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Coexpression cluster:C1905: Difference between revisions

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|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0002346!1.13e-24!90;UBERON:0003075!5.44e-23!86;UBERON:0007284!5.44e-23!86;UBERON:0003056!4.02e-22!61;UBERON:0000073!1.30e-19!94;UBERON:0001016!1.30e-19!94;UBERON:0005743!7.17e-16!86;UBERON:0002616!2.49e-15!59;UBERON:0001049!5.15e-15!57;UBERON:0005068!5.15e-15!57;UBERON:0006241!5.15e-15!57;UBERON:0007135!5.15e-15!57;UBERON:0002780!2.03e-14!41;UBERON:0001890!2.03e-14!41;UBERON:0006240!2.03e-14!41;UBERON:0000924!3.52e-14!173;UBERON:0006601!3.52e-14!173;UBERON:0003080!7.79e-14!42;UBERON:0000955!1.91e-13!69;UBERON:0006238!1.91e-13!69;UBERON:0000033!2.42e-13!123;UBERON:0001017!3.62e-13!82;UBERON:0004121!5.84e-13!169;UBERON:0000153!7.74e-13!129;UBERON:0007811!7.74e-13!129;UBERON:0007625!2.20e-12!11;UBERON:0002104!2.78e-11!21;UBERON:0000970!1.70e-10!20;UBERON:0000019!1.30e-09!19;UBERON:0000047!1.30e-09!19;UBERON:0004088!1.30e-09!19;UBERON:0003072!1.30e-09!19;UBERON:0003071!1.30e-09!19;UBERON:0004128!1.30e-09!19;UBERON:0001893!2.94e-09!34;UBERON:0001032!3.89e-09!24;UBERON:0004456!3.89e-09!24;UBERON:0001869!3.99e-09!32;UBERON:0002791!5.38e-09!33;UBERON:0000020!2.03e-08!23;UBERON:0002020!2.96e-08!34;UBERON:0003528!2.96e-08!34;UBERON:0001456!3.18e-08!21;UBERON:0001894!4.72e-08!7;UBERON:0006222!4.72e-08!7;UBERON:0000966!8.99e-07!5;UBERON:0005388!8.99e-07!5;UBERON:0001802!8.99e-07!5
|ontology_enrichment_uberon=UBERON:0002346!1.13e-24!90;UBERON:0003075!5.44e-23!86;UBERON:0007284!5.44e-23!86;UBERON:0003056!4.02e-22!61;UBERON:0000073!1.30e-19!94;UBERON:0001016!1.30e-19!94;UBERON:0005743!7.17e-16!86;UBERON:0002616!2.49e-15!59;UBERON:0001049!5.15e-15!57;UBERON:0005068!5.15e-15!57;UBERON:0006241!5.15e-15!57;UBERON:0007135!5.15e-15!57;UBERON:0002780!2.03e-14!41;UBERON:0001890!2.03e-14!41;UBERON:0006240!2.03e-14!41;UBERON:0000924!3.52e-14!173;UBERON:0006601!3.52e-14!173;UBERON:0003080!7.79e-14!42;UBERON:0000955!1.91e-13!69;UBERON:0006238!1.91e-13!69;UBERON:0000033!2.42e-13!123;UBERON:0001017!3.62e-13!82;UBERON:0004121!5.84e-13!169;UBERON:0000153!7.74e-13!129;UBERON:0007811!7.74e-13!129;UBERON:0007625!2.20e-12!11;UBERON:0002104!2.78e-11!21;UBERON:0000970!1.70e-10!20;UBERON:0000019!1.30e-09!19;UBERON:0000047!1.30e-09!19;UBERON:0004088!1.30e-09!19;UBERON:0003072!1.30e-09!19;UBERON:0003071!1.30e-09!19;UBERON:0004128!1.30e-09!19;UBERON:0001893!2.94e-09!34;UBERON:0001032!3.89e-09!24;UBERON:0004456!3.89e-09!24;UBERON:0001869!3.99e-09!32;UBERON:0002791!5.38e-09!33;UBERON:0000020!2.03e-08!23;UBERON:0002020!2.96e-08!34;UBERON:0003528!2.96e-08!34;UBERON:0001456!3.18e-08!21;UBERON:0001894!4.72e-08!7;UBERON:0006222!4.72e-08!7;UBERON:0000966!8.99e-07!5;UBERON:0005388!8.99e-07!5;UBERON:0001802!8.99e-07!5
|tf_chipseq_enrich=GATA2#2624;4:10.1959453868432:0.000177544777760982:0.00215762148528964!PBX3#5090;3:13.1487076120465:0.000886046932280843:0.00660560036836883!SUZ12#23512;5:50.1157809110629:3.15480790456198e-09:2.62747195171092e-07!ZNF263#10127;4:6.57747330960854:0.000987510323790016:0.00709365091865366
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}}
}}

Revision as of 12:45, 5 September 2012


Full id: C1905_caudate_putamen_embryonic_pituitary_globus_cord_rhabdomyosarcoma



Phase1 CAGE Peaks

Hg19::chr2:45168959..45168990,+p6@SIX3
Hg19::chr2:45168997..45169020,+p4@SIX3
Hg19::chr2:45169024..45169033,+p12@SIX3
Hg19::chr2:45169317..45169326,+p13@SIX3
Hg19::chr2:45169684..45169715,+p9@SIX3


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
neurectoderm1.13e-2490
neural plate5.44e-2386
presumptive neural plate5.44e-2386
pre-chordal neural plate4.02e-2261
regional part of nervous system1.30e-1994
nervous system1.30e-1994
regional part of brain2.49e-1559
neural tube5.15e-1557
neural rod5.15e-1557
future spinal cord5.15e-1557
neural keel5.15e-1557
regional part of forebrain2.03e-1441
forebrain2.03e-1441
future forebrain2.03e-1441
ectoderm3.52e-14173
presumptive ectoderm3.52e-14173
anterior neural tube7.79e-1442
brain1.91e-1369
future brain1.91e-1369
head2.42e-13123
central nervous system3.62e-1382
ectoderm-derived structure5.84e-13169
anterior region of body7.74e-13129
craniocervical region7.74e-13129
pigment epithelium of eye2.20e-1211
visual system2.78e-1121
eye1.70e-1020
camera-type eye1.30e-0919
simple eye1.30e-0919
ocular region1.30e-0919
optic cup1.30e-0919
eye primordium1.30e-0919
optic vesicle1.30e-0919
telencephalon2.94e-0934
sensory system3.89e-0924
entire sense organ system3.89e-0924
cerebral hemisphere3.99e-0932
regional part of telencephalon5.38e-0933
sense organ2.03e-0823
gray matter2.96e-0834
brain grey matter2.96e-0834
face3.18e-0821
diencephalon4.72e-087
future diencephalon4.72e-087
retina8.99e-075
photoreceptor array8.99e-075
posterior segment of eyeball8.99e-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
GATA2#2624410.19594538684320.0001775447777609820.00215762148528964
PBX3#5090313.14870761204650.0008860469322808430.00660560036836883
SUZ12#23512550.11578091106293.15480790456198e-092.62747195171092e-07
ZNF263#1012746.577473309608540.0009875103237900160.00709365091865366



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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