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Coexpression cluster:C4419: Difference between revisions

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|ontology_enrichment_uberon=UBERON:0001049!2.79e-83!56;UBERON:0005068!2.79e-83!56;UBERON:0006241!2.79e-83!56;UBERON:0007135!2.79e-83!56;UBERON:0000073!1.18e-75!53;UBERON:0002616!1.18e-75!53;UBERON:0001869!1.62e-72!32;UBERON:0001893!1.90e-72!34;UBERON:0003528!2.47e-72!34;UBERON:0002020!2.47e-72!34;UBERON:0001017!5.17e-72!81;UBERON:0002780!1.21e-71!41;UBERON:0001890!1.21e-71!41;UBERON:0003080!1.21e-71!41;UBERON:0006240!1.21e-71!41;UBERON:0002791!1.77e-67!32;UBERON:0000955!8.56e-66!68;UBERON:0006238!8.56e-66!68;UBERON:0001016!9.41e-64!89;UBERON:0002619!1.97e-61!22;UBERON:0001950!2.40e-55!20;UBERON:0003075!1.24e-53!82;UBERON:0007284!1.24e-53!82;UBERON:0000956!1.35e-53!25;UBERON:0000203!1.35e-53!25;UBERON:0002346!1.20e-50!86;UBERON:0003056!1.70e-45!61;UBERON:0007023!9.87e-42!114;UBERON:0010371!4.91e-40!104;UBERON:0011216!1.69e-38!223;UBERON:0010314!9.92e-33!132;UBERON:0004121!6.70e-28!171;UBERON:0000924!6.70e-28!171;UBERON:0006601!6.70e-28!171;UBERON:0002420!6.89e-21!9;UBERON:0007245!6.89e-21!9;UBERON:0010009!6.89e-21!9;UBERON:0010011!6.89e-21!9;UBERON:0000454!6.89e-21!9;UBERON:0000125!1.13e-19!9;UBERON:0002308!1.13e-19!9;UBERON:0000477!2.70e-19!373;UBERON:0000025!6.66e-19!192;UBERON:0000200!1.21e-18!6;UBERON:0000349!1.98e-16!5;UBERON:0001871!3.24e-16!6;UBERON:0002021!1.27e-15!5;UBERON:0001872!2.68e-15!5;UBERON:0009663!4.92e-15!7;UBERON:0004111!1.09e-14!240;UBERON:0000160!2.98e-14!17;UBERON:0000481!5.59e-14!342;UBERON:0000064!8.78e-14!218;UBERON:0003076!1.64e-13!15;UBERON:0003057!1.64e-13!15;UBERON:0000369!1.26e-12!4;UBERON:0002435!1.26e-12!4;UBERON:0000204!1.26e-12!4;UBERON:0010082!1.26e-12!4;UBERON:0000483!3.76e-12!306;UBERON:0000119!6.42e-12!309;UBERON:0001870!2.22e-10!3;UBERON:0000062!5.95e-10!503;UBERON:0005383!6.24e-10!3;UBERON:0005382!6.24e-10!3;UBERON:0002240!2.36e-09!3;UBERON:0005174!2.36e-09!3;UBERON:0001137!2.36e-09!3;UBERON:0002108!2.56e-09!4;UBERON:0005409!3.09e-09!25;UBERON:0000988!1.36e-08!3;UBERON:0005423!1.85e-08!581;UBERON:0000922!5.01e-08!592;UBERON:0002050!5.93e-08!564;UBERON:0001876!9.47e-08!2;UBERON:0004733!1.09e-07!12;UBERON:0002028!1.09e-07!12;UBERON:0007277!1.09e-07!12;UBERON:0001954!1.11e-07!2;UBERON:0003022!1.11e-07!2;UBERON:0002421!1.11e-07!2;UBERON:0002600!1.11e-07!2;UBERON:0002771!1.43e-07!2;UBERON:0000923!1.61e-07!560;UBERON:0010316!1.61e-07!560;UBERON:0005291!1.61e-07!560;UBERON:0006598!1.61e-07!560;UBERON:0010317!1.61e-07!560;UBERON:0002532!1.61e-07!560;UBERON:0002680!1.80e-07!9;UBERON:0001895!1.80e-07!9;UBERON:0010092!1.80e-07!9;UBERON:0002702!1.83e-07!2;UBERON:0002298!2.59e-07!6;UBERON:0001873!2.66e-07!2;UBERON:0010122!2.66e-07!2;UBERON:0004732!4.77e-07!13;UBERON:0002360!9.92e-07!2;UBERON:0001875!9.92e-07!2;UBERON:0000094!9.92e-07!2;UBERON:0006514!9.92e-07!2;UBERON:0010743!9.92e-07!2
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}}
}}

Revision as of 16:43, 26 November 2012


Full id: C4419_colon_argyrophil_hippocampus_amygdala_parietal_medial_caudate



Phase1 CAGE Peaks

Hg19::chr4:46391040..46391059,-p10@GABRA2
Hg19::chr4:46391367..46391436,-p3@GABRA2
Hg19::chr4:46391457..46391464,-p22@GABRA2


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
neural tube2.79e-8356
neural rod2.79e-8356
future spinal cord2.79e-8356
neural keel2.79e-8356
regional part of nervous system1.18e-7553
regional part of brain1.18e-7553
cerebral hemisphere1.62e-7232
telencephalon1.90e-7234
brain grey matter2.47e-7234
gray matter2.47e-7234
central nervous system5.17e-7281
regional part of forebrain1.21e-7141
forebrain1.21e-7141
anterior neural tube1.21e-7141
future forebrain1.21e-7141
regional part of telencephalon1.77e-6732
brain8.56e-6668
future brain8.56e-6668
nervous system9.41e-6489
regional part of cerebral cortex1.97e-6122
neocortex2.40e-5520
neural plate1.24e-5382
presumptive neural plate1.24e-5382
cerebral cortex1.35e-5325
pallium1.35e-5325
neurectoderm1.20e-5086
pre-chordal neural plate1.70e-4561
adult organism9.87e-42114
ecto-epithelium4.91e-40104
organ system subdivision1.69e-38223
structure with developmental contribution from neural crest9.92e-33132
ectoderm-derived structure6.70e-28171
ectoderm6.70e-28171
presumptive ectoderm6.70e-28171
basal ganglion6.89e-219
nuclear complex of neuraxis6.89e-219
aggregate regional part of brain6.89e-219
collection of basal ganglia6.89e-219
cerebral subcortex6.89e-219
neural nucleus1.13e-199
nucleus of brain1.13e-199
anatomical cluster2.70e-19373
tube6.66e-19192
gyrus1.21e-186
limbic system1.98e-165
temporal lobe3.24e-166
occipital lobe1.27e-155
parietal lobe2.68e-155
telencephalic nucleus4.92e-157
anatomical conduit1.09e-14240
intestine2.98e-1417
multi-tissue structure5.59e-14342
organ part8.78e-14218
posterior neural tube1.64e-1315
chordal neural plate1.64e-1315
corpus striatum1.26e-124
striatum1.26e-124
ventral part of telencephalon1.26e-124
future corpus striatum1.26e-124
epithelium3.76e-12306
cell layer6.42e-12309
frontal cortex2.22e-103
organ5.95e-10503
caudate-putamen6.24e-103
dorsal striatum6.24e-103
spinal cord2.36e-093
dorsal region element2.36e-093
dorsum2.36e-093
small intestine2.56e-094
gastrointestinal system3.09e-0925
pons1.36e-083
developing anatomical structure1.85e-08581
embryo5.01e-08592
embryonic structure5.93e-08564
amygdala9.47e-082
segmental subdivision of hindbrain1.09e-0712
hindbrain1.09e-0712
presumptive hindbrain1.09e-0712
Ammon's horn1.11e-072
lobe parts of cerebral cortex1.11e-072
hippocampal formation1.11e-072
limbic lobe1.11e-072
middle temporal gyrus1.43e-072
germ layer1.61e-07560
germ layer / neural crest1.61e-07560
embryonic tissue1.61e-07560
presumptive structure1.61e-07560
germ layer / neural crest derived structure1.61e-07560
epiblast (generic)1.61e-07560
regional part of metencephalon1.80e-079
metencephalon1.80e-079
future metencephalon1.80e-079
middle frontal gyrus1.83e-072
brainstem2.59e-076
caudate nucleus2.66e-072
future caudate nucleus2.66e-072
segmental subdivision of nervous system4.77e-0713
meninx9.92e-072
globus pallidus9.92e-072
membrane organ9.92e-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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