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Coexpression cluster:C2658: Difference between revisions

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|ontology_enrichment_uberon=UBERON:0001049!3.02e-111!56;UBERON:0005068!3.02e-111!56;UBERON:0006241!3.02e-111!56;UBERON:0007135!3.02e-111!56;UBERON:0000073!2.81e-99!53;UBERON:0002616!2.81e-99!53;UBERON:0001017!2.36e-86!81;UBERON:0000955!3.58e-79!68;UBERON:0006238!3.58e-79!68;UBERON:0001016!4.26e-77!89;UBERON:0002780!1.39e-76!41;UBERON:0001890!1.39e-76!41;UBERON:0003080!1.39e-76!41;UBERON:0006240!1.39e-76!41;UBERON:0003075!7.11e-74!82;UBERON:0007284!7.11e-74!82;UBERON:0002346!4.17e-70!86;UBERON:0003528!8.26e-68!34;UBERON:0002020!8.26e-68!34;UBERON:0001893!2.06e-67!34;UBERON:0002791!4.60e-60!32;UBERON:0001869!1.29e-59!32;UBERON:0010371!1.08e-56!104;UBERON:0007023!3.91e-54!114;UBERON:0003056!9.62e-50!61;UBERON:0010314!1.34e-45!132;UBERON:0002619!2.25e-45!22;UBERON:0000956!1.05e-39!25;UBERON:0000203!1.05e-39!25;UBERON:0001950!1.07e-37!20;UBERON:0004121!8.02e-37!171;UBERON:0000924!8.02e-37!171;UBERON:0006601!8.02e-37!171;UBERON:0003076!4.26e-34!15;UBERON:0003057!4.26e-34!15;UBERON:0000125!1.69e-31!9;UBERON:0002308!1.69e-31!9;UBERON:0011216!1.59e-29!223;UBERON:0000025!4.26e-27!192;UBERON:0002298!1.86e-26!6;UBERON:0000200!1.47e-25!6;UBERON:0002420!2.47e-24!9;UBERON:0007245!2.47e-24!9;UBERON:0010009!2.47e-24!9;UBERON:0010011!2.47e-24!9;UBERON:0000454!2.47e-24!9;UBERON:0009663!3.99e-23!7;UBERON:0004733!1.19e-22!12;UBERON:0002028!1.19e-22!12;UBERON:0007277!1.19e-22!12;UBERON:0004732!8.28e-21!13;UBERON:0004111!4.79e-20!240;UBERON:0000369!1.95e-18!4;UBERON:0002435!1.95e-18!4;UBERON:0000204!1.95e-18!4;UBERON:0010082!1.95e-18!4;UBERON:0000349!5.07e-15!5;UBERON:0005383!1.46e-14!3;UBERON:0005382!1.46e-14!3;UBERON:0002240!2.01e-14!3;UBERON:0005174!2.01e-14!3;UBERON:0001137!2.01e-14!3;UBERON:0000477!2.61e-14!373;UBERON:0000988!3.15e-14!3;UBERON:0001896!5.38e-14!3;UBERON:0001870!5.38e-14!3;UBERON:0005290!5.38e-14!3;UBERON:0010096!5.38e-14!3;UBERON:0000483!6.07e-14!306;UBERON:0000119!9.97e-14!309;UBERON:0000064!2.04e-12!218;UBERON:0002680!2.56e-12!9;UBERON:0001895!2.56e-12!9;UBERON:0010092!2.56e-12!9;UBERON:0002784!9.89e-11!4;UBERON:0000481!1.37e-10!342;UBERON:0001894!1.64e-10!7;UBERON:0006222!1.64e-10!7;UBERON:0001897!2.02e-10!2;UBERON:0010225!2.02e-10!2;UBERON:0001871!2.05e-10!6;UBERON:0001873!2.12e-10!2;UBERON:0010122!2.12e-10!2;UBERON:0001954!2.22e-10!2;UBERON:0003022!2.22e-10!2;UBERON:0002421!2.22e-10!2;UBERON:0002600!2.22e-10!2;UBERON:0002148!2.92e-10!2;UBERON:0006331!2.92e-10!2;UBERON:0009662!2.92e-10!2;UBERON:0002702!4.39e-10!2;UBERON:0002771!8.22e-10!2;UBERON:0002021!1.96e-08!5;UBERON:0001872!2.81e-08!5;UBERON:0000062!6.20e-07!503
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}}
}}

Revision as of 15:38, 26 November 2012


Full id: C2658_hippocampus_amygdala_medulla_thalamus_locus_substantia_medial



Phase1 CAGE Peaks

Hg19::chr2:131684411..131684414,+p@chr2:131684411..131684414
+
Hg19::chr5:82155695..82155706,-p@chr5:82155695..82155706
-
Hg19::chr5:82155710..82155724,-p@chr5:82155710..82155724
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Hg19::chr5:82155725..82155739,-p@chr5:82155725..82155739
-


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 tube3.02e-11156
neural rod3.02e-11156
future spinal cord3.02e-11156
neural keel3.02e-11156
regional part of nervous system2.81e-9953
regional part of brain2.81e-9953
central nervous system2.36e-8681
brain3.58e-7968
future brain3.58e-7968
nervous system4.26e-7789
regional part of forebrain1.39e-7641
forebrain1.39e-7641
anterior neural tube1.39e-7641
future forebrain1.39e-7641
neural plate7.11e-7482
presumptive neural plate7.11e-7482
neurectoderm4.17e-7086
brain grey matter8.26e-6834
gray matter8.26e-6834
telencephalon2.06e-6734
regional part of telencephalon4.60e-6032
cerebral hemisphere1.29e-5932
ecto-epithelium1.08e-56104
adult organism3.91e-54114
pre-chordal neural plate9.62e-5061
structure with developmental contribution from neural crest1.34e-45132
regional part of cerebral cortex2.25e-4522
cerebral cortex1.05e-3925
pallium1.05e-3925
neocortex1.07e-3720
ectoderm-derived structure8.02e-37171
ectoderm8.02e-37171
presumptive ectoderm8.02e-37171
posterior neural tube4.26e-3415
chordal neural plate4.26e-3415
neural nucleus1.69e-319
nucleus of brain1.69e-319
organ system subdivision1.59e-29223
tube4.26e-27192
brainstem1.86e-266
gyrus1.47e-256
basal ganglion2.47e-249
nuclear complex of neuraxis2.47e-249
aggregate regional part of brain2.47e-249
collection of basal ganglia2.47e-249
cerebral subcortex2.47e-249
telencephalic nucleus3.99e-237
segmental subdivision of hindbrain1.19e-2212
hindbrain1.19e-2212
presumptive hindbrain1.19e-2212
segmental subdivision of nervous system8.28e-2113
anatomical conduit4.79e-20240
corpus striatum1.95e-184
striatum1.95e-184
ventral part of telencephalon1.95e-184
future corpus striatum1.95e-184
limbic system5.07e-155
caudate-putamen1.46e-143
dorsal striatum1.46e-143
spinal cord2.01e-143
dorsal region element2.01e-143
dorsum2.01e-143
anatomical cluster2.61e-14373
pons3.15e-143
medulla oblongata5.38e-143
frontal cortex5.38e-143
myelencephalon5.38e-143
future myelencephalon5.38e-143
epithelium6.07e-14306
cell layer9.97e-14309
organ part2.04e-12218
regional part of metencephalon2.56e-129
metencephalon2.56e-129
future metencephalon2.56e-129
regional part of diencephalon9.89e-114
multi-tissue structure1.37e-10342
diencephalon1.64e-107
future diencephalon1.64e-107
dorsal plus ventral thalamus2.02e-102
thalamic complex2.02e-102
temporal lobe2.05e-106
caudate nucleus2.12e-102
future caudate nucleus2.12e-102
Ammon's horn2.22e-102
lobe parts of cerebral cortex2.22e-102
hippocampal formation2.22e-102
limbic lobe2.22e-102
locus ceruleus2.92e-102
brainstem nucleus2.92e-102
hindbrain nucleus2.92e-102
middle frontal gyrus4.39e-102
middle temporal gyrus8.22e-102
occipital lobe1.96e-085
parietal lobe2.81e-085
organ6.20e-07503


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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