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Coexpression cluster:C2239: Difference between revisions

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{{Coexpression_clusters
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biosynthetic process from tryptophan!0.00476793112366575!121278$GO:0042428!serotonin metabolic process!0.00476793112366575!121278$GO:0042427!serotonin biosynthetic process!0.00476793112366575!121278$GO:0004510!tryptophan 5-monooxygenase activity!0.00476793112366575!121278$GO:0042435!indole derivative biosynthetic process!0.00476793112366575!121278$GO:0046219!indolalkylamine biosynthetic process!0.00476793112366575!121278$GO:0006568!tryptophan metabolic process!0.00476793112366575!121278$GO:0016714!oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, reduced pteridine as one donor, and incorporation of one atom of oxygen!0.00476793112366575!121278$GO:0042430!indole and derivative metabolic process!0.00476793112366575!121278$GO:0006586!indolalkylamine metabolic process!0.00476793112366575!121278$GO:0042434!indole derivative metabolic process!0.00476793112366575!121278$GO:0042136!neurotransmitter biosynthetic 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|full_id=C2239_locus_pons_medulla_gastrointestinal_thalamus_globus_medial
|id=C2239
}}

Latest revision as of 12:01, 17 September 2013


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)
MA0003.10.0214529
MA0004.10.71247
MA0006.10.532262
MA0007.10.6918
MA0009.11.20602
MA0014.10.0695829
MA0017.10.577281
MA0019.10.873355
MA0024.11.09684
MA0025.11.34373
MA0027.12.83281
MA0028.10.550763
MA0029.11.11704
MA0030.11.10506
MA0031.11.03735
MA0038.10.824639
MA0040.11.12314
MA0041.10.732902
MA0042.10.697662
MA0043.11.20635
MA0046.11.19471
MA0048.10.709734
MA0050.10.69864
MA0051.10.820063
MA0052.11.12718
MA0055.10.396851
MA0056.10
MA0057.10.69331
MA0058.10.605914
MA0059.10.604454
MA0060.10.393285
MA0061.10.360128
MA0063.10
MA0066.10.825101
MA0067.11.53181
MA0068.10.313194
MA0069.11.19071
MA0070.11.17908
MA0071.10.782546
MA0072.11.1744
MA0073.10.0343867
MA0074.10.819248
MA0076.10.623864
MA0077.11.16637
MA0078.10.926725
MA0081.11.4709
MA0083.11.21381
MA0084.11.72172
MA0087.11.17185
MA0088.10.182167
MA0089.10
MA0090.10.640115
MA0091.10.715356
MA0092.10.673508
MA0093.11.32557
MA0095.10
MA0098.10
MA0100.10.83965
MA0101.10.539569
MA0103.10.521546
MA0105.10.656404
MA0106.10.869173
MA0107.10.453492
MA0108.21.03412
MA0109.10
MA0111.10.655276
MA0113.10.886811
MA0114.10.447443
MA0115.11.45393
MA0116.10.457606
MA0117.11.24497
MA0119.10.586221
MA0122.11.27173
MA0124.11.41151
MA0125.11.32534
MA0130.10
MA0131.10.94608
MA0132.10
MA0133.10
MA0135.11.23748
MA0136.10.832277
MA0139.10.344952
MA0140.10.779643
MA0141.10.602484
MA0142.11.00381
MA0143.10.887001
MA0144.10.430413
MA0145.10.195821
MA0146.10.061409
MA0147.10.46175
MA0148.10.739888
MA0149.10.769072
MA0062.20.353589
MA0035.20.778873
MA0039.20.257871
MA0138.20.928035
MA0002.20.379056
MA0137.20.558189
MA0104.20.392359
MA0047.20.856092
MA0112.20.187982
MA0065.20.199162
MA0150.10.633493
MA0151.10
MA0152.10.78681
MA0153.11.30799
MA0154.10.229241
MA0155.10.533581
MA0156.10.560797
MA0157.10.97481
MA0158.10
MA0159.10.462502
MA0160.10.756582
MA0161.10
MA0162.10.309472
MA0163.10.0725493
MA0164.10.90014
MA0080.20.535868
MA0018.20.870662
MA0099.20.7872
MA0079.20.476674
MA0102.21.75932
MA0258.10.418966
MA0259.10.471671
MA0442.10



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.

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