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Coexpression cluster:C1247: Difference between revisions

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|ontology_enrichment_uberon=UBERON:0001049!3.92e-136!56;UBERON:0005068!3.92e-136!56;UBERON:0006241!3.92e-136!56;UBERON:0007135!3.92e-136!56;UBERON:0000073!1.18e-124!53;UBERON:0002616!1.18e-124!53;UBERON:0003528!9.50e-107!34;UBERON:0002020!9.50e-107!34;UBERON:0001893!5.58e-106!34;UBERON:0002780!1.15e-105!41;UBERON:0001890!1.15e-105!41;UBERON:0003080!1.15e-105!41;UBERON:0006240!1.15e-105!41;UBERON:0001017!1.02e-99!81;UBERON:0000955!4.44e-99!68;UBERON:0006238!4.44e-99!68;UBERON:0001869!5.24e-99!32;UBERON:0002791!5.85e-99!32;UBERON:0003075!1.23e-90!82;UBERON:0007284!1.23e-90!82;UBERON:0001016!4.66e-89!89;UBERON:0002346!4.78e-86!86;UBERON:0002619!1.77e-82!22;UBERON:0001950!1.72e-74!20;UBERON:0000956!2.57e-72!25;UBERON:0000203!2.57e-72!25;UBERON:0010371!1.01e-69!104;UBERON:0003056!5.37e-69!61;UBERON:0007023!2.36e-60!114;UBERON:0010314!5.48e-56!132;UBERON:0004121!1.10e-42!171;UBERON:0000924!1.10e-42!171;UBERON:0006601!1.10e-42!171;UBERON:0002420!6.26e-36!9;UBERON:0007245!6.26e-36!9;UBERON:0010009!6.26e-36!9;UBERON:0010011!6.26e-36!9;UBERON:0000454!6.26e-36!9;UBERON:0000025!1.75e-35!192;UBERON:0000125!2.05e-35!9;UBERON:0002308!2.05e-35!9;UBERON:0011216!5.39e-34!223;UBERON:0003076!9.66e-30!15;UBERON:0003057!9.66e-30!15;UBERON:0009663!7.20e-28!7;UBERON:0004111!1.56e-26!240;UBERON:0000200!1.05e-24!6;UBERON:0002298!2.57e-23!6;UBERON:0001871!2.39e-21!6;UBERON:0000349!5.84e-21!5;UBERON:0001872!1.22e-20!5;UBERON:0002021!1.44e-20!5;UBERON:0004733!1.02e-19!12;UBERON:0002028!1.02e-19!12;UBERON:0007277!1.02e-19!12;UBERON:0000483!8.90e-19!306;UBERON:0000119!1.67e-18!309;UBERON:0000064!1.92e-18!218;UBERON:0004732!4.20e-18!13;UBERON:0000477!1.20e-17!373;UBERON:0000369!3.83e-17!4;UBERON:0002435!3.83e-17!4;UBERON:0000204!3.83e-17!4;UBERON:0010082!3.83e-17!4;UBERON:0000481!9.80e-15!342;UBERON:0005383!8.54e-14!3;UBERON:0005382!8.54e-14!3;UBERON:0001870!2.44e-13!3;UBERON:0002240!6.81e-13!3;UBERON:0005174!6.81e-13!3;UBERON:0001137!6.81e-13!3;UBERON:0000988!8.02e-13!3;UBERON:0001896!3.01e-12!3;UBERON:0005290!3.01e-12!3;UBERON:0010096!3.01e-12!3;UBERON:0002680!7.76e-11!9;UBERON:0001895!7.76e-11!9;UBERON:0010092!7.76e-11!9;UBERON:0002702!8.13e-10!2;UBERON:0001876!8.48e-10!2;UBERON:0002771!8.85e-10!2;UBERON:0000062!9.70e-10!503;UBERON:0001873!1.05e-09!2;UBERON:0010122!1.05e-09!2;UBERON:0001954!1.54e-09!2;UBERON:0003022!1.54e-09!2;UBERON:0002421!1.54e-09!2;UBERON:0002600!1.54e-09!2;UBERON:0001897!2.75e-09!2;UBERON:0010225!2.75e-09!2;UBERON:0002148!2.87e-09!2;UBERON:0006331!2.87e-09!2;UBERON:0009662!2.87e-09!2;UBERON:0001875!3.83e-09!2;UBERON:0006514!3.83e-09!2;UBERON:0000923!1.84e-08!560;UBERON:0010316!1.84e-08!560;UBERON:0005291!1.84e-08!560;UBERON:0006598!1.84e-08!560;UBERON:0010317!1.84e-08!560;UBERON:0002532!1.84e-08!560;UBERON:0002050!2.49e-08!564;UBERON:0005423!8.58e-08!581;UBERON:0000922!1.84e-07!592
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}}
}}

Revision as of 14:46, 26 November 2012


Full id: C1247_parietal_thalamus_hippocampus_olfactory_middle_amygdala_medial



Phase1 CAGE Peaks

Hg19::chr1:14819044..14819065,+p@chr1:14819044..14819065
+
Hg19::chr2:210526133..210526141,+p52@MAP2
Hg19::chr3:10369338..10369362,-p@chr3:10369338..10369362
-
Hg19::chr5:58148556..58148559,+p@chr5:58148556..58148559
+
Hg19::chr5:71502197..71502220,+p@chr5:71502197..71502220
+
Hg19::chr8:91969565..91969587,+p@chr8:91969565..91969587
+
Hg19::chr8:91969795..91969807,+p@chr8:91969795..91969807
+


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 tube3.92e-13656
neural rod3.92e-13656
future spinal cord3.92e-13656
neural keel3.92e-13656
regional part of nervous system1.18e-12453
regional part of brain1.18e-12453
brain grey matter9.50e-10734
gray matter9.50e-10734
telencephalon5.58e-10634
regional part of forebrain1.15e-10541
forebrain1.15e-10541
anterior neural tube1.15e-10541
future forebrain1.15e-10541
central nervous system1.02e-9981
brain4.44e-9968
future brain4.44e-9968
cerebral hemisphere5.24e-9932
regional part of telencephalon5.85e-9932
neural plate1.23e-9082
presumptive neural plate1.23e-9082
nervous system4.66e-8989
neurectoderm4.78e-8686
regional part of cerebral cortex1.77e-8222
neocortex1.72e-7420
cerebral cortex2.57e-7225
pallium2.57e-7225
ecto-epithelium1.01e-69104
pre-chordal neural plate5.37e-6961
adult organism2.36e-60114
structure with developmental contribution from neural crest5.48e-56132
ectoderm-derived structure1.10e-42171
ectoderm1.10e-42171
presumptive ectoderm1.10e-42171
basal ganglion6.26e-369
nuclear complex of neuraxis6.26e-369
aggregate regional part of brain6.26e-369
collection of basal ganglia6.26e-369
cerebral subcortex6.26e-369
tube1.75e-35192
neural nucleus2.05e-359
nucleus of brain2.05e-359
organ system subdivision5.39e-34223
posterior neural tube9.66e-3015
chordal neural plate9.66e-3015
telencephalic nucleus7.20e-287
anatomical conduit1.56e-26240
gyrus1.05e-246
brainstem2.57e-236
temporal lobe2.39e-216
limbic system5.84e-215
parietal lobe1.22e-205
occipital lobe1.44e-205
segmental subdivision of hindbrain1.02e-1912
hindbrain1.02e-1912
presumptive hindbrain1.02e-1912
epithelium8.90e-19306
cell layer1.67e-18309
organ part1.92e-18218
segmental subdivision of nervous system4.20e-1813
anatomical cluster1.20e-17373
corpus striatum3.83e-174
striatum3.83e-174
ventral part of telencephalon3.83e-174
future corpus striatum3.83e-174
multi-tissue structure9.80e-15342
caudate-putamen8.54e-143
dorsal striatum8.54e-143
frontal cortex2.44e-133
spinal cord6.81e-133
dorsal region element6.81e-133
dorsum6.81e-133
pons8.02e-133
medulla oblongata3.01e-123
myelencephalon3.01e-123
future myelencephalon3.01e-123
regional part of metencephalon7.76e-119
metencephalon7.76e-119
future metencephalon7.76e-119
middle frontal gyrus8.13e-102
amygdala8.48e-102
middle temporal gyrus8.85e-102
organ9.70e-10503
caudate nucleus1.05e-092
future caudate nucleus1.05e-092
Ammon's horn1.54e-092
lobe parts of cerebral cortex1.54e-092
hippocampal formation1.54e-092
limbic lobe1.54e-092
dorsal plus ventral thalamus2.75e-092
thalamic complex2.75e-092
locus ceruleus2.87e-092
brainstem nucleus2.87e-092
hindbrain nucleus2.87e-092
globus pallidus3.83e-092
pallidum3.83e-092
germ layer1.84e-08560
germ layer / neural crest1.84e-08560
embryonic tissue1.84e-08560
presumptive structure1.84e-08560
germ layer / neural crest derived structure1.84e-08560


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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