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Coexpression cluster:C2296: Difference between revisions

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|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0005743!7.06e-47!86;UBERON:0001017!8.30e-45!82;UBERON:0002346!1.30e-44!90;UBERON:0000073!4.40e-44!94;UBERON:0001016!4.40e-44!94;UBERON:0003075!1.71e-42!86;UBERON:0007284!1.71e-42!86;UBERON:0001049!4.26e-42!57;UBERON:0005068!4.26e-42!57;UBERON:0006241!4.26e-42!57;UBERON:0007135!4.26e-42!57;UBERON:0000955!5.82e-37!69;UBERON:0006238!5.82e-37!69;UBERON:0002616!3.22e-36!59;UBERON:0003056!1.76e-33!61;UBERON:0002780!4.05e-33!41;UBERON:0001890!4.05e-33!41;UBERON:0006240!4.05e-33!41;UBERON:0000924!1.69e-32!173;UBERON:0006601!1.69e-32!173;UBERON:0003080!8.79e-32!42;UBERON:0004121!1.34e-30!169;UBERON:0000033!2.90e-28!123;UBERON:0002020!5.64e-28!34;UBERON:0003528!5.64e-28!34;UBERON:0001893!6.64e-28!34;UBERON:0000153!7.37e-28!129;UBERON:0007811!7.37e-28!129;UBERON:0002791!4.22e-27!33;UBERON:0001869!1.62e-26!32;UBERON:0007023!2.38e-22!115;UBERON:0000956!3.06e-21!25;UBERON:0000203!3.06e-21!25;UBERON:0002619!2.10e-19!22;UBERON:0001950!6.50e-18!20;UBERON:0003076!3.38e-11!15;UBERON:0003057!3.38e-11!15;UBERON:0004732!1.16e-09!13;UBERON:0004733!5.86e-09!12;UBERON:0002028!5.86e-09!12;UBERON:0007277!5.86e-09!12;UBERON:0002308!3.79e-08!9;UBERON:0002420!3.79e-08!9;UBERON:0000125!3.79e-08!9;UBERON:0007245!3.79e-08!9;UBERON:0010009!3.79e-08!9;UBERON:0010011!3.79e-08!9;UBERON:0000454!3.79e-08!9;UBERON:0000064!5.66e-08!219;UBERON:0000475!7.82e-08!365;UBERON:0000025!9.08e-08!194;UBERON:0001871!1.08e-07!7;UBERON:0007625!5.00e-07!11;UBERON:0002680!6.50e-07!9;UBERON:0001895!6.50e-07!9;UBERON:0010092!6.50e-07!9;UBERON:0000119!6.50e-07!312
|ontology_enrichment_uberon=UBERON:0005743!7.06e-47!86;UBERON:0001017!8.30e-45!82;UBERON:0002346!1.30e-44!90;UBERON:0000073!4.40e-44!94;UBERON:0001016!4.40e-44!94;UBERON:0003075!1.71e-42!86;UBERON:0007284!1.71e-42!86;UBERON:0001049!4.26e-42!57;UBERON:0005068!4.26e-42!57;UBERON:0006241!4.26e-42!57;UBERON:0007135!4.26e-42!57;UBERON:0000955!5.82e-37!69;UBERON:0006238!5.82e-37!69;UBERON:0002616!3.22e-36!59;UBERON:0003056!1.76e-33!61;UBERON:0002780!4.05e-33!41;UBERON:0001890!4.05e-33!41;UBERON:0006240!4.05e-33!41;UBERON:0000924!1.69e-32!173;UBERON:0006601!1.69e-32!173;UBERON:0003080!8.79e-32!42;UBERON:0004121!1.34e-30!169;UBERON:0000033!2.90e-28!123;UBERON:0002020!5.64e-28!34;UBERON:0003528!5.64e-28!34;UBERON:0001893!6.64e-28!34;UBERON:0000153!7.37e-28!129;UBERON:0007811!7.37e-28!129;UBERON:0002791!4.22e-27!33;UBERON:0001869!1.62e-26!32;UBERON:0007023!2.38e-22!115;UBERON:0000956!3.06e-21!25;UBERON:0000203!3.06e-21!25;UBERON:0002619!2.10e-19!22;UBERON:0001950!6.50e-18!20;UBERON:0003076!3.38e-11!15;UBERON:0003057!3.38e-11!15;UBERON:0004732!1.16e-09!13;UBERON:0004733!5.86e-09!12;UBERON:0002028!5.86e-09!12;UBERON:0007277!5.86e-09!12;UBERON:0002308!3.79e-08!9;UBERON:0002420!3.79e-08!9;UBERON:0000125!3.79e-08!9;UBERON:0007245!3.79e-08!9;UBERON:0010009!3.79e-08!9;UBERON:0010011!3.79e-08!9;UBERON:0000454!3.79e-08!9;UBERON:0000064!5.66e-08!219;UBERON:0000475!7.82e-08!365;UBERON:0000025!9.08e-08!194;UBERON:0001871!1.08e-07!7;UBERON:0007625!5.00e-07!11;UBERON:0002680!6.50e-07!9;UBERON:0001895!6.50e-07!9;UBERON:0010092!6.50e-07!9;UBERON:0000119!6.50e-07!312
|tf_chipseq_enrich=CTBP2#1488;2:31.3585001696641:0.00149267688204723:0.00953886562345534
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}}
}}

Revision as of 12:56, 5 September 2012


Full id: C2296_pineal_temporal_occipital_parietal_duodenum_spinal_optic



Phase1 CAGE Peaks

Hg19::chr14:48006773..48006777,-p@chr14:48006773..48006777
-
Hg19::chr14:48144799..48144820,-p@chr14:48144799..48144820
-
Hg19::chr1:178340501..178340532,+p@chr1:178340501..178340532
+
Hg19::chr4:165305086..165305179,-p2@MARCH1


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 system8.30e-4582
neurectoderm1.30e-4490
regional part of nervous system4.40e-4494
nervous system4.40e-4494
neural plate1.71e-4286
presumptive neural plate1.71e-4286
neural tube4.26e-4257
neural rod4.26e-4257
future spinal cord4.26e-4257
neural keel4.26e-4257
brain5.82e-3769
future brain5.82e-3769
regional part of brain3.22e-3659
pre-chordal neural plate1.76e-3361
regional part of forebrain4.05e-3341
forebrain4.05e-3341
future forebrain4.05e-3341
ectoderm1.69e-32173
presumptive ectoderm1.69e-32173
anterior neural tube8.79e-3242
ectoderm-derived structure1.34e-30169
head2.90e-28123
gray matter5.64e-2834
brain grey matter5.64e-2834
telencephalon6.64e-2834
anterior region of body7.37e-28129
craniocervical region7.37e-28129
regional part of telencephalon4.22e-2733
cerebral hemisphere1.62e-2632
adult organism2.38e-22115
cerebral cortex3.06e-2125
pallium3.06e-2125
regional part of cerebral cortex2.10e-1922
neocortex6.50e-1820
posterior neural tube3.38e-1115
chordal neural plate3.38e-1115
segmental subdivision of nervous system1.16e-0913
segmental subdivision of hindbrain5.86e-0912
hindbrain5.86e-0912
presumptive hindbrain5.86e-0912
nucleus of brain3.79e-089
basal ganglion3.79e-089
neural nucleus3.79e-089
nuclear complex of neuraxis3.79e-089
aggregate regional part of brain3.79e-089
collection of basal ganglia3.79e-089
cerebral subcortex3.79e-089
organ part5.66e-08219
organism subdivision7.82e-08365
tube9.08e-08194
temporal lobe1.08e-077
pigment epithelium of eye5.00e-0711
regional part of metencephalon6.50e-079
metencephalon6.50e-079
future metencephalon6.50e-079
cell layer6.50e-07312


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


(#promoters = Number of promoters in this coexpression cluster that have ChIP signal of the TF)

TF#promotersEnrichmentp-valueq-value
CTBP2#1488231.35850016966410.001492676882047230.00953886562345534



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.