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Coexpression cluster:C1298: Difference between revisions

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|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0007023!2.92e-25!115;UBERON:0001049!1.26e-21!57;UBERON:0005068!1.26e-21!57;UBERON:0006241!1.26e-21!57;UBERON:0007135!1.26e-21!57;UBERON:0002616!1.43e-21!59;UBERON:0003080!3.68e-21!42;UBERON:0002780!1.14e-20!41;UBERON:0001890!1.14e-20!41;UBERON:0006240!1.14e-20!41;UBERON:0001017!2.30e-20!82;UBERON:0005743!2.81e-20!86;UBERON:0002346!3.41e-19!90;UBERON:0003075!3.77e-19!86;UBERON:0007284!3.77e-19!86;UBERON:0000955!5.08e-19!69;UBERON:0006238!5.08e-19!69;UBERON:0001893!9.63e-19!34;UBERON:0000475!1.06e-18!365;UBERON:0000073!2.72e-18!94;UBERON:0001016!2.72e-18!94;UBERON:0002020!2.78e-18!34;UBERON:0003528!2.78e-18!34;UBERON:0002791!3.56e-18!33;UBERON:0003056!4.56e-18!61;UBERON:0001869!8.08e-18!32;UBERON:0002199!7.57e-16!45;UBERON:0002416!7.57e-16!45;UBERON:0000956!5.85e-14!25;UBERON:0000203!5.85e-14!25;UBERON:0000924!1.67e-13!173;UBERON:0006601!1.67e-13!173;UBERON:0004121!3.01e-13!169;UBERON:0002097!3.25e-13!40;UBERON:0002619!2.75e-12!22;UBERON:0000033!8.68e-12!123;UBERON:0000153!1.35e-11!129;UBERON:0007811!1.35e-11!129;UBERON:0001950!4.36e-11!20;UBERON:0000468!2.44e-09!659;UBERON:0003102!7.19e-09!95;UBERON:0000064!1.32e-08!219;UBERON:0001013!1.67e-08!14;UBERON:0000119!1.07e-07!312;UBERON:0000062!2.03e-07!511;UBERON:0000483!2.31e-07!309;UBERON:0000467!3.13e-07!625;UBERON:0000489!3.22e-07!32;UBERON:0000480!4.20e-07!626;UBERON:0002113!6.31e-07!27;UBERON:0003918!6.31e-07!27;UBERON:0005095!6.31e-07!27;UBERON:0007687!6.31e-07!27;UBERON:0000479!8.97e-07!787
|ontology_enrichment_uberon=UBERON:0007023!2.92e-25!115;UBERON:0001049!1.26e-21!57;UBERON:0005068!1.26e-21!57;UBERON:0006241!1.26e-21!57;UBERON:0007135!1.26e-21!57;UBERON:0002616!1.43e-21!59;UBERON:0003080!3.68e-21!42;UBERON:0002780!1.14e-20!41;UBERON:0001890!1.14e-20!41;UBERON:0006240!1.14e-20!41;UBERON:0001017!2.30e-20!82;UBERON:0005743!2.81e-20!86;UBERON:0002346!3.41e-19!90;UBERON:0003075!3.77e-19!86;UBERON:0007284!3.77e-19!86;UBERON:0000955!5.08e-19!69;UBERON:0006238!5.08e-19!69;UBERON:0001893!9.63e-19!34;UBERON:0000475!1.06e-18!365;UBERON:0000073!2.72e-18!94;UBERON:0001016!2.72e-18!94;UBERON:0002020!2.78e-18!34;UBERON:0003528!2.78e-18!34;UBERON:0002791!3.56e-18!33;UBERON:0003056!4.56e-18!61;UBERON:0001869!8.08e-18!32;UBERON:0002199!7.57e-16!45;UBERON:0002416!7.57e-16!45;UBERON:0000956!5.85e-14!25;UBERON:0000203!5.85e-14!25;UBERON:0000924!1.67e-13!173;UBERON:0006601!1.67e-13!173;UBERON:0004121!3.01e-13!169;UBERON:0002097!3.25e-13!40;UBERON:0002619!2.75e-12!22;UBERON:0000033!8.68e-12!123;UBERON:0000153!1.35e-11!129;UBERON:0007811!1.35e-11!129;UBERON:0001950!4.36e-11!20;UBERON:0000468!2.44e-09!659;UBERON:0003102!7.19e-09!95;UBERON:0000064!1.32e-08!219;UBERON:0001013!1.67e-08!14;UBERON:0000119!1.07e-07!312;UBERON:0000062!2.03e-07!511;UBERON:0000483!2.31e-07!309;UBERON:0000467!3.13e-07!625;UBERON:0000489!3.22e-07!32;UBERON:0000480!4.20e-07!626;UBERON:0002113!6.31e-07!27;UBERON:0003918!6.31e-07!27;UBERON:0005095!6.31e-07!27;UBERON:0007687!6.31e-07!27;UBERON:0000479!8.97e-07!787
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}}
}}

Revision as of 17:07, 8 August 2012


Full id: C1298_ductus_seminal_Fibroblast_kidney_uterus_epididymis_mesenchymal



Phase1 CAGE Peaks

Hg19::chr10:119301691..119301711,-p7@EMX2OS
Hg19::chr10:119301716..119301729,-p10@EMX2OS
Hg19::chr10:119301735..119301746,-p9@EMX2OS
Hg19::chr10:119301771..119301798,-p1@EMX2OS
Hg19::chr10:119301800..119301823,-p2@EMX2OS
Hg19::chr10:119303078..119303169,+p2@EMX2


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
skin fibroblast1.35e-1223
fibroblast1.07e-0975
fat cell1.22e-0915
Uber Anatomy
Ontology termp-valuen
adult organism2.92e-25115
neural tube1.26e-2157
neural rod1.26e-2157
future spinal cord1.26e-2157
neural keel1.26e-2157
regional part of brain1.43e-2159
anterior neural tube3.68e-2142
regional part of forebrain1.14e-2041
forebrain1.14e-2041
future forebrain1.14e-2041
central nervous system2.30e-2082
neurectoderm3.41e-1990
neural plate3.77e-1986
presumptive neural plate3.77e-1986
brain5.08e-1969
future brain5.08e-1969
telencephalon9.63e-1934
organism subdivision1.06e-18365
regional part of nervous system2.72e-1894
nervous system2.72e-1894
gray matter2.78e-1834
brain grey matter2.78e-1834
regional part of telencephalon3.56e-1833
pre-chordal neural plate4.56e-1861
cerebral hemisphere8.08e-1832
integument7.57e-1645
integumental system7.57e-1645
cerebral cortex5.85e-1425
pallium5.85e-1425
ectoderm1.67e-13173
presumptive ectoderm1.67e-13173
ectoderm-derived structure3.01e-13169
skin of body3.25e-1340
regional part of cerebral cortex2.75e-1222
head8.68e-12123
anterior region of body1.35e-11129
craniocervical region1.35e-11129
neocortex4.36e-1120
multi-cellular organism2.44e-09659
surface structure7.19e-0995
organ part1.32e-08219
adipose tissue1.67e-0814
cell layer1.07e-07312
organ2.03e-07511
epithelium2.31e-07309
anatomical system3.13e-07625
cavitated compound organ3.22e-0732
anatomical group4.20e-07626
kidney6.31e-0727
kidney mesenchyme6.31e-0727
kidney rudiment6.31e-0727
kidney field6.31e-0727
tissue8.97e-07787


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.