Coexpression cluster:C2239

Full id: C2239_locus_pons_medulla_gastrointestinal_thalamus_globus_medial

Phase1 CAGE Peaks

Hg19::chr12:72332618..72332632,+	p1@TPH2
Hg19::chr15:60296481..60296492,+	p7@FOXB1
Hg19::chr2:234077664..234077672,+	p@chr2:234077664..234077672 +
Hg19::chr2:237146889..237146895,-	p@chr2:237146889..237146895 -

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:0006587	serotonin biosynthetic process from tryptophan	0.00476793112366575
GO:0042428	serotonin metabolic process	0.00476793112366575
GO:0042427	serotonin biosynthetic process	0.00476793112366575
GO:0004510	tryptophan 5-monooxygenase activity	0.00476793112366575
GO:0042435	indole derivative biosynthetic process	0.00476793112366575
GO:0046219	indolalkylamine biosynthetic process	0.00476793112366575
GO:0006568	tryptophan metabolic process	0.00476793112366575
GO:0016714	oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, reduced pteridine as one donor, and incorporation of one atom of oxygen	0.00476793112366575
GO:0042430	indole and derivative metabolic process	0.00476793112366575
GO:0006586	indolalkylamine metabolic process	0.00476793112366575
GO:0042434	indole derivative metabolic process	0.00476793112366575
GO:0042136	neurotransmitter biosynthetic process	0.00635677358608103
GO:0016597	amino acid binding	0.00733430683427203
GO:0042133	neurotransmitter metabolic process	0.0108036514740413
GO:0042401	biogenic amine biosynthetic process	0.0108036514740413
GO:0042398	amino acid derivative biosynthetic process	0.0116492810098451
GO:0042446	hormone biosynthetic process	0.0116492810098451
GO:0043176	amine binding	0.0116492810098451
GO:0009072	aromatic amino acid family metabolic process	0.0117881056163774
GO:0006576	biogenic amine metabolic process	0.0176249846095899
GO:0001505	regulation of neurotransmitter levels	0.0176919919675915
GO:0042445	hormone metabolic process	0.0186354249057678
GO:0006575	amino acid derivative metabolic process	0.0186354249057678
GO:0009309	amine biosynthetic process	0.0236034067788678
GO:0046483	heterocycle metabolic process	0.0247498102382317
GO:0044271	nitrogen compound biosynthetic process	0.0269031807789839
GO:0016705	oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen	0.0310829355447597
GO:0006725	aromatic compound metabolic process	0.0310829355447597
GO:0004497	monooxygenase activity	0.0381826713210847
GO:0007268	synaptic transmission	0.0459007070058853

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><br>uberon_data<br><br>

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Uber Anatomy

Ontology term	p-value	n
neural tube	5.57e-64	56
neural rod	5.57e-64	56
future spinal cord	5.57e-64	56
neural keel	5.57e-64	56
regional part of nervous system	3.57e-61	53
regional part of brain	3.57e-61	53
brainstem	2.91e-53	6
central nervous system	2.03e-47	81
brain	1.62e-46	68
future brain	1.62e-46	68
neural plate	5.36e-43	82
presumptive neural plate	5.36e-43	82
nervous system	1.77e-42	89
neurectoderm	7.03e-41	86
regional part of forebrain	1.16e-37	41
forebrain	1.16e-37	41
anterior neural tube	1.16e-37	41
future forebrain	1.16e-37	41
neural nucleus	1.05e-34	9
nucleus of brain	1.05e-34	9
brain grey matter	1.60e-33	34
gray matter	1.60e-33	34
ecto-epithelium	2.42e-33	104
adult organism	1.78e-30	114
posterior neural tube	1.94e-28	15
chordal neural plate	1.94e-28	15
telencephalon	9.71e-28	34
medulla oblongata	1.34e-27	3
myelencephalon	1.34e-27	3
future myelencephalon	1.34e-27	3
pons	1.75e-27	3
segmental subdivision of hindbrain	1.76e-26	12
hindbrain	1.76e-26	12
presumptive hindbrain	1.76e-26	12
structure with developmental contribution from neural crest	1.17e-25	132
pre-chordal neural plate	8.91e-25	61
segmental subdivision of nervous system	2.05e-24	13
regional part of telencephalon	2.10e-24	32
gyrus	4.97e-23	6
ectoderm-derived structure	5.87e-21	171
ectoderm	5.87e-21	171
presumptive ectoderm	5.87e-21	171
telencephalic nucleus	4.84e-20	7
cerebral hemisphere	1.08e-19	32
locus ceruleus	3.43e-19	2
brainstem nucleus	3.43e-19	2
hindbrain nucleus	3.43e-19	2
dorsal plus ventral thalamus	7.68e-19	2
thalamic complex	7.68e-19	2
globus pallidus	1.43e-18	2
pallidum	1.43e-18	2
middle frontal gyrus	2.22e-18	2
tube	1.12e-16	192
basal ganglion	1.20e-15	9
nuclear complex of neuraxis	1.20e-15	9
aggregate regional part of brain	1.20e-15	9
collection of basal ganglia	1.20e-15	9
cerebral subcortex	1.20e-15	9
organ system subdivision	2.74e-15	223
regional part of cerebral cortex	6.25e-13	22
anatomical conduit	1.09e-12	240
frontal cortex	1.41e-12	3
diencephalon	6.05e-12	7
future diencephalon	6.05e-12	7
cerebral cortex	2.17e-11	25
pallium	2.17e-11	25
substantia nigra	3.71e-10	1
midbrain nucleus	3.71e-10	1
regional part of midbrain	3.71e-10	1
midbrain	3.71e-10	1
presumptive midbrain	3.71e-10	1
midbrain neural tube	3.71e-10	1
neocortex	4.80e-10	20
regional part of diencephalon	6.93e-10	4
occipital pole	8.99e-10	1
pole of cerebral hemisphere	8.99e-10	1
corpus callosum	9.82e-10	1
central nervous system cell part cluster	9.82e-10	1
axon tract	9.82e-10	1
intercerebral commissure	9.82e-10	1
dorsal telencephalic commissure	9.82e-10	1
brain white matter	9.82e-10	1
brain commissure	9.82e-10	1
white matter	9.82e-10	1
nervous system commissure	9.82e-10	1
cerebral hemisphere white matter	9.82e-10	1
postcentral gyrus	1.07e-09	1
nucleus accumbens	1.17e-09	1
ventral striatum	1.17e-09	1
regional part of metencephalon	1.53e-09	9
metencephalon	1.53e-09	9
future metencephalon	1.53e-09	9
epithelium	3.18e-09	306
cell layer	4.21e-09	309
anatomical cluster	8.12e-08	373
limbic system	1.09e-07	5
organ part	1.96e-07	218
multi-tissue structure	7.18e-07	342

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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No analysis results for this cluster

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.