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Coexpression cluster:C3927: Difference between revisions

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|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0007023!1.20e-87!115;UBERON:0001049!1.19e-47!57;UBERON:0005068!1.19e-47!57;UBERON:0006241!1.19e-47!57;UBERON:0007135!1.19e-47!57;UBERON:0000955!1.51e-39!69;UBERON:0006238!1.51e-39!69;UBERON:0002616!2.51e-39!59;UBERON:0005743!2.35e-38!86;UBERON:0001017!3.92e-38!82;UBERON:0003080!4.82e-38!42;UBERON:0003075!8.60e-38!86;UBERON:0007284!8.60e-38!86;UBERON:0002780!5.45e-37!41;UBERON:0001890!5.45e-37!41;UBERON:0006240!5.45e-37!41;UBERON:0000073!2.28e-35!94;UBERON:0001016!2.28e-35!94;UBERON:0002346!3.64e-35!90;UBERON:0001893!8.83e-30!34;UBERON:0002020!1.54e-29!34;UBERON:0003528!1.54e-29!34;UBERON:0002791!1.67e-28!33;UBERON:0001869!6.20e-28!32;UBERON:0000153!1.55e-26!129;UBERON:0007811!1.55e-26!129;UBERON:0003056!3.78e-26!61;UBERON:0002619!1.16e-25!22;UBERON:0000033!9.14e-25!123;UBERON:0001950!2.98e-23!20;UBERON:0000956!1.05e-21!25;UBERON:0000203!1.05e-21!25;UBERON:0004121!1.77e-20!169;UBERON:0000924!1.77e-19!173;UBERON:0006601!1.77e-19!173;UBERON:0004111!7.64e-16!241;UBERON:0000062!1.07e-14!511;UBERON:0000025!1.82e-13!194;UBERON:0000477!2.28e-13!286;UBERON:0000922!1.26e-11!612;UBERON:0000064!1.66e-11!219;UBERON:0000468!2.33e-11!659;UBERON:0000467!2.49e-11!625;UBERON:0000480!3.05e-11!626;UBERON:0000481!4.70e-11!347;UBERON:0001871!9.81e-11!7;UBERON:0003076!1.29e-10!15;UBERON:0003057!1.29e-10!15;UBERON:0000923!2.05e-10!604;UBERON:0005291!2.05e-10!604;UBERON:0006598!2.05e-10!604;UBERON:0002532!2.05e-10!604;UBERON:0002050!2.50e-10!605;UBERON:0005423!2.50e-10!605;UBERON:0002420!1.02e-09!9;UBERON:0007245!1.02e-09!9;UBERON:0010009!1.02e-09!9;UBERON:0010011!1.02e-09!9;UBERON:0000454!1.02e-09!9;UBERON:0002298!1.49e-09!8;UBERON:0002308!3.04e-09!9;UBERON:0000125!3.04e-09!9;UBERON:0000200!5.11e-09!6;UBERON:0004732!7.36e-09!13;UBERON:0000483!1.28e-08!309;UBERON:0001894!1.33e-08!7;UBERON:0006222!1.33e-08!7;UBERON:0000475!1.95e-08!365;UBERON:0000119!2.53e-08!312;UBERON:0004733!6.64e-08!12;UBERON:0002028!6.64e-08!12;UBERON:0007277!6.64e-08!12;UBERON:0000349!9.49e-08!5;UBERON:0009663!3.00e-07!7;UBERON:0002021!6.16e-07!5
|ontology_enrichment_uberon=UBERON:0007023!1.20e-87!115;UBERON:0001049!1.19e-47!57;UBERON:0005068!1.19e-47!57;UBERON:0006241!1.19e-47!57;UBERON:0007135!1.19e-47!57;UBERON:0000955!1.51e-39!69;UBERON:0006238!1.51e-39!69;UBERON:0002616!2.51e-39!59;UBERON:0005743!2.35e-38!86;UBERON:0001017!3.92e-38!82;UBERON:0003080!4.82e-38!42;UBERON:0003075!8.60e-38!86;UBERON:0007284!8.60e-38!86;UBERON:0002780!5.45e-37!41;UBERON:0001890!5.45e-37!41;UBERON:0006240!5.45e-37!41;UBERON:0000073!2.28e-35!94;UBERON:0001016!2.28e-35!94;UBERON:0002346!3.64e-35!90;UBERON:0001893!8.83e-30!34;UBERON:0002020!1.54e-29!34;UBERON:0003528!1.54e-29!34;UBERON:0002791!1.67e-28!33;UBERON:0001869!6.20e-28!32;UBERON:0000153!1.55e-26!129;UBERON:0007811!1.55e-26!129;UBERON:0003056!3.78e-26!61;UBERON:0002619!1.16e-25!22;UBERON:0000033!9.14e-25!123;UBERON:0001950!2.98e-23!20;UBERON:0000956!1.05e-21!25;UBERON:0000203!1.05e-21!25;UBERON:0004121!1.77e-20!169;UBERON:0000924!1.77e-19!173;UBERON:0006601!1.77e-19!173;UBERON:0004111!7.64e-16!241;UBERON:0000062!1.07e-14!511;UBERON:0000025!1.82e-13!194;UBERON:0000477!2.28e-13!286;UBERON:0000922!1.26e-11!612;UBERON:0000064!1.66e-11!219;UBERON:0000468!2.33e-11!659;UBERON:0000467!2.49e-11!625;UBERON:0000480!3.05e-11!626;UBERON:0000481!4.70e-11!347;UBERON:0001871!9.81e-11!7;UBERON:0003076!1.29e-10!15;UBERON:0003057!1.29e-10!15;UBERON:0000923!2.05e-10!604;UBERON:0005291!2.05e-10!604;UBERON:0006598!2.05e-10!604;UBERON:0002532!2.05e-10!604;UBERON:0002050!2.50e-10!605;UBERON:0005423!2.50e-10!605;UBERON:0002420!1.02e-09!9;UBERON:0007245!1.02e-09!9;UBERON:0010009!1.02e-09!9;UBERON:0010011!1.02e-09!9;UBERON:0000454!1.02e-09!9;UBERON:0002298!1.49e-09!8;UBERON:0002308!3.04e-09!9;UBERON:0000125!3.04e-09!9;UBERON:0000200!5.11e-09!6;UBERON:0004732!7.36e-09!13;UBERON:0000483!1.28e-08!309;UBERON:0001894!1.33e-08!7;UBERON:0006222!1.33e-08!7;UBERON:0000475!1.95e-08!365;UBERON:0000119!2.53e-08!312;UBERON:0004733!6.64e-08!12;UBERON:0002028!6.64e-08!12;UBERON:0007277!6.64e-08!12;UBERON:0000349!9.49e-08!5;UBERON:0009663!3.00e-07!7;UBERON:0002021!6.16e-07!5
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}}
}}

Revision as of 14:20, 5 September 2012


Full id: C3927_stomach_brain_temporal_occipital_insula_kidney_frontal



Phase1 CAGE Peaks

Hg19::chr1:205538132..205538150,+p1@MFSD4
Hg19::chr1:205538165..205538193,+p2@MFSD4
Hg19::chr1:205538351..205538398,-p@chr1:205538351..205538398
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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 organism1.20e-87115
neural tube1.19e-4757
neural rod1.19e-4757
future spinal cord1.19e-4757
neural keel1.19e-4757
brain1.51e-3969
future brain1.51e-3969
regional part of brain2.51e-3959
central nervous system3.92e-3882
anterior neural tube4.82e-3842
neural plate8.60e-3886
presumptive neural plate8.60e-3886
regional part of forebrain5.45e-3741
forebrain5.45e-3741
future forebrain5.45e-3741
regional part of nervous system2.28e-3594
nervous system2.28e-3594
neurectoderm3.64e-3590
telencephalon8.83e-3034
gray matter1.54e-2934
brain grey matter1.54e-2934
regional part of telencephalon1.67e-2833
cerebral hemisphere6.20e-2832
anterior region of body1.55e-26129
craniocervical region1.55e-26129
pre-chordal neural plate3.78e-2661
regional part of cerebral cortex1.16e-2522
head9.14e-25123
neocortex2.98e-2320
cerebral cortex1.05e-2125
pallium1.05e-2125
ectoderm-derived structure1.77e-20169
ectoderm1.77e-19173
presumptive ectoderm1.77e-19173
anatomical conduit7.64e-16241
organ1.07e-14511
tube1.82e-13194
anatomical cluster2.28e-13286
embryo1.26e-11612
organ part1.66e-11219
multi-cellular organism2.33e-11659
anatomical system2.49e-11625
anatomical group3.05e-11626
multi-tissue structure4.70e-11347
temporal lobe9.81e-117
posterior neural tube1.29e-1015
chordal neural plate1.29e-1015
germ layer2.05e-10604
embryonic tissue2.05e-10604
presumptive structure2.05e-10604
epiblast (generic)2.05e-10604
embryonic structure2.50e-10605
developing anatomical structure2.50e-10605
basal ganglion1.02e-099
nuclear complex of neuraxis1.02e-099
aggregate regional part of brain1.02e-099
collection of basal ganglia1.02e-099
cerebral subcortex1.02e-099
brainstem1.49e-098
nucleus of brain3.04e-099
neural nucleus3.04e-099
gyrus5.11e-096
segmental subdivision of nervous system7.36e-0913
epithelium1.28e-08309
diencephalon1.33e-087
future diencephalon1.33e-087
organism subdivision1.95e-08365
cell layer2.53e-08312
segmental subdivision of hindbrain6.64e-0812
hindbrain6.64e-0812
presumptive hindbrain6.64e-0812
limbic system9.49e-085
telencephalic nucleus3.00e-077
occipital lobe6.16e-075


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
CTCF#1066435.360256373075030.0064925092527670.0279605448785507
MYC#460935.22228187160940.007020843755740150.0294714590436393
SUZ12#23512350.11578091106297.93834897779404e-060.000222569994333378



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.