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	3.22e-54	57
neural rod	3.22e-54	57
future spinal cord	3.22e-54	57
neural keel	3.22e-54	57
central nervous system	8.90e-46	82
regional part of brain	1.01e-42	59
regional part of nervous system	4.04e-38	94
nervous system	4.04e-38	94
brain	7.22e-37	69
future brain	7.22e-37	69
neurectoderm	3.98e-35	90
neural plate	5.28e-35	86
presumptive neural plate	5.28e-35	86
regional part of forebrain	1.82e-34	41
forebrain	1.82e-34	41
future forebrain	1.82e-34	41
anterior neural tube	1.68e-33	42
adult organism	2.36e-30	115
gray matter	2.68e-29	34
brain grey matter	2.68e-29	34
telencephalon	9.81e-29	34
regional part of telencephalon	1.20e-26	33
cerebral hemisphere	9.06e-25	32
anterior region of body	2.54e-23	129
craniocervical region	2.54e-23	129
posterior neural tube	2.57e-22	15
chordal neural plate	2.57e-22	15
head	4.25e-22	123
pre-chordal neural plate	4.24e-21	61
ectoderm	1.46e-20	173
presumptive ectoderm	1.46e-20	173
ectoderm-derived structure	4.58e-20	169
regional part of cerebral cortex	1.82e-19	22
brainstem	1.25e-18	8
cerebral cortex	7.97e-17	25
pallium	7.97e-17	25
gyrus	3.80e-16	6
neocortex	2.22e-15	20
nucleus of brain	2.55e-15	9
neural nucleus	2.55e-15	9
segmental subdivision of hindbrain	3.22e-15	12
hindbrain	3.22e-15	12
presumptive hindbrain	3.22e-15	12
segmental subdivision of nervous system	6.37e-14	13
tube	1.09e-13	194
basal ganglion	7.03e-11	9
nuclear complex of neuraxis	7.03e-11	9
aggregate regional part of brain	7.03e-11	9
collection of basal ganglia	7.03e-11	9
cerebral subcortex	7.03e-11	9
anatomical conduit	1.86e-10	241
pons	2.94e-10	3
medulla oblongata	3.22e-10	3
myelencephalon	3.22e-10	3
future myelencephalon	3.22e-10	3
brainstem nucleus	3.62e-10	3
telencephalic nucleus	4.06e-10	7
spinal cord	1.73e-09	3
limbic system	3.02e-09	5
anatomical cluster	4.94e-09	286
middle temporal gyrus	1.48e-08	3
regional part of metencephalon	3.25e-08	9
metencephalon	3.25e-08	9
future metencephalon	3.25e-08	9
temporal lobe	4.87e-08	7
locus ceruleus	1.99e-07	2
hindbrain nucleus	1.99e-07	2
globus pallidus	3.39e-07	2
pallidum	3.39e-07	2
dorsal plus ventral thalamus	3.50e-07	2
organ part	4.02e-07	219
epithelium	4.19e-07	309
diencephalon	4.38e-07	7
future diencephalon	4.38e-07	7
pituitary gland	6.08e-07	2
cell layer	6.12e-07	312
Ammon's horn	6.44e-07	2
lobe parts of cerebral cortex	6.44e-07	2
hippocampal formation	6.44e-07	2
limbic lobe	6.44e-07	2

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.