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Coexpression cluster:C4153: Difference between revisions

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|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0007023!1.47e-56!115;UBERON:0001049!2.20e-40!57;UBERON:0005068!2.20e-40!57;UBERON:0006241!2.20e-40!57;UBERON:0007135!2.20e-40!57;UBERON:0001017!1.55e-38!82;UBERON:0005743!3.33e-37!86;UBERON:0000955!1.45e-36!69;UBERON:0006238!1.45e-36!69;UBERON:0002616!5.19e-34!59;UBERON:0000073!2.21e-33!94;UBERON:0001016!2.21e-33!94;UBERON:0003080!3.66e-33!42;UBERON:0002780!2.21e-32!41;UBERON:0001890!2.21e-32!41;UBERON:0006240!2.21e-32!41;UBERON:0003075!1.09e-30!86;UBERON:0007284!1.09e-30!86;UBERON:0000153!3.90e-30!129;UBERON:0007811!3.90e-30!129;UBERON:0000033!3.73e-29!123;UBERON:0002346!3.16e-28!90;UBERON:0001893!2.93e-27!34;UBERON:0002020!5.40e-27!34;UBERON:0003528!5.40e-27!34;UBERON:0001869!1.77e-26!32;UBERON:0002791!2.81e-26!33;UBERON:0003056!2.09e-24!61;UBERON:0002619!1.45e-22!22;UBERON:0004121!2.94e-22!169;UBERON:0001950!4.53e-21!20;UBERON:0000924!4.88e-21!173;UBERON:0006601!4.88e-21!173;UBERON:0000956!3.36e-20!25;UBERON:0000203!3.36e-20!25;UBERON:0004111!2.71e-16!241;UBERON:0000481!3.58e-15!347;UBERON:0000477!6.11e-15!286;UBERON:0000064!7.42e-15!219;UBERON:0000062!6.24e-14!511;UBERON:0000025!8.00e-13!194;UBERON:0000475!6.27e-11!365;UBERON:0000922!7.22e-10!612;UBERON:0000468!1.73e-09!659;UBERON:0000483!9.19e-09!309;UBERON:0003076!1.70e-08!15;UBERON:0003057!1.70e-08!15;UBERON:0001871!1.99e-08!7;UBERON:0000119!2.09e-08!312;UBERON:0002308!3.25e-08!9;UBERON:0000125!3.25e-08!9;UBERON:0002420!3.34e-08!9;UBERON:0007245!3.34e-08!9;UBERON:0010009!3.34e-08!9;UBERON:0010011!3.34e-08!9;UBERON:0000454!3.34e-08!9;UBERON:0002050!9.63e-08!605;UBERON:0005423!9.63e-08!605;UBERON:0000467!1.04e-07!625;UBERON:0000480!1.29e-07!626;UBERON:0000200!1.59e-07!6;UBERON:0000923!1.63e-07!604;UBERON:0005291!1.63e-07!604;UBERON:0006598!1.63e-07!604;UBERON:0002532!1.63e-07!604;UBERON:0004733!2.68e-07!12;UBERON:0002028!2.68e-07!12;UBERON:0007277!2.68e-07!12;UBERON:0002298!5.50e-07!8;UBERON:0001007!6.02e-07!155;UBERON:0001555!6.02e-07!155;UBERON:0007026!6.02e-07!155;UBERON:0009663!7.00e-07!7
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}}
}}

Revision as of 19:46, 8 August 2012


Full id: C4153_cerebellum_Burkitt_eye_occipital_colon_caudate_retina



Phase1 CAGE Peaks

Hg19::chr2:180726040..180726052,-p2@ZNF385B
Hg19::chr2:180726058..180726098,-p3@ZNF385B
Hg19::chr2:180726254..180726275,-p4@ZNF385B


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
adult organism1.47e-56115
neural tube2.20e-4057
neural rod2.20e-4057
future spinal cord2.20e-4057
neural keel2.20e-4057
central nervous system1.55e-3882
brain1.45e-3669
future brain1.45e-3669
regional part of brain5.19e-3459
regional part of nervous system2.21e-3394
nervous system2.21e-3394
anterior neural tube3.66e-3342
regional part of forebrain2.21e-3241
forebrain2.21e-3241
future forebrain2.21e-3241
neural plate1.09e-3086
presumptive neural plate1.09e-3086
anterior region of body3.90e-30129
craniocervical region3.90e-30129
head3.73e-29123
neurectoderm3.16e-2890
telencephalon2.93e-2734
gray matter5.40e-2734
brain grey matter5.40e-2734
cerebral hemisphere1.77e-2632
regional part of telencephalon2.81e-2633
pre-chordal neural plate2.09e-2461
regional part of cerebral cortex1.45e-2222
ectoderm-derived structure2.94e-22169
neocortex4.53e-2120
ectoderm4.88e-21173
presumptive ectoderm4.88e-21173
cerebral cortex3.36e-2025
pallium3.36e-2025
anatomical conduit2.71e-16241
multi-tissue structure3.58e-15347
anatomical cluster6.11e-15286
organ part7.42e-15219
organ6.24e-14511
tube8.00e-13194
organism subdivision6.27e-11365
embryo7.22e-10612
multi-cellular organism1.73e-09659
epithelium9.19e-09309
posterior neural tube1.70e-0815
chordal neural plate1.70e-0815
temporal lobe1.99e-087
cell layer2.09e-08312
nucleus of brain3.25e-089
neural nucleus3.25e-089
basal ganglion3.34e-089
nuclear complex of neuraxis3.34e-089
aggregate regional part of brain3.34e-089
collection of basal ganglia3.34e-089
cerebral subcortex3.34e-089
embryonic structure9.63e-08605
developing anatomical structure9.63e-08605
anatomical system1.04e-07625
anatomical group1.29e-07626
gyrus1.59e-076
germ layer1.63e-07604
embryonic tissue1.63e-07604
presumptive structure1.63e-07604
epiblast (generic)1.63e-07604
segmental subdivision of hindbrain2.68e-0712
hindbrain2.68e-0712
presumptive hindbrain2.68e-0712
brainstem5.50e-078
digestive system6.02e-07155
digestive tract6.02e-07155
primitive gut6.02e-07155
telencephalic nucleus7.00e-077


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.