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Coexpression cluster:C2239

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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


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


GO IDGO nameFDR corrected p-value
GO:0006587serotonin biosynthetic process from tryptophan0.00476793112366575
GO:0042428serotonin metabolic process0.00476793112366575
GO:0042427serotonin biosynthetic process0.00476793112366575
GO:0004510tryptophan 5-monooxygenase activity0.00476793112366575
GO:0042435indole derivative biosynthetic process0.00476793112366575
GO:0046219indolalkylamine biosynthetic process0.00476793112366575
GO:0006568tryptophan metabolic process0.00476793112366575
GO:0016714oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, reduced pteridine as one donor, and incorporation of one atom of oxygen0.00476793112366575
GO:0042430indole and derivative metabolic process0.00476793112366575
GO:0006586indolalkylamine metabolic process0.00476793112366575
GO:0042434indole derivative metabolic process0.00476793112366575
GO:0042136neurotransmitter biosynthetic process0.00635677358608103
GO:0016597amino acid binding0.00733430683427203
GO:0042133neurotransmitter metabolic process0.0108036514740413
GO:0042401biogenic amine biosynthetic process0.0108036514740413
GO:0042398amino acid derivative biosynthetic process0.0116492810098451
GO:0042446hormone biosynthetic process0.0116492810098451
GO:0043176amine binding0.0116492810098451
GO:0009072aromatic amino acid family metabolic process0.0117881056163774
GO:0006576biogenic amine metabolic process0.0176249846095899
GO:0001505regulation of neurotransmitter levels0.0176919919675915
GO:0042445hormone metabolic process0.0186354249057678
GO:0006575amino acid derivative metabolic process0.0186354249057678
GO:0009309amine biosynthetic process0.0236034067788678
GO:0046483heterocycle metabolic process0.0247498102382317
GO:0044271nitrogen compound biosynthetic process0.0269031807789839
GO:0016705oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen0.0310829355447597
GO:0006725aromatic compound metabolic process0.0310829355447597
GO:0004497monooxygenase activity0.0381826713210847
GO:0007268synaptic transmission0.0459007070058853



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>


Uber Anatomy
Ontology termp-valuen
neural tube5.57e-6456
neural rod5.57e-6456
future spinal cord5.57e-6456
neural keel5.57e-6456
regional part of nervous system3.57e-6153
regional part of brain3.57e-6153
brainstem2.91e-536
central nervous system2.03e-4781
brain1.62e-4668
future brain1.62e-4668
neural plate5.36e-4382
presumptive neural plate5.36e-4382
nervous system1.77e-4289
neurectoderm7.03e-4186
regional part of forebrain1.16e-3741
forebrain1.16e-3741
anterior neural tube1.16e-3741
future forebrain1.16e-3741
neural nucleus1.05e-349
nucleus of brain1.05e-349
brain grey matter1.60e-3334
gray matter1.60e-3334
ecto-epithelium2.42e-33104
adult organism1.78e-30114
posterior neural tube1.94e-2815
chordal neural plate1.94e-2815
telencephalon9.71e-2834
medulla oblongata1.34e-273
myelencephalon1.34e-273
future myelencephalon1.34e-273
pons1.75e-273
segmental subdivision of hindbrain1.76e-2612
hindbrain1.76e-2612
presumptive hindbrain1.76e-2612
structure with developmental contribution from neural crest1.17e-25132
pre-chordal neural plate8.91e-2561
segmental subdivision of nervous system2.05e-2413
regional part of telencephalon2.10e-2432
gyrus4.97e-236
ectoderm-derived structure5.87e-21171
ectoderm5.87e-21171
presumptive ectoderm5.87e-21171
telencephalic nucleus4.84e-207
cerebral hemisphere1.08e-1932
locus ceruleus3.43e-192
brainstem nucleus3.43e-192
hindbrain nucleus3.43e-192
dorsal plus ventral thalamus7.68e-192
thalamic complex7.68e-192
globus pallidus1.43e-182
pallidum1.43e-182
middle frontal gyrus2.22e-182
tube1.12e-16192
basal ganglion1.20e-159
nuclear complex of neuraxis1.20e-159
aggregate regional part of brain1.20e-159
collection of basal ganglia1.20e-159
cerebral subcortex1.20e-159
organ system subdivision2.74e-15223
regional part of cerebral cortex6.25e-1322
anatomical conduit1.09e-12240
frontal cortex1.41e-123
diencephalon6.05e-127
future diencephalon6.05e-127
cerebral cortex2.17e-1125
pallium2.17e-1125
substantia nigra3.71e-101
midbrain nucleus3.71e-101
regional part of midbrain3.71e-101
midbrain3.71e-101
presumptive midbrain3.71e-101
midbrain neural tube3.71e-101
neocortex4.80e-1020
regional part of diencephalon6.93e-104
occipital pole8.99e-101
pole of cerebral hemisphere8.99e-101
corpus callosum9.82e-101
central nervous system cell part cluster9.82e-101
axon tract9.82e-101
intercerebral commissure9.82e-101
dorsal telencephalic commissure9.82e-101
brain white matter9.82e-101
brain commissure9.82e-101
white matter9.82e-101
nervous system commissure9.82e-101
cerebral hemisphere white matter9.82e-101
postcentral gyrus1.07e-091
nucleus accumbens1.17e-091
ventral striatum1.17e-091
regional part of metencephalon1.53e-099
metencephalon1.53e-099
future metencephalon1.53e-099
epithelium3.18e-09306
cell layer4.21e-09309
anatomical cluster8.12e-08373
limbic system1.09e-075
organ part1.96e-07218
multi-tissue structure7.18e-07342


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


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


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


This analysis result is provided for C0 - C305 clusters.