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Coexpression cluster:C2316: Difference between revisions

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|ontology_enrichment_uberon=UBERON:0001049!3.00e-74!56;UBERON:0005068!3.00e-74!56;UBERON:0006241!3.00e-74!56;UBERON:0007135!3.00e-74!56;UBERON:0000073!7.36e-71!53;UBERON:0002616!7.36e-71!53;UBERON:0001017!1.30e-59!81;UBERON:0000955!4.87e-59!68;UBERON:0006238!4.87e-59!68;UBERON:0001893!5.22e-56!34;UBERON:0003528!1.51e-55!34;UBERON:0002020!1.51e-55!34;UBERON:0007023!1.28e-53!114;UBERON:0002780!1.10e-52!41;UBERON:0001890!1.10e-52!41;UBERON:0003080!1.10e-52!41;UBERON:0006240!1.10e-52!41;UBERON:0001016!1.11e-52!89;UBERON:0001869!4.53e-51!32;UBERON:0002791!1.51e-50!32;UBERON:0003075!2.70e-50!82;UBERON:0007284!2.70e-50!82;UBERON:0002619!8.91e-48!22;UBERON:0002346!1.71e-47!86;UBERON:0001950!3.10e-42!20;UBERON:0000956!1.23e-41!25;UBERON:0000203!1.23e-41!25;UBERON:0010371!1.55e-37!104;UBERON:0003056!1.34e-35!61;UBERON:0010314!2.08e-34!132;UBERON:0004121!3.20e-25!171;UBERON:0000924!3.20e-25!171;UBERON:0006601!3.20e-25!171;UBERON:0011216!2.48e-22!223;UBERON:0003076!9.64e-22!15;UBERON:0003057!9.64e-22!15;UBERON:0000200!3.53e-20!6;UBERON:0004733!1.02e-18!12;UBERON:0002028!1.02e-18!12;UBERON:0007277!1.02e-18!12;UBERON:0002298!2.01e-17!6;UBERON:0004732!3.84e-17!13;UBERON:0000025!8.84e-17!192;UBERON:0000349!7.71e-16!5;UBERON:0002420!1.91e-15!9;UBERON:0007245!1.91e-15!9;UBERON:0010009!1.91e-15!9;UBERON:0010011!1.91e-15!9;UBERON:0000454!1.91e-15!9;UBERON:0000125!4.71e-15!9;UBERON:0002308!4.71e-15!9;UBERON:0000064!1.16e-12!218;UBERON:0004111!3.18e-12!240;UBERON:0001871!1.38e-11!6;UBERON:0002680!1.46e-11!9;UBERON:0001895!1.46e-11!9;UBERON:0010092!1.46e-11!9;UBERON:0000477!2.43e-11!373;UBERON:0001872!3.66e-11!5;UBERON:0002021!4.48e-11!5;UBERON:0001870!5.64e-11!3;UBERON:0009663!2.64e-10!7;UBERON:0000988!1.45e-09!3;UBERON:0001896!1.45e-09!3;UBERON:0005290!1.45e-09!3;UBERON:0010096!1.45e-09!3;UBERON:0000483!2.15e-09!306;UBERON:0000119!3.35e-09!309;UBERON:0000481!4.25e-09!342;UBERON:0002702!8.14e-08!2;UBERON:0002771!8.69e-08!2;UBERON:0000369!2.43e-07!4;UBERON:0002435!2.43e-07!4;UBERON:0000204!2.43e-07!4;UBERON:0010082!2.43e-07!4;UBERON:0001876!2.58e-07!2;UBERON:0001954!2.83e-07!2;UBERON:0003022!2.83e-07!2;UBERON:0002421!2.83e-07!2;UBERON:0002600!2.83e-07!2;UBERON:0002360!3.63e-07!2;UBERON:0000094!3.63e-07!2;UBERON:0010743!3.63e-07!2;UBERON:0002370!4.13e-07!4;UBERON:0005058!4.13e-07!4;UBERON:0009113!4.13e-07!4;UBERON:0003295!4.13e-07!4;UBERON:0005562!4.13e-07!4;UBERON:0002148!8.78e-07!2;UBERON:0006331!8.78e-07!2;UBERON:0009662!8.78e-07!2
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}}
}}

Revision as of 15:25, 26 November 2012


Full id: C2316_mycosis_occipital_frontal_parietal_paracentral_postcentral_medial



Phase1 CAGE Peaks

Hg19::chr14:78870030..78870098,+p5@NRXN3
Hg19::chr6:128134199..128134253,-p3@THEMIS
Hg19::chrX:21977968..21977978,+p@chrX:21977968..21977978
+
Hg19::chrX:21977990..21978030,+p@chrX:21977990..21978030
+


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 tube3.00e-7456
neural rod3.00e-7456
future spinal cord3.00e-7456
neural keel3.00e-7456
regional part of nervous system7.36e-7153
regional part of brain7.36e-7153
central nervous system1.30e-5981
brain4.87e-5968
future brain4.87e-5968
telencephalon5.22e-5634
brain grey matter1.51e-5534
gray matter1.51e-5534
adult organism1.28e-53114
regional part of forebrain1.10e-5241
forebrain1.10e-5241
anterior neural tube1.10e-5241
future forebrain1.10e-5241
nervous system1.11e-5289
cerebral hemisphere4.53e-5132
regional part of telencephalon1.51e-5032
neural plate2.70e-5082
presumptive neural plate2.70e-5082
regional part of cerebral cortex8.91e-4822
neurectoderm1.71e-4786
neocortex3.10e-4220
cerebral cortex1.23e-4125
pallium1.23e-4125
ecto-epithelium1.55e-37104
pre-chordal neural plate1.34e-3561
structure with developmental contribution from neural crest2.08e-34132
ectoderm-derived structure3.20e-25171
ectoderm3.20e-25171
presumptive ectoderm3.20e-25171
organ system subdivision2.48e-22223
posterior neural tube9.64e-2215
chordal neural plate9.64e-2215
gyrus3.53e-206
segmental subdivision of hindbrain1.02e-1812
hindbrain1.02e-1812
presumptive hindbrain1.02e-1812
brainstem2.01e-176
segmental subdivision of nervous system3.84e-1713
tube8.84e-17192
limbic system7.71e-165
basal ganglion1.91e-159
nuclear complex of neuraxis1.91e-159
aggregate regional part of brain1.91e-159
collection of basal ganglia1.91e-159
cerebral subcortex1.91e-159
neural nucleus4.71e-159
nucleus of brain4.71e-159
organ part1.16e-12218
anatomical conduit3.18e-12240
temporal lobe1.38e-116
regional part of metencephalon1.46e-119
metencephalon1.46e-119
future metencephalon1.46e-119
anatomical cluster2.43e-11373
parietal lobe3.66e-115
occipital lobe4.48e-115
frontal cortex5.64e-113
telencephalic nucleus2.64e-107
pons1.45e-093
medulla oblongata1.45e-093
myelencephalon1.45e-093
future myelencephalon1.45e-093
epithelium2.15e-09306
cell layer3.35e-09309
multi-tissue structure4.25e-09342
middle frontal gyrus8.14e-082
middle temporal gyrus8.69e-082
corpus striatum2.43e-074
striatum2.43e-074
ventral part of telencephalon2.43e-074
future corpus striatum2.43e-074
amygdala2.58e-072
Ammon's horn2.83e-072
lobe parts of cerebral cortex2.83e-072
hippocampal formation2.83e-072
limbic lobe2.83e-072
meninx3.63e-072
membrane organ3.63e-072
meningeal cluster3.63e-072
thymus4.13e-074
hemolymphoid system gland4.13e-074
thymic region4.13e-074
pharyngeal gland4.13e-074
thymus primordium4.13e-074
locus ceruleus8.78e-072
brainstem nucleus8.78e-072
hindbrain nucleus8.78e-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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