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Coexpression cluster:C2239: Difference between revisions

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|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0001049!3.22e-54!57;UBERON:0005068!3.22e-54!57;UBERON:0006241!3.22e-54!57;UBERON:0007135!3.22e-54!57;UBERON:0001017!8.90e-46!82;UBERON:0005743!3.53e-43!86;UBERON:0002616!1.01e-42!59;UBERON:0000073!4.04e-38!94;UBERON:0001016!4.04e-38!94;UBERON:0000955!7.22e-37!69;UBERON:0006238!7.22e-37!69;UBERON:0002346!3.98e-35!90;UBERON:0003075!5.28e-35!86;UBERON:0007284!5.28e-35!86;UBERON:0002780!1.82e-34!41;UBERON:0001890!1.82e-34!41;UBERON:0006240!1.82e-34!41;UBERON:0003080!1.68e-33!42;UBERON:0007023!2.36e-30!115;UBERON:0002020!2.68e-29!34;UBERON:0003528!2.68e-29!34;UBERON:0001893!9.81e-29!34;UBERON:0002791!1.20e-26!33;UBERON:0001869!9.06e-25!32;UBERON:0000153!2.54e-23!129;UBERON:0007811!2.54e-23!129;UBERON:0003076!2.57e-22!15;UBERON:0003057!2.57e-22!15;UBERON:0000033!4.25e-22!123;UBERON:0003056!4.24e-21!61;UBERON:0000924!1.46e-20!173;UBERON:0006601!1.46e-20!173;UBERON:0004121!4.58e-20!169;UBERON:0002619!1.82e-19!22;UBERON:0002298!1.25e-18!8;UBERON:0000956!7.97e-17!25;UBERON:0000203!7.97e-17!25;UBERON:0000200!3.80e-16!6;UBERON:0001950!2.22e-15!20;UBERON:0002308!2.55e-15!9;UBERON:0000125!2.55e-15!9;UBERON:0004733!3.22e-15!12;UBERON:0002028!3.22e-15!12;UBERON:0007277!3.22e-15!12;UBERON:0004732!6.37e-14!13;UBERON:0000025!1.09e-13!194;UBERON:0002420!7.03e-11!9;UBERON:0007245!7.03e-11!9;UBERON:0010009!7.03e-11!9;UBERON:0010011!7.03e-11!9;UBERON:0000454!7.03e-11!9;UBERON:0004111!1.86e-10!241;UBERON:0000988!2.94e-10!3;UBERON:0001896!3.22e-10!3;UBERON:0005290!3.22e-10!3;UBERON:0010096!3.22e-10!3;UBERON:0006331!3.62e-10!3;UBERON:0009663!4.06e-10!7;UBERON:0002240!1.73e-09!3;UBERON:0000349!3.02e-09!5;UBERON:0000477!4.94e-09!286;UBERON:0002771!1.48e-08!3;UBERON:0002680!3.25e-08!9;UBERON:0001895!3.25e-08!9;UBERON:0010092!3.25e-08!9;UBERON:0001871!4.87e-08!7;UBERON:0002148!1.99e-07!2;UBERON:0009662!1.99e-07!2;UBERON:0001875!3.39e-07!2;UBERON:0006514!3.39e-07!2;UBERON:0001897!3.50e-07!2;UBERON:0000064!4.02e-07!219;UBERON:0000483!4.19e-07!309;UBERON:0001894!4.38e-07!7;UBERON:0006222!4.38e-07!7;UBERON:0000007!6.08e-07!2;UBERON:0000119!6.12e-07!312;UBERON:0001954!6.44e-07!2;UBERON:0003022!6.44e-07!2;UBERON:0002421!6.44e-07!2;UBERON:0002600!6.44e-07!2
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}}
}}

Revision as of 18:07, 8 August 2012


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 tube3.22e-5457
neural rod3.22e-5457
future spinal cord3.22e-5457
neural keel3.22e-5457
central nervous system8.90e-4682
regional part of brain1.01e-4259
regional part of nervous system4.04e-3894
nervous system4.04e-3894
brain7.22e-3769
future brain7.22e-3769
neurectoderm3.98e-3590
neural plate5.28e-3586
presumptive neural plate5.28e-3586
regional part of forebrain1.82e-3441
forebrain1.82e-3441
future forebrain1.82e-3441
anterior neural tube1.68e-3342
adult organism2.36e-30115
gray matter2.68e-2934
brain grey matter2.68e-2934
telencephalon9.81e-2934
regional part of telencephalon1.20e-2633
cerebral hemisphere9.06e-2532
anterior region of body2.54e-23129
craniocervical region2.54e-23129
posterior neural tube2.57e-2215
chordal neural plate2.57e-2215
head4.25e-22123
pre-chordal neural plate4.24e-2161
ectoderm1.46e-20173
presumptive ectoderm1.46e-20173
ectoderm-derived structure4.58e-20169
regional part of cerebral cortex1.82e-1922
brainstem1.25e-188
cerebral cortex7.97e-1725
pallium7.97e-1725
gyrus3.80e-166
neocortex2.22e-1520
nucleus of brain2.55e-159
neural nucleus2.55e-159
segmental subdivision of hindbrain3.22e-1512
hindbrain3.22e-1512
presumptive hindbrain3.22e-1512
segmental subdivision of nervous system6.37e-1413
tube1.09e-13194
basal ganglion7.03e-119
nuclear complex of neuraxis7.03e-119
aggregate regional part of brain7.03e-119
collection of basal ganglia7.03e-119
cerebral subcortex7.03e-119
anatomical conduit1.86e-10241
pons2.94e-103
medulla oblongata3.22e-103
myelencephalon3.22e-103
future myelencephalon3.22e-103
brainstem nucleus3.62e-103
telencephalic nucleus4.06e-107
spinal cord1.73e-093
limbic system3.02e-095
anatomical cluster4.94e-09286
middle temporal gyrus1.48e-083
regional part of metencephalon3.25e-089
metencephalon3.25e-089
future metencephalon3.25e-089
temporal lobe4.87e-087
locus ceruleus1.99e-072
hindbrain nucleus1.99e-072
globus pallidus3.39e-072
pallidum3.39e-072
dorsal plus ventral thalamus3.50e-072
organ part4.02e-07219
epithelium4.19e-07309
diencephalon4.38e-077
future diencephalon4.38e-077
pituitary gland6.08e-072
cell layer6.12e-07312
Ammon's horn6.44e-072
lobe parts of cerebral cortex6.44e-072
hippocampal formation6.44e-072
limbic lobe6.44e-072


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.