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Coexpression cluster:C1168: Difference between revisions

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|ontology_enrichment_uberon=UBERON:0001049!5.77e-101!56;UBERON:0005068!5.77e-101!56;UBERON:0006241!5.77e-101!56;UBERON:0007135!5.77e-101!56;UBERON:0000073!5.46e-94!53;UBERON:0002616!5.46e-94!53;UBERON:0001017!4.94e-84!81;UBERON:0000955!3.15e-80!68;UBERON:0006238!3.15e-80!68;UBERON:0001016!5.41e-80!89;UBERON:0002780!4.08e-78!41;UBERON:0001890!4.08e-78!41;UBERON:0003080!4.08e-78!41;UBERON:0006240!4.08e-78!41;UBERON:0003075!9.98e-71!82;UBERON:0007284!9.98e-71!82;UBERON:0002346!8.10e-67!86;UBERON:0003528!2.24e-66!34;UBERON:0002020!2.24e-66!34;UBERON:0001893!9.52e-66!34;UBERON:0001869!1.33e-61!32;UBERON:0002791!1.67e-61!32;UBERON:0007023!4.98e-54!114;UBERON:0010371!6.39e-53!104;UBERON:0003056!3.77e-52!61;UBERON:0002619!4.58e-52!22;UBERON:0001950!4.70e-47!20;UBERON:0000956!2.82e-45!25;UBERON:0000203!2.82e-45!25;UBERON:0010314!2.49e-44!132;UBERON:0004121!3.51e-38!171;UBERON:0000924!3.51e-38!171;UBERON:0006601!3.51e-38!171;UBERON:0011216!2.37e-29!223;UBERON:0000025!1.15e-24!192;UBERON:0003076!9.32e-23!15;UBERON:0003057!9.32e-23!15;UBERON:0002420!1.21e-22!9;UBERON:0007245!1.21e-22!9;UBERON:0010009!1.21e-22!9;UBERON:0010011!1.21e-22!9;UBERON:0000454!1.21e-22!9;UBERON:0000125!2.06e-22!9;UBERON:0002308!2.06e-22!9;UBERON:0004111!6.28e-18!240;UBERON:0009663!1.15e-17!7;UBERON:0004733!1.56e-16!12;UBERON:0002028!1.56e-16!12;UBERON:0007277!1.56e-16!12;UBERON:0000200!3.68e-16!6;UBERON:0000477!8.24e-16!373;UBERON:0004732!4.13e-15!13;UBERON:0002298!6.22e-15!6;UBERON:0000349!7.62e-14!5;UBERON:0002021!8.24e-14!5;UBERON:0001872!1.02e-13!5;UBERON:0001871!1.13e-13!6;UBERON:0001894!2.43e-13!7;UBERON:0006222!2.43e-13!7;UBERON:0000483!8.03e-12!306;UBERON:0000119!1.41e-11!309;UBERON:0000369!3.38e-11!4;UBERON:0002435!3.38e-11!4;UBERON:0000204!3.38e-11!4;UBERON:0010082!3.38e-11!4;UBERON:0002784!4.49e-11!4;UBERON:0002680!1.16e-10!9;UBERON:0001895!1.16e-10!9;UBERON:0010092!1.16e-10!9;UBERON:0000064!3.82e-10!218;UBERON:0000481!1.01e-09!342;UBERON:0005383!5.82e-09!3;UBERON:0005382!5.82e-09!3;UBERON:0001870!7.18e-09!3;UBERON:0000988!1.24e-08!3;UBERON:0002240!3.42e-08!3;UBERON:0005174!3.42e-08!3;UBERON:0001137!3.42e-08!3;UBERON:0001896!5.48e-08!3;UBERON:0005290!5.48e-08!3;UBERON:0010096!5.48e-08!3;UBERON:0002771!9.47e-07!2
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}}
}}

Revision as of 14:43, 26 November 2012


Full id: C1168_cerebellum_amygdala_hippocampus_occipital_medial_parietal_pineal



Phase1 CAGE Peaks

Hg19::chr12:175930..175960,+p2@IQSEC3
Hg19::chr16:29826201..29826227,+p@chr16:29826201..29826227
+
Hg19::chr16:58546898..58546921,+p@chr16:58546898..58546921
+
Hg19::chr6:31512426..31512437,-p@chr6:31512426..31512437
-
Hg19::chr6:31512450..31512515,-p@chr6:31512450..31512515
-
Hg19::chrX:101906316..101906354,+p2@GPRASP1
Hg19::chrX:75651278..75651282,+p1@AF086039


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:0016010dystrophin-associated glycoprotein complex0.0398091642367653
GO:0005086ARF guanyl-nucleotide exchange factor activity0.0398091642367653
GO:0030425dendrite0.0398091642367653
GO:0005605basal lamina0.0398091642367653
GO:0048471perinuclear region of cytoplasm0.0398091642367653
GO:0005604basement membrane0.0398091642367653
GO:0043005neuron projection0.0398091642367653
GO:0032011ARF protein signal transduction0.0398091642367653
GO:0032012regulation of ARF protein signal transduction0.0398091642367653



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 tube5.77e-10156
neural rod5.77e-10156
future spinal cord5.77e-10156
neural keel5.77e-10156
regional part of nervous system5.46e-9453
regional part of brain5.46e-9453
central nervous system4.94e-8481
brain3.15e-8068
future brain3.15e-8068
nervous system5.41e-8089
regional part of forebrain4.08e-7841
forebrain4.08e-7841
anterior neural tube4.08e-7841
future forebrain4.08e-7841
neural plate9.98e-7182
presumptive neural plate9.98e-7182
neurectoderm8.10e-6786
brain grey matter2.24e-6634
gray matter2.24e-6634
telencephalon9.52e-6634
cerebral hemisphere1.33e-6132
regional part of telencephalon1.67e-6132
adult organism4.98e-54114
ecto-epithelium6.39e-53104
pre-chordal neural plate3.77e-5261
regional part of cerebral cortex4.58e-5222
neocortex4.70e-4720
cerebral cortex2.82e-4525
pallium2.82e-4525
structure with developmental contribution from neural crest2.49e-44132
ectoderm-derived structure3.51e-38171
ectoderm3.51e-38171
presumptive ectoderm3.51e-38171
organ system subdivision2.37e-29223
tube1.15e-24192
posterior neural tube9.32e-2315
chordal neural plate9.32e-2315
basal ganglion1.21e-229
nuclear complex of neuraxis1.21e-229
aggregate regional part of brain1.21e-229
collection of basal ganglia1.21e-229
cerebral subcortex1.21e-229
neural nucleus2.06e-229
nucleus of brain2.06e-229
anatomical conduit6.28e-18240
telencephalic nucleus1.15e-177
segmental subdivision of hindbrain1.56e-1612
hindbrain1.56e-1612
presumptive hindbrain1.56e-1612
gyrus3.68e-166
anatomical cluster8.24e-16373
segmental subdivision of nervous system4.13e-1513
brainstem6.22e-156
limbic system7.62e-145
occipital lobe8.24e-145
parietal lobe1.02e-135
temporal lobe1.13e-136
diencephalon2.43e-137
future diencephalon2.43e-137
epithelium8.03e-12306
cell layer1.41e-11309
corpus striatum3.38e-114
striatum3.38e-114
ventral part of telencephalon3.38e-114
future corpus striatum3.38e-114
regional part of diencephalon4.49e-114
regional part of metencephalon1.16e-109
metencephalon1.16e-109
future metencephalon1.16e-109
organ part3.82e-10218
multi-tissue structure1.01e-09342
caudate-putamen5.82e-093
dorsal striatum5.82e-093
frontal cortex7.18e-093
pons1.24e-083
spinal cord3.42e-083
dorsal region element3.42e-083
dorsum3.42e-083
medulla oblongata5.48e-083
myelencephalon5.48e-083
future myelencephalon5.48e-083
middle temporal gyrus9.47e-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.

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