Coexpression cluster:C1753

Full id: C1753_neuroblastoma_pineal_rectum_retina_merkel_carcinosarcoma_eye

Phase1 CAGE Peaks

Hg19::chr15:78913289..78913302,-	p4@CHRNA3
Hg19::chr15:78913306..78913349,-	p1@CHRNA3
Hg19::chr15:78913353..78913365,-	p3@CHRNA3
Hg19::chr15:78933542..78933562,-	p2@CHRNB4
Hg19::chr15:78933567..78933604,-	p1@CHRNB4

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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p.value	FDR	nGenes	nPathway	Name
9.04613128104753e-05	0.0190873370030103	2	272	Neuroactive ligand-receptor interaction (KEGG):04080
4.73856659734924e-05	0.0149975632806103	2	197	Synaptic Transmission (Reactome):REACT_13685
1.91447319275479e-07	0.000121186153101378	2	13	{CHRNA1,13} (Static Module):NA

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:0005892	nicotinic acetylcholine-gated receptor-channel complex	9.64592211467951e-06
GO:0015464	acetylcholine receptor activity	9.64592211467951e-06
GO:0042166	acetylcholine binding	9.64592211467951e-06
GO:0004889	nicotinic acetylcholine-activated cation-selective channel activity	9.64592211467951e-06
GO:0043176	amine binding	2.88538887604326e-05
GO:0005231	excitatory extracellular ligand-gated ion channel activity	6.4967001120213e-05
GO:0043235	receptor complex	0.000130609380186344
GO:0005230	extracellular ligand-gated ion channel activity	0.000145598413308646
GO:0030594	neurotransmitter receptor activity	0.000145598413308646
GO:0042165	neurotransmitter binding	0.000145598413308646
GO:0045211	postsynaptic membrane	0.000145598413308646
GO:0044456	synapse part	0.000145598413308646
GO:0015276	ligand-gated ion channel activity	0.000145598413308646
GO:0022834	ligand-gated channel activity	0.000145598413308646
GO:0035095	behavioral response to nicotine	0.00030474923985843
GO:0060073	micturition	0.00030474923985843
GO:0060084	synaptic transmission involved in micturition	0.00030474923985843
GO:0005261	cation channel activity	0.000736886645026226
GO:0030054	cell junction	0.000736886645026226
GO:0046873	metal ion transmembrane transporter activity	0.000924178466639651
GO:0022836	gated channel activity	0.000924178466639651
GO:0035094	response to nicotine	0.00117737092459055
GO:0005216	ion channel activity	0.00142681635278938
GO:0022838	substrate specific channel activity	0.00142681635278938
GO:0022803	passive transmembrane transporter activity	0.00142681635278938
GO:0015267	channel activity	0.00142681635278938
GO:0043279	response to alkaloid	0.00153487505515621
GO:0003014	renal system process	0.00160762563893901
GO:0007274	neuromuscular synaptic transmission	0.00160762563893901
GO:0014070	response to organic cyclic substance	0.00186392717093987
GO:0008324	cation transmembrane transporter activity	0.00186392717093987
GO:0046928	regulation of neurotransmitter secretion	0.00188359938245719
GO:0007271	synaptic transmission, cholinergic	0.00188359938245719
GO:0006940	regulation of smooth muscle contraction	0.00304664016645142
GO:0015075	ion transmembrane transporter activity	0.00363495337446202
GO:0005887	integral to plasma membrane	0.00363495337446202
GO:0031226	intrinsic to plasma membrane	0.00363495337446202
GO:0030534	adult behavior	0.00363495337446202
GO:0006811	ion transport	0.00363495337446202
GO:0022891	substrate-specific transmembrane transporter activity	0.00440723325204938
GO:0006939	smooth muscle contraction	0.00470705748726614
GO:0006937	regulation of muscle contraction	0.00470705748726614
GO:0022857	transmembrane transporter activity	0.00470705748726614
GO:0007269	neurotransmitter secretion	0.00470705748726614
GO:0022892	substrate-specific transporter activity	0.00528172907724811
GO:0045055	regulated secretory pathway	0.0059645416008552
GO:0051046	regulation of secretion	0.00649792663916262
GO:0004888	transmembrane receptor activity	0.00649813937510364
GO:0010033	response to organic substance	0.00654933290669141
GO:0003001	generation of a signal involved in cell-cell signaling	0.00724566593174309
GO:0044459	plasma membrane part	0.00776229847011137
GO:0001505	regulation of neurotransmitter levels	0.00776229847011137
GO:0043234	protein complex	0.0119540749559224
GO:0004872	receptor activity	0.0134608779566729
GO:0003012	muscle system process	0.0152278255222535
GO:0006936	muscle contraction	0.0152278255222535
GO:0007626	locomotory behavior	0.01640752823724
GO:0060089	molecular transducer activity	0.0177936923627931
GO:0004871	signal transducer activity	0.0177936923627931
GO:0005886	plasma membrane	0.0185014123823964
GO:0032991	macromolecular complex	0.0188428378990201
GO:0045045	secretory pathway	0.0197011740994843
GO:0006810	transport	0.0197011740994843
GO:0051234	establishment of localization	0.0203666329991751
GO:0051239	regulation of multicellular organismal process	0.021988223475816
GO:0007268	synaptic transmission	0.0222025422545425
GO:0007610	behavior	0.0222025422545425
GO:0051179	localization	0.0222025422545425
GO:0032940	secretion by cell	0.0222025422545425
GO:0019226	transmission of nerve impulse	0.0243052074014842
GO:0046903	secretion	0.0278618091882116
GO:0007165	signal transduction	0.027996284948599
GO:0007154	cell communication	0.0322850773249661
GO:0042221	response to chemical stimulus	0.040878993381908
GO:0007267	cell-cell signaling	0.0437931675882937
GO:0016021	integral to membrane	0.0448731129004987
GO:0031224	intrinsic to membrane	0.0448731129004987

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
neuron	3.83e-10	6
neuroblast	3.83e-10	6
electrically signaling cell	3.83e-10	6
embryonic stem cell	3.31e-09	5
neurectodermal cell	1.67e-07	59
neuronal stem cell	2.33e-07	8

Uber Anatomy

Ontology term	p-value	n
neural plate	8.73e-31	82
presumptive neural plate	8.73e-31	82
neurectoderm	1.10e-28	86
nervous system	4.02e-28	89
central nervous system	2.54e-27	81
neural tube	1.14e-25	56
neural rod	1.14e-25	56
future spinal cord	1.14e-25	56
neural keel	1.14e-25	56
adult organism	1.60e-24	114
regional part of nervous system	3.83e-24	53
regional part of brain	3.83e-24	53
ecto-epithelium	4.37e-24	104
ectoderm-derived structure	3.14e-21	171
ectoderm	3.14e-21	171
presumptive ectoderm	3.14e-21	171
organ system subdivision	1.12e-20	223
pre-chordal neural plate	2.69e-20	61
brain	9.72e-19	68
future brain	9.72e-19	68
structure with developmental contribution from neural crest	2.54e-17	132
regional part of forebrain	3.98e-15	41
forebrain	3.98e-15	41
anterior neural tube	3.98e-15	41
future forebrain	3.98e-15	41
anatomical cluster	5.96e-15	373
posterior neural tube	1.29e-12	15
chordal neural plate	1.29e-12	15
diencephalon	1.04e-11	7
future diencephalon	1.04e-11	7
segmental subdivision of hindbrain	2.75e-11	12
hindbrain	2.75e-11	12
presumptive hindbrain	2.75e-11	12
gastrointestinal system	5.69e-11	25
organ part	1.26e-10	218
segmental subdivision of nervous system	3.06e-10	13
intestine	1.38e-09	17
organ segment	3.84e-09	98
multi-tissue structure	4.73e-09	342
embryo	5.36e-09	592
brainstem	1.24e-08	6
pigment epithelium of eye	1.67e-08	11
brain grey matter	2.30e-08	34
gray matter	2.30e-08	34
telencephalon	2.84e-08	34
gland of diencephalon	6.08e-08	4
neuroendocrine gland	6.08e-08	4
cerebral hemisphere	7.99e-08	32
regional part of metencephalon	8.46e-08	9
metencephalon	8.46e-08	9
future metencephalon	8.46e-08	9
basal ganglion	9.81e-08	9
nuclear complex of neuraxis	9.81e-08	9
aggregate regional part of brain	9.81e-08	9
collection of basal ganglia	9.81e-08	9
cerebral subcortex	9.81e-08	9
regional part of diencephalon	1.43e-07	4
multi-cellular organism	1.51e-07	656
eye	1.60e-07	21
visual system	1.60e-07	21
neural nucleus	1.93e-07	9
nucleus of brain	1.93e-07	9
retina	2.96e-07	6
photoreceptor array	2.96e-07	6
posterior segment of eyeball	2.96e-07	6
organ	5.92e-07	503
regional part of telencephalon	8.12e-07	32

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
NANOG#79923	2	11.6979113924051	0.0109116495195608	0.0402217119321431

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.