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Coexpression cluster:C2799: Difference between revisions

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|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0007023!4.38e-37!115;UBERON:0001049!2.70e-32!57;UBERON:0005068!2.70e-32!57;UBERON:0006241!2.70e-32!57;UBERON:0007135!2.70e-32!57;UBERON:0001017!3.61e-32!82;UBERON:0005743!4.88e-32!86;UBERON:0000073!2.01e-31!94;UBERON:0001016!2.01e-31!94;UBERON:0002780!8.96e-27!41;UBERON:0001890!8.96e-27!41;UBERON:0006240!8.96e-27!41;UBERON:0003075!1.39e-26!86;UBERON:0007284!1.39e-26!86;UBERON:0003080!1.25e-25!42;UBERON:0002616!1.77e-25!59;UBERON:0002346!2.03e-25!90;UBERON:0000955!6.52e-25!69;UBERON:0006238!6.52e-25!69;UBERON:0001893!1.00e-21!34;UBERON:0002020!1.38e-21!34;UBERON:0003528!1.38e-21!34;UBERON:0002791!5.32e-21!33;UBERON:0001869!2.05e-20!32;UBERON:0004121!2.62e-19!169;UBERON:0003056!2.68e-19!61;UBERON:0000924!7.06e-19!173;UBERON:0006601!7.06e-19!173;UBERON:0002619!1.36e-17!22;UBERON:0004111!3.31e-17!241;UBERON:0000956!5.11e-16!25;UBERON:0000203!5.11e-16!25;UBERON:0001950!5.81e-16!20;UBERON:0000033!2.27e-15!123;UBERON:0000153!3.58e-15!129;UBERON:0007811!3.58e-15!129;UBERON:0000025!5.56e-15!194;UBERON:0000477!1.04e-14!286;UBERON:0000481!4.59e-10!347;UBERON:0000483!6.01e-10!309;UBERON:0000119!1.18e-09!312;UBERON:0000475!5.17e-08!365;UBERON:0000468!6.03e-08!659;UBERON:0003076!7.65e-08!15;UBERON:0003057!7.65e-08!15;UBERON:0000064!1.71e-07!219;UBERON:0002420!2.82e-07!9;UBERON:0007245!2.82e-07!9;UBERON:0010009!2.82e-07!9;UBERON:0010011!2.82e-07!9;UBERON:0000454!2.82e-07!9;UBERON:0001871!3.54e-07!7;UBERON:0002308!4.96e-07!9;UBERON:0000125!4.96e-07!9;UBERON:0000922!5.14e-07!612;UBERON:0000467!8.82e-07!625
|ontology_enrichment_uberon=UBERON:0007023!4.38e-37!115;UBERON:0001049!2.70e-32!57;UBERON:0005068!2.70e-32!57;UBERON:0006241!2.70e-32!57;UBERON:0007135!2.70e-32!57;UBERON:0001017!3.61e-32!82;UBERON:0005743!4.88e-32!86;UBERON:0000073!2.01e-31!94;UBERON:0001016!2.01e-31!94;UBERON:0002780!8.96e-27!41;UBERON:0001890!8.96e-27!41;UBERON:0006240!8.96e-27!41;UBERON:0003075!1.39e-26!86;UBERON:0007284!1.39e-26!86;UBERON:0003080!1.25e-25!42;UBERON:0002616!1.77e-25!59;UBERON:0002346!2.03e-25!90;UBERON:0000955!6.52e-25!69;UBERON:0006238!6.52e-25!69;UBERON:0001893!1.00e-21!34;UBERON:0002020!1.38e-21!34;UBERON:0003528!1.38e-21!34;UBERON:0002791!5.32e-21!33;UBERON:0001869!2.05e-20!32;UBERON:0004121!2.62e-19!169;UBERON:0003056!2.68e-19!61;UBERON:0000924!7.06e-19!173;UBERON:0006601!7.06e-19!173;UBERON:0002619!1.36e-17!22;UBERON:0004111!3.31e-17!241;UBERON:0000956!5.11e-16!25;UBERON:0000203!5.11e-16!25;UBERON:0001950!5.81e-16!20;UBERON:0000033!2.27e-15!123;UBERON:0000153!3.58e-15!129;UBERON:0007811!3.58e-15!129;UBERON:0000025!5.56e-15!194;UBERON:0000477!1.04e-14!286;UBERON:0000481!4.59e-10!347;UBERON:0000483!6.01e-10!309;UBERON:0000119!1.18e-09!312;UBERON:0000475!5.17e-08!365;UBERON:0000468!6.03e-08!659;UBERON:0003076!7.65e-08!15;UBERON:0003057!7.65e-08!15;UBERON:0000064!1.71e-07!219;UBERON:0002420!2.82e-07!9;UBERON:0007245!2.82e-07!9;UBERON:0010009!2.82e-07!9;UBERON:0010011!2.82e-07!9;UBERON:0000454!2.82e-07!9;UBERON:0001871!3.54e-07!7;UBERON:0002308!4.96e-07!9;UBERON:0000125!4.96e-07!9;UBERON:0000922!5.14e-07!612;UBERON:0000467!8.82e-07!625
|tf_chipseq_enrich=JUND#3727;3:5.24599795640327:0.0104343275174842:0.0387095315287913!MYC#4609;4:5.2222818716094:0.00134430939527274:0.00889216093057758!TAF1#6872;4:3.34304628574529:0.00800566489870165:0.0323056928385882!TAF7#6879;4:11.4330694049239:5.85061525419808e-05:0.00097128025199999!TBP#6908;4:3.70677068709639:0.00529637781478435:0.0244842600300222!ZNF143#7702;4:13.5008765522279:3.00867915035614e-05:0.00062160918255993
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}}
}}

Revision as of 14:17, 5 September 2012


Full id: C2799_hippocampus_cerebellum_pituitary_amygdala_olfactory_middle_medial



Phase1 CAGE Peaks

Hg19::chr5:113697717..113697728,+p6@KCNN2
Hg19::chr5:113697740..113697793,+p1@KCNN2
Hg19::chr5:113697798..113697814,+p3@KCNN2
Hg19::chr5:113697983..113698024,+p4@KCNN2


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 organism4.38e-37115
neural tube2.70e-3257
neural rod2.70e-3257
future spinal cord2.70e-3257
neural keel2.70e-3257
central nervous system3.61e-3282
regional part of nervous system2.01e-3194
nervous system2.01e-3194
regional part of forebrain8.96e-2741
forebrain8.96e-2741
future forebrain8.96e-2741
neural plate1.39e-2686
presumptive neural plate1.39e-2686
anterior neural tube1.25e-2542
regional part of brain1.77e-2559
neurectoderm2.03e-2590
brain6.52e-2569
future brain6.52e-2569
telencephalon1.00e-2134
gray matter1.38e-2134
brain grey matter1.38e-2134
regional part of telencephalon5.32e-2133
cerebral hemisphere2.05e-2032
ectoderm-derived structure2.62e-19169
pre-chordal neural plate2.68e-1961
ectoderm7.06e-19173
presumptive ectoderm7.06e-19173
regional part of cerebral cortex1.36e-1722
anatomical conduit3.31e-17241
cerebral cortex5.11e-1625
pallium5.11e-1625
neocortex5.81e-1620
head2.27e-15123
anterior region of body3.58e-15129
craniocervical region3.58e-15129
tube5.56e-15194
anatomical cluster1.04e-14286
multi-tissue structure4.59e-10347
epithelium6.01e-10309
cell layer1.18e-09312
organism subdivision5.17e-08365
multi-cellular organism6.03e-08659
posterior neural tube7.65e-0815
chordal neural plate7.65e-0815
organ part1.71e-07219
basal ganglion2.82e-079
nuclear complex of neuraxis2.82e-079
aggregate regional part of brain2.82e-079
collection of basal ganglia2.82e-079
cerebral subcortex2.82e-079
temporal lobe3.54e-077
nucleus of brain4.96e-079
neural nucleus4.96e-079
embryo5.14e-07612
anatomical system8.82e-07625


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
JUND#372735.245997956403270.01043432751748420.0387095315287913
MYC#460945.22228187160940.001344309395272740.00889216093057758
TAF1#687243.343046285745290.008005664898701650.0323056928385882
TAF7#6879411.43306940492395.85061525419808e-050.00097128025199999
TBP#690843.706770687096390.005296377814784350.0244842600300222
ZNF143#7702413.50087655222793.00867915035614e-050.00062160918255993



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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