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Coexpression cluster:C4396: Difference between revisions

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|ontology_enrichment_uberon=UBERON:0001017!8.07e-100!81;UBERON:0001893!1.10e-99!34;UBERON:0003528!1.95e-99!34;UBERON:0002020!1.95e-99!34;UBERON:0001869!2.34e-99!32;UBERON:0000073!4.01e-95!53;UBERON:0002616!4.01e-95!53;UBERON:0001049!9.32e-95!56;UBERON:0005068!9.32e-95!56;UBERON:0006241!9.32e-95!56;UBERON:0007135!9.32e-95!56;UBERON:0002780!3.22e-93!41;UBERON:0001890!3.22e-93!41;UBERON:0003080!3.22e-93!41;UBERON:0006240!3.22e-93!41;UBERON:0002791!2.78e-92!32;UBERON:0000955!5.59e-90!68;UBERON:0006238!5.59e-90!68;UBERON:0001016!3.76e-89!89;UBERON:0002619!1.56e-83!22;UBERON:0000956!6.43e-80!25;UBERON:0000203!6.43e-80!25;UBERON:0001950!5.28e-76!20;UBERON:0003075!2.14e-62!82;UBERON:0007284!2.14e-62!82;UBERON:0003056!1.15e-60!61;UBERON:0002346!3.92e-59!86;UBERON:0010371!1.59e-47!104;UBERON:0007023!3.61e-43!114;UBERON:0004121!9.83e-43!171;UBERON:0000924!9.83e-43!171;UBERON:0006601!9.83e-43!171;UBERON:0010314!3.08e-40!132;UBERON:0011216!2.77e-32!223;UBERON:0000200!1.84e-25!6;UBERON:0000025!6.28e-22!192;UBERON:0001871!1.31e-21!6;UBERON:0002420!1.76e-21!9;UBERON:0007245!1.76e-21!9;UBERON:0010009!1.76e-21!9;UBERON:0010011!1.76e-21!9;UBERON:0000454!1.76e-21!9;UBERON:0000349!8.45e-21!5;UBERON:0001872!9.18e-21!5;UBERON:0002021!1.08e-20!5;UBERON:0000125!1.09e-20!9;UBERON:0002308!1.09e-20!9;UBERON:0004111!7.49e-16!240;UBERON:0000477!1.36e-15!373;UBERON:0009663!3.46e-14!7;UBERON:0001870!6.62e-14!3;UBERON:0000064!9.82e-14!218;UBERON:0000988!5.43e-12!3;UBERON:0000483!1.29e-10!306;UBERON:0000119!1.97e-10!309;UBERON:0002298!2.99e-10!6;UBERON:0002702!7.46e-10!2;UBERON:0000369!7.75e-10!4;UBERON:0002435!7.75e-10!4;UBERON:0000204!7.75e-10!4;UBERON:0010082!7.75e-10!4;UBERON:0002771!8.48e-10!2;UBERON:0001876!1.10e-09!2;UBERON:0001954!4.70e-09!2;UBERON:0003022!4.70e-09!2;UBERON:0002421!4.70e-09!2;UBERON:0002600!4.70e-09!2;UBERON:0002360!6.24e-09!2;UBERON:0000094!6.24e-09!2;UBERON:0010743!6.24e-09!2;UBERON:0001875!1.01e-08!2;UBERON:0006514!1.01e-08!2;UBERON:0002148!1.23e-08!2;UBERON:0006331!1.23e-08!2;UBERON:0009662!1.23e-08!2;UBERON:0000481!1.28e-08!342;UBERON:0003076!1.57e-08!15;UBERON:0003057!1.57e-08!15;UBERON:0004733!1.17e-07!12;UBERON:0002028!1.17e-07!12;UBERON:0007277!1.17e-07!12;UBERON:0000923!4.31e-07!560;UBERON:0010316!4.31e-07!560;UBERON:0005291!4.31e-07!560;UBERON:0006598!4.31e-07!560;UBERON:0010317!4.31e-07!560;UBERON:0002532!4.31e-07!560;UBERON:0004732!4.76e-07!13;UBERON:0002050!5.70e-07!564;UBERON:0002680!6.77e-07!9;UBERON:0001895!6.77e-07!9;UBERON:0010092!6.77e-07!9
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}}
}}

Revision as of 16:43, 26 November 2012


Full id: C4396_glioblastoma_medial_amygdala_insula_olfactory_brain_parietal



Phase1 CAGE Peaks

Hg19::chr4:176734117..176734124,-p30@GPM6A
Hg19::chr4:176734149..176734174,-p12@GPM6A
Hg19::chr4:176734191..176734204,-p21@GPM6A


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

No GOStat results

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
central nervous system8.07e-10081
telencephalon1.10e-9934
brain grey matter1.95e-9934
gray matter1.95e-9934
cerebral hemisphere2.34e-9932
regional part of nervous system4.01e-9553
regional part of brain4.01e-9553
neural tube9.32e-9556
neural rod9.32e-9556
future spinal cord9.32e-9556
neural keel9.32e-9556
regional part of forebrain3.22e-9341
forebrain3.22e-9341
anterior neural tube3.22e-9341
future forebrain3.22e-9341
regional part of telencephalon2.78e-9232
brain5.59e-9068
future brain5.59e-9068
nervous system3.76e-8989
regional part of cerebral cortex1.56e-8322
cerebral cortex6.43e-8025
pallium6.43e-8025
neocortex5.28e-7620
neural plate2.14e-6282
presumptive neural plate2.14e-6282
pre-chordal neural plate1.15e-6061
neurectoderm3.92e-5986
ecto-epithelium1.59e-47104
adult organism3.61e-43114
ectoderm-derived structure9.83e-43171
ectoderm9.83e-43171
presumptive ectoderm9.83e-43171
structure with developmental contribution from neural crest3.08e-40132
organ system subdivision2.77e-32223
gyrus1.84e-256
tube6.28e-22192
temporal lobe1.31e-216
basal ganglion1.76e-219
nuclear complex of neuraxis1.76e-219
aggregate regional part of brain1.76e-219
collection of basal ganglia1.76e-219
cerebral subcortex1.76e-219
limbic system8.45e-215
parietal lobe9.18e-215
occipital lobe1.08e-205
neural nucleus1.09e-209
nucleus of brain1.09e-209
anatomical conduit7.49e-16240
anatomical cluster1.36e-15373
telencephalic nucleus3.46e-147
frontal cortex6.62e-143
organ part9.82e-14218
pons5.43e-123
epithelium1.29e-10306
cell layer1.97e-10309
brainstem2.99e-106
middle frontal gyrus7.46e-102
corpus striatum7.75e-104
striatum7.75e-104
ventral part of telencephalon7.75e-104
future corpus striatum7.75e-104
middle temporal gyrus8.48e-102
amygdala1.10e-092
Ammon's horn4.70e-092
lobe parts of cerebral cortex4.70e-092
hippocampal formation4.70e-092
limbic lobe4.70e-092
meninx6.24e-092
membrane organ6.24e-092
meningeal cluster6.24e-092
globus pallidus1.01e-082
pallidum1.01e-082
locus ceruleus1.23e-082
brainstem nucleus1.23e-082
hindbrain nucleus1.23e-082
multi-tissue structure1.28e-08342
posterior neural tube1.57e-0815
chordal neural plate1.57e-0815
segmental subdivision of hindbrain1.17e-0712
hindbrain1.17e-0712
presumptive hindbrain1.17e-0712
germ layer4.31e-07560
germ layer / neural crest4.31e-07560
embryonic tissue4.31e-07560
presumptive structure4.31e-07560
germ layer / neural crest derived structure4.31e-07560
epiblast (generic)4.31e-07560
segmental subdivision of nervous system4.76e-0713
embryonic structure5.70e-07564
regional part of metencephalon6.77e-079
metencephalon6.77e-079
future metencephalon6.77e-079


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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