Coexpression cluster:C1405

Full id: C1405_smallcell_pineal_small_occipital_somatostatinoma_medial_amygdala

Phase1 CAGE Peaks

Hg19::chr15:51973680..51973707,+	p1@SCG3
Hg19::chr15:51973708..51973725,+	p3@SCG3
Hg19::chr1:154540296..154540327,+	p1@CHRNB2
Hg19::chr1:42846443..42846502,+	p1@RIMKLA
Hg19::chr20:17207640..17207661,+	p2@PCSK2
Hg19::chr2:220408724..220408789,+	p1@TMEM198

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:0004286	proprotein convertase 2 activity	0.00588650804177389
GO:0014059	regulation of dopamine secretion	0.00588650804177389
GO:0021955	central nervous system neuron axonogenesis	0.00588650804177389
GO:0014046	dopamine secretion	0.00588650804177389
GO:0021952	central nervous system projection neuron axonogenesis	0.00588650804177389
GO:0032225	regulation of synaptic transmission, dopaminergic	0.00588650804177389
GO:0048814	regulation of dendrite morphogenesis	0.00588650804177389
GO:0016808	proprotein convertase activity	0.00588650804177389
GO:0050433	regulation of catecholamine secretion	0.00588650804177389
GO:0050773	regulation of dendrite development	0.00588650804177389
GO:0050432	catecholamine secretion	0.00588650804177389
GO:0048813	dendrite morphogenesis	0.00588650804177389
GO:0035094	response to nicotine	0.00588650804177389
GO:0008306	associative learning	0.00588650804177389
GO:0021954	central nervous system neuron development	0.00588650804177389
GO:0001963	synaptic transmission, dopaminergic	0.00727114064039783
GO:0021953	central nervous system neuron differentiation	0.00727114064039783
GO:0043279	response to alkaloid	0.00784706013717014
GO:0030890	positive regulation of B cell proliferation	0.00784706013717014
GO:0051899	membrane depolarization	0.00784706013717014
GO:0030888	regulation of B cell proliferation	0.00784706013717014
GO:0007613	memory	0.00784706013717014
GO:0014070	response to organic cyclic substance	0.00784706013717014
GO:0007267	cell-cell signaling	0.00784706013717014
GO:0016358	dendrite development	0.00784706013717014
GO:0046928	regulation of neurotransmitter secretion	0.00784706013717014
GO:0007271	synaptic transmission, cholinergic	0.00784706013717014
GO:0005892	nicotinic acetylcholine-gated receptor-channel complex	0.00819713399072745
GO:0050804	regulation of synaptic transmission	0.00962878184772167
GO:0007612	learning	0.00962878184772167
GO:0051969	regulation of transmission of nerve impulse	0.00962878184772167
GO:0050871	positive regulation of B cell activation	0.00962878184772167
GO:0042100	B cell proliferation	0.00962878184772167
GO:0007270	nerve-nerve synaptic transmission	0.00986449096606127
GO:0015464	acetylcholine receptor activity	0.0105907245387965
GO:0042166	acetylcholine binding	0.0107865314738784
GO:0004889	nicotinic acetylcholine-activated cation-selective channel activity	0.010971726164849
GO:0031644	regulation of neurological process	0.0113135441234759
GO:0050864	regulation of B cell activation	0.0113135441234759
GO:0032946	positive regulation of mononuclear cell proliferation	0.0129120955954723
GO:0050671	positive regulation of lymphocyte proliferation	0.0129120955954723
GO:0042391	regulation of membrane potential	0.0130244367204868
GO:0046879	hormone secretion	0.0139514273861003
GO:0004289	subtilase activity	0.0140349464792311
GO:0050767	regulation of neurogenesis	0.0148980047794665
GO:0007269	neurotransmitter secretion	0.0153402913403732
GO:0050670	regulation of lymphocyte proliferation	0.0154352590373835
GO:0032944	regulation of mononuclear cell proliferation	0.0154352590373835
GO:0043176	amine binding	0.0155225462346516
GO:0007611	learning and/or memory	0.0155225462346516
GO:0001666	response to hypoxia	0.016599698156691
GO:0009897	external side of plasma membrane	0.0166898725144052
GO:0051251	positive regulation of lymphocyte activation	0.0166898725144052
GO:0045055	regulated secretory pathway	0.0166898725144052
GO:0032943	mononuclear cell proliferation	0.0166898725144052
GO:0046651	lymphocyte proliferation	0.0166898725144052
GO:0051046	regulation of secretion	0.018250114138437
GO:0042113	B cell activation	0.0185263443156412
GO:0010033	response to organic substance	0.0185263443156412
GO:0003001	generation of a signal involved in cell-cell signaling	0.0205633800705441
GO:0005231	excitatory extracellular ligand-gated ion channel activity	0.0208029434278018
GO:0051249	regulation of lymphocyte activation	0.0216019449595088
GO:0001505	regulation of neurotransmitter levels	0.0218172203414233
GO:0050865	regulation of cell activation	0.0220257035271641
GO:0043235	receptor complex	0.0297930673958638
GO:0007409	axonogenesis	0.0304050423764427
GO:0048667	neuron morphogenesis during differentiation	0.0310584828125304
GO:0048812	neurite morphogenesis	0.0310584828125304
GO:0000904	cellular morphogenesis during differentiation	0.0321330951278089
GO:0005230	extracellular ligand-gated ion channel activity	0.0329261050180939
GO:0031175	neurite development	0.0334496300870671
GO:0030594	neurotransmitter receptor activity	0.0344449617093647
GO:0042165	neurotransmitter binding	0.0349327699114972
GO:0009986	cell surface	0.0349350746353671
GO:0045211	postsynaptic membrane	0.0349350746353671
GO:0048666	neuron development	0.0353916510545207
GO:0046649	lymphocyte activation	0.0353916510545207
GO:0044456	synapse part	0.0360328383118421
GO:0015276	ligand-gated ion channel activity	0.0360328383118421
GO:0022834	ligand-gated channel activity	0.0360328383118421
GO:0045321	leukocyte activation	0.0390415637659016
GO:0006816	calcium ion transport	0.0392047360730927
GO:0032990	cell part morphogenesis	0.0421350544475285
GO:0048858	cell projection morphogenesis	0.0421350544475285
GO:0030030	cell projection organization and biogenesis	0.0421350544475285
GO:0001775	cell activation	0.0423697106789525
GO:0030182	neuron differentiation	0.0423697106789525
GO:0007601	visual perception	0.0439646645802476
GO:0050953	sensory perception of light stimulus	0.0439646645802476
GO:0008284	positive regulation of cell proliferation	0.0442068515711884
GO:0007417	central nervous system development	0.0442068515711884
GO:0050793	regulation of developmental process	0.0442068515711884
GO:0055082	cellular chemical homeostasis	0.0442068515711884
GO:0006873	cellular ion homeostasis	0.0442068515711884
GO:0045045	secretory pathway	0.0442068515711884
GO:0048699	generation of neurons	0.0442068515711884
GO:0015674	di-, tri-valent inorganic cation transport	0.0446484715958753
GO:0022008	neurogenesis	0.0468559071508107
GO:0050801	ion homeostasis	0.0472608049517232
GO:0051239	regulation of multicellular organismal process	0.0485262389823197

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>disease_data<br>

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Cell Type

Ontology term	p-value	n
neuronal stem cell	2.69e-08	8

Uber Anatomy

Ontology term	p-value	n
adult organism	1.33e-60	114
nervous system	7.62e-56	89
central nervous system	1.22e-53	81
neural tube	2.51e-50	56
neural rod	2.51e-50	56
future spinal cord	2.51e-50	56
neural keel	2.51e-50	56
regional part of nervous system	1.22e-47	53
regional part of brain	1.22e-47	53
neurectoderm	4.12e-43	86
brain	5.73e-42	68
future brain	5.73e-42	68
regional part of forebrain	2.01e-41	41
forebrain	2.01e-41	41
anterior neural tube	2.01e-41	41
future forebrain	2.01e-41	41
neural plate	1.75e-40	82
presumptive neural plate	1.75e-40	82
ectoderm-derived structure	3.46e-35	171
ectoderm	3.46e-35	171
presumptive ectoderm	3.46e-35	171
organ system subdivision	4.90e-35	223
telencephalon	1.27e-34	34
brain grey matter	1.61e-34	34
gray matter	1.61e-34	34
cerebral hemisphere	4.19e-33	32
ecto-epithelium	1.21e-32	104
regional part of telencephalon	1.22e-32	32
pre-chordal neural plate	9.98e-32	61
cerebral cortex	3.86e-26	25
pallium	3.86e-26	25
regional part of cerebral cortex	2.27e-25	22
structure with developmental contribution from neural crest	8.45e-24	132
neocortex	1.76e-23	20
anatomical cluster	8.57e-20	373
tube	6.77e-12	192
multi-tissue structure	9.79e-12	342
embryo	1.13e-10	592
organ part	1.91e-10	218
posterior neural tube	3.61e-10	15
chordal neural plate	3.61e-10	15
anatomical conduit	4.78e-10	240
basal ganglion	5.86e-10	9
nuclear complex of neuraxis	5.86e-10	9
aggregate regional part of brain	5.86e-10	9
collection of basal ganglia	5.86e-10	9
cerebral subcortex	5.86e-10	9
neural nucleus	9.72e-10	9
nucleus of brain	9.72e-10	9
developing anatomical structure	9.17e-09	581
segmental subdivision of nervous system	1.73e-08	13
temporal lobe	2.04e-08	6
organ	3.08e-08	503
diencephalon	4.21e-08	7
future diencephalon	4.21e-08	7
gyrus	5.23e-08	6
telencephalic nucleus	6.22e-08	7
multi-cellular organism	8.10e-08	656
segmental subdivision of hindbrain	8.92e-08	12
hindbrain	8.92e-08	12
presumptive hindbrain	8.92e-08	12
embryonic structure	1.74e-07	564
germ layer	1.80e-07	560
germ layer / neural crest	1.80e-07	560
embryonic tissue	1.80e-07	560
presumptive structure	1.80e-07	560
germ layer / neural crest derived structure	1.80e-07	560
epiblast (generic)	1.80e-07	560
parietal lobe	4.71e-07	5
brainstem	5.59e-07	6
occipital lobe	5.67e-07	5
epithelium	9.67e-07	306

Disease

Ontology term	p-value	n
neuroectodermal tumor	7.47e-09	10
germ cell and embryonal cancer	5.69e-08	22
germ cell cancer	5.69e-08	22

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
BCL3#602	2	11.5157009345794	0.0116272534680164	0.0424801904759729
HDAC2#3066	3	6.70781011831313	0.00697394002796266	0.029487907796777
JUND#3727	4	4.66310929458068	0.00491764340826023	0.0229888438259384
NRF1#4899	3	6.10513972385545	0.00909016207939674	0.0344048502359251
POLR2A#5430	6	2.14745317655807	0.0101957067681878	0.0380187596102102
REST#5978	5	8.04169059677335	6.54774545315482e-05	0.00106153366560391
SIN3A#25942	5	4.50740393901261	0.00109611006120864	0.00765986207310597
SMARCA4#6597	2	52.2553011026293	0.000599565921574195	0.00500984601034381
SMARCB1#6598	3	9.12635789057871	0.00290024715036702	0.0156779975226284
SRF#6722	3	6.8985891310839	0.0064424516893037	0.0280001336653845
TAF1#6872	6	3.34304628574529	0.000716247428463562	0.00573080251140014
TAF7#6879	3	5.71653470246196	0.0109272937988966	0.0402112553138706
ZNF263#10127	4	5.48122775800712	0.00267560938060723	0.014745288802767

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.