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Coexpression cluster:C1667: Difference between revisions

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|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0007023!1.67e-34!115;UBERON:0000475!3.41e-30!365;UBERON:0005743!4.64e-26!86;UBERON:0000073!1.10e-25!94;UBERON:0001016!1.10e-25!94;UBERON:0001049!2.12e-25!57;UBERON:0005068!2.12e-25!57;UBERON:0006241!2.12e-25!57;UBERON:0007135!2.12e-25!57;UBERON:0001017!3.30e-25!82;UBERON:0000955!6.53e-24!69;UBERON:0006238!6.53e-24!69;UBERON:0000481!7.42e-24!347;UBERON:0003075!1.64e-23!86;UBERON:0007284!1.64e-23!86;UBERON:0002616!4.72e-23!59;UBERON:0000033!1.24e-21!123;UBERON:0004121!5.48e-21!169;UBERON:0002346!1.05e-20!90;UBERON:0000153!1.14e-20!129;UBERON:0007811!1.14e-20!129;UBERON:0000924!3.13e-19!173;UBERON:0006601!3.13e-19!173;UBERON:0002780!1.25e-18!41;UBERON:0001890!1.25e-18!41;UBERON:0006240!1.25e-18!41;UBERON:0003080!2.96e-18!42;UBERON:0000477!3.56e-18!286;UBERON:0000483!5.30e-18!309;UBERON:0000119!7.55e-18!312;UBERON:0000468!5.44e-17!659;UBERON:0003056!1.88e-16!61;UBERON:0004111!3.37e-16!241;UBERON:0002020!3.47e-16!34;UBERON:0003528!3.47e-16!34;UBERON:0001893!3.47e-16!34;UBERON:0002791!1.31e-15!33;UBERON:0000025!1.82e-15!194;UBERON:0000467!5.51e-15!625;UBERON:0001869!7.02e-15!32;UBERON:0000480!9.62e-15!626;UBERON:0000923!3.94e-11!604;UBERON:0005291!3.94e-11!604;UBERON:0006598!3.94e-11!604;UBERON:0002532!3.94e-11!604;UBERON:0002050!4.63e-11!605;UBERON:0005423!4.63e-11!605;UBERON:0000922!6.01e-11!612;UBERON:0002619!7.34e-11!22;UBERON:0000956!8.85e-11!25;UBERON:0000203!8.85e-11!25;UBERON:0000064!4.29e-10!219;UBERON:0001950!1.25e-09!20;UBERON:0000062!3.77e-09!511;UBERON:0003076!2.38e-08!15;UBERON:0003057!2.38e-08!15;UBERON:0002100!5.27e-08!216;UBERON:0000914!5.87e-08!83;UBERON:0002329!5.87e-08!83;UBERON:0003077!5.87e-08!83;UBERON:0003059!5.87e-08!83;UBERON:0007282!5.87e-08!83;UBERON:0009618!5.87e-08!83;UBERON:0007285!5.87e-08!83;UBERON:0005256!9.87e-08!143;UBERON:0004732!2.86e-07!13;UBERON:0002308!3.89e-07!9;UBERON:0000125!3.89e-07!9;UBERON:0002420!5.21e-07!9;UBERON:0007245!5.21e-07!9;UBERON:0010009!5.21e-07!9;UBERON:0010011!5.21e-07!9;UBERON:0000454!5.21e-07!9
|ontology_enrichment_uberon=UBERON:0007023!1.67e-34!115;UBERON:0000475!3.41e-30!365;UBERON:0005743!4.64e-26!86;UBERON:0000073!1.10e-25!94;UBERON:0001016!1.10e-25!94;UBERON:0001049!2.12e-25!57;UBERON:0005068!2.12e-25!57;UBERON:0006241!2.12e-25!57;UBERON:0007135!2.12e-25!57;UBERON:0001017!3.30e-25!82;UBERON:0000955!6.53e-24!69;UBERON:0006238!6.53e-24!69;UBERON:0000481!7.42e-24!347;UBERON:0003075!1.64e-23!86;UBERON:0007284!1.64e-23!86;UBERON:0002616!4.72e-23!59;UBERON:0000033!1.24e-21!123;UBERON:0004121!5.48e-21!169;UBERON:0002346!1.05e-20!90;UBERON:0000153!1.14e-20!129;UBERON:0007811!1.14e-20!129;UBERON:0000924!3.13e-19!173;UBERON:0006601!3.13e-19!173;UBERON:0002780!1.25e-18!41;UBERON:0001890!1.25e-18!41;UBERON:0006240!1.25e-18!41;UBERON:0003080!2.96e-18!42;UBERON:0000477!3.56e-18!286;UBERON:0000483!5.30e-18!309;UBERON:0000119!7.55e-18!312;UBERON:0000468!5.44e-17!659;UBERON:0003056!1.88e-16!61;UBERON:0004111!3.37e-16!241;UBERON:0002020!3.47e-16!34;UBERON:0003528!3.47e-16!34;UBERON:0001893!3.47e-16!34;UBERON:0002791!1.31e-15!33;UBERON:0000025!1.82e-15!194;UBERON:0000467!5.51e-15!625;UBERON:0001869!7.02e-15!32;UBERON:0000480!9.62e-15!626;UBERON:0000923!3.94e-11!604;UBERON:0005291!3.94e-11!604;UBERON:0006598!3.94e-11!604;UBERON:0002532!3.94e-11!604;UBERON:0002050!4.63e-11!605;UBERON:0005423!4.63e-11!605;UBERON:0000922!6.01e-11!612;UBERON:0002619!7.34e-11!22;UBERON:0000956!8.85e-11!25;UBERON:0000203!8.85e-11!25;UBERON:0000064!4.29e-10!219;UBERON:0001950!1.25e-09!20;UBERON:0000062!3.77e-09!511;UBERON:0003076!2.38e-08!15;UBERON:0003057!2.38e-08!15;UBERON:0002100!5.27e-08!216;UBERON:0000914!5.87e-08!83;UBERON:0002329!5.87e-08!83;UBERON:0003077!5.87e-08!83;UBERON:0003059!5.87e-08!83;UBERON:0007282!5.87e-08!83;UBERON:0009618!5.87e-08!83;UBERON:0007285!5.87e-08!83;UBERON:0005256!9.87e-08!143;UBERON:0004732!2.86e-07!13;UBERON:0002308!3.89e-07!9;UBERON:0000125!3.89e-07!9;UBERON:0002420!5.21e-07!9;UBERON:0007245!5.21e-07!9;UBERON:0010009!5.21e-07!9;UBERON:0010011!5.21e-07!9;UBERON:0000454!5.21e-07!9
|tf_chipseq_enrich=BHLHE40#8553;2:17.948725418791:0.00474781285983895:0.022317797608638!HNF4G#3174;2:11.5013690105787:0.0112743830492105:0.0413718875400194!NANOG#79923;2:11.6979113924051:0.0109116495195608:0.0402146151518601
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}}
}}

Revision as of 14:12, 5 September 2012


Full id: C1667_corpus_diaphragm_globus_tongue_diencephalon_optic_thalamus



Phase1 CAGE Peaks

Hg19::chr12:21680455..21680478,+p2@C12orf39
Hg19::chr12:21680481..21680499,+p7@C12orf39
Hg19::chr14:35183743..35183754,-p9@CFL2
Hg19::chr14:35183755..35183770,-p7@CFL2
Hg19::chr1:201857798..201857813,+p2@SHISA4


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>cell_data<br>uberon_data<br><br>


Cell Type
Ontology termp-valuen
non-terminally differentiated cell2.55e-13180
Uber Anatomy
Ontology termp-valuen
adult organism1.67e-34115
organism subdivision3.41e-30365
regional part of nervous system1.10e-2594
nervous system1.10e-2594
neural tube2.12e-2557
neural rod2.12e-2557
future spinal cord2.12e-2557
neural keel2.12e-2557
central nervous system3.30e-2582
brain6.53e-2469
future brain6.53e-2469
multi-tissue structure7.42e-24347
neural plate1.64e-2386
presumptive neural plate1.64e-2386
regional part of brain4.72e-2359
head1.24e-21123
ectoderm-derived structure5.48e-21169
neurectoderm1.05e-2090
anterior region of body1.14e-20129
craniocervical region1.14e-20129
ectoderm3.13e-19173
presumptive ectoderm3.13e-19173
regional part of forebrain1.25e-1841
forebrain1.25e-1841
future forebrain1.25e-1841
anterior neural tube2.96e-1842
anatomical cluster3.56e-18286
epithelium5.30e-18309
cell layer7.55e-18312
multi-cellular organism5.44e-17659
pre-chordal neural plate1.88e-1661
anatomical conduit3.37e-16241
gray matter3.47e-1634
brain grey matter3.47e-1634
telencephalon3.47e-1634
regional part of telencephalon1.31e-1533
tube1.82e-15194
anatomical system5.51e-15625
cerebral hemisphere7.02e-1532
anatomical group9.62e-15626
germ layer3.94e-11604
embryonic tissue3.94e-11604
presumptive structure3.94e-11604
epiblast (generic)3.94e-11604
embryonic structure4.63e-11605
developing anatomical structure4.63e-11605
embryo6.01e-11612
regional part of cerebral cortex7.34e-1122
cerebral cortex8.85e-1125
pallium8.85e-1125
organ part4.29e-10219
neocortex1.25e-0920
organ3.77e-09511
posterior neural tube2.38e-0815
chordal neural plate2.38e-0815
trunk5.27e-08216
somite5.87e-0883
paraxial mesoderm5.87e-0883
presomitic mesoderm5.87e-0883
presumptive segmental plate5.87e-0883
trunk paraxial mesoderm5.87e-0883
presumptive paraxial mesoderm5.87e-0883
trunk mesenchyme9.87e-08143
segmental subdivision of nervous system2.86e-0713
nucleus of brain3.89e-079
neural nucleus3.89e-079
basal ganglion5.21e-079
nuclear complex of neuraxis5.21e-079
aggregate regional part of brain5.21e-079
collection of basal ganglia5.21e-079
cerebral subcortex5.21e-079


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
BHLHE40#8553217.9487254187910.004747812859838950.022317797608638
HNF4G#3174211.50136901057870.01127438304921050.0413718875400194
NANOG#79923211.69791139240510.01091164951956080.0402146151518601



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.