	0.00410469730419261	0.0195865345525916
ZNF263#10127	3	6.16638122775801	0.00653981434797598	0.027983106796471

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.