Coexpression cluster:C759

Full id: C759_nonsmall_gastrointestinal_occipital_pineal_cerebellum_small_argyrophil

Phase1 CAGE Peaks

Hg19::chr15:48483855..48483892,+	p1@CTXN2 p2@SLC12A1
Hg19::chr18:40857274..40857292,-	p5@SYT4
Hg19::chr18:40857296..40857305,-	p8@SYT4
Hg19::chr18:40857329..40857357,-	p2@SYT4
Hg19::chr18:40857368..40857384,-	p6@SYT4
Hg19::chr18:40857389..40857405,-	p3@SYT4
Hg19::chr18:40857447..40857461,-	p1@SYT4
Hg19::chr18:40857470..40857481,-	p7@SYT4
Hg19::chr18:40857484..40857491,-	p9@SYT4
Hg19::chr18:40857493..40857505,-	p4@SYT4
Hg19::chr6:158957739..158957759,+	p3@TMEM181

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:0007269	neurotransmitter secretion	0.0360628509212003
GO:0045055	regulated secretory pathway	0.0360628509212003
GO:0048471	perinuclear region of cytoplasm	0.0360628509212003
GO:0003001	generation of a signal involved in cell-cell signaling	0.0360628509212003
GO:0008021	synaptic vesicle	0.0360628509212003
GO:0001505	regulation of neurotransmitter levels	0.0360628509212003
GO:0043005	neuron projection	0.0360628509212003
GO:0030136	clathrin-coated vesicle	0.0447778552108827

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	1.91e-11	8
neuron	2.88e-11	6
neuroblast	2.88e-11	6
electrically signaling cell	2.88e-11	6

Uber Anatomy

Ontology term	p-value	n
nervous system	3.45e-86	89
central nervous system	2.23e-85	81
neural tube	7.41e-81	56
neural rod	7.41e-81	56
future spinal cord	7.41e-81	56
neural keel	7.41e-81	56
regional part of nervous system	8.21e-76	53
regional part of brain	8.21e-76	53
brain	3.48e-66	68
future brain	3.48e-66	68
regional part of forebrain	6.22e-64	41
forebrain	6.22e-64	41
anterior neural tube	6.22e-64	41
future forebrain	6.22e-64	41
neurectoderm	2.69e-56	86
neural plate	8.68e-53	82
presumptive neural plate	8.68e-53	82
telencephalon	1.46e-50	34
adult organism	1.70e-50	114
brain grey matter	1.85e-50	34
gray matter	1.85e-50	34
cerebral hemisphere	1.04e-47	32
regional part of telencephalon	4.30e-47	32
ectoderm-derived structure	2.74e-45	171
ectoderm	2.74e-45	171
presumptive ectoderm	2.74e-45	171
ecto-epithelium	3.80e-42	104
pre-chordal neural plate	1.56e-41	61
regional part of cerebral cortex	6.48e-41	22
organ system subdivision	1.42e-38	223
neocortex	2.38e-37	20
cerebral cortex	2.29e-35	25
pallium	2.29e-35	25
structure with developmental contribution from neural crest	6.23e-30	132
anatomical cluster	1.75e-18	373
tube	6.77e-18	192
posterior neural tube	2.05e-17	15
chordal neural plate	2.05e-17	15
basal ganglion	1.07e-16	9
nuclear complex of neuraxis	1.07e-16	9
aggregate regional part of brain	1.07e-16	9
collection of basal ganglia	1.07e-16	9
cerebral subcortex	1.07e-16	9
neural nucleus	2.07e-16	9
nucleus of brain	2.07e-16	9
diencephalon	1.28e-14	7
future diencephalon	1.28e-14	7
anatomical conduit	2.22e-13	240
telencephalic nucleus	3.71e-13	7
gyrus	3.91e-13	6
segmental subdivision of hindbrain	6.28e-13	12
hindbrain	6.28e-13	12
presumptive hindbrain	6.28e-13	12
segmental subdivision of nervous system	8.89e-12	13
brainstem	9.74e-12	6
occipital lobe	3.66e-11	5
parietal lobe	4.07e-11	5
temporal lobe	8.56e-11	6
limbic system	1.34e-10	5
gland of diencephalon	9.13e-10	4
neuroendocrine gland	9.13e-10	4
organ part	6.43e-09	218
regional part of diencephalon	7.14e-09	4
corpus striatum	7.59e-09	4
striatum	7.59e-09	4
ventral part of telencephalon	7.59e-09	4
future corpus striatum	7.59e-09	4
embryo	1.17e-08	592
epithelium	1.35e-08	306
regional part of metencephalon	2.01e-08	9
metencephalon	2.01e-08	9
future metencephalon	2.01e-08	9
cell layer	2.24e-08	309
germ layer	2.53e-08	560
germ layer / neural crest	2.53e-08	560
embryonic tissue	2.53e-08	560
presumptive structure	2.53e-08	560
germ layer / neural crest derived structure	2.53e-08	560
epiblast (generic)	2.53e-08	560
embryonic structure	4.10e-08	564
developing anatomical structure	9.82e-08	581
frontal cortex	1.71e-07	3
multi-tissue structure	2.29e-07	342
caudate-putamen	5.97e-07	3
dorsal striatum	5.97e-07	3
pons	7.02e-07	3

Disease

Ontology term	p-value	n
neuroectodermal tumor	2.80e-11	10
neuroendocrine tumor	3.21e-08	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
CTCF#10664	9	4.3856643052432	1.04204760534736e-05	0.000270857167383953
RAD21#5885	9	8.47230045991881	3.34431965405885e-08	2.24039384445319e-06
REST#5978	11	9.65002871612802	1.47593496597899e-11	1.80709462968206e-09
SIN3A#25942	7	3.44201755342781	0.00120675394335343	0.00818284476625688
TBP#6908	9	3.03281238035159	0.000238825863057691	0.00260063959043709
YY1#7528	7	3.12529047717973	0.00219383950773288	0.0126447243017723
ZNF263#10127	10	7.47440148819152	6.91943485229632e-09	5.40103779177112e-07

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.