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Coexpression cluster:C4604: Difference between revisions

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|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0000475!2.60e-19!365;UBERON:0003102!4.20e-14!95;UBERON:0002100!3.25e-12!216;UBERON:0002097!1.98e-11!40;UBERON:0000468!2.61e-11!659;UBERON:0002199!2.72e-11!45;UBERON:0002416!2.72e-11!45;UBERON:0005256!7.59e-11!143;UBERON:0005085!3.23e-09!29;UBERON:0000481!6.67e-09!347;UBERON:0000119!1.99e-08!312;UBERON:0000486!3.42e-08!82;UBERON:0000483!4.60e-08!309;UBERON:0003104!6.31e-08!238;UBERON:0009142!6.31e-08!238;UBERON:0004923!9.59e-08!57;UBERON:0000914!9.78e-08!83;UBERON:0002329!9.78e-08!83;UBERON:0003077!9.78e-08!83;UBERON:0003059!9.78e-08!83;UBERON:0007282!9.78e-08!83;UBERON:0009618!9.78e-08!83;UBERON:0007285!9.78e-08!83;UBERON:0000464!1.89e-07!104;UBERON:0001444!2.26e-07!48;UBERON:0000064!2.86e-07!219;UBERON:0000466!3.39e-07!126;UBERON:0000467!5.95e-07!625
|ontology_enrichment_uberon=UBERON:0000475!2.60e-19!365;UBERON:0003102!4.20e-14!95;UBERON:0002100!3.25e-12!216;UBERON:0002097!1.98e-11!40;UBERON:0000468!2.61e-11!659;UBERON:0002199!2.72e-11!45;UBERON:0002416!2.72e-11!45;UBERON:0005256!7.59e-11!143;UBERON:0005085!3.23e-09!29;UBERON:0000481!6.67e-09!347;UBERON:0000119!1.99e-08!312;UBERON:0000486!3.42e-08!82;UBERON:0000483!4.60e-08!309;UBERON:0003104!6.31e-08!238;UBERON:0009142!6.31e-08!238;UBERON:0004923!9.59e-08!57;UBERON:0000914!9.78e-08!83;UBERON:0002329!9.78e-08!83;UBERON:0003077!9.78e-08!83;UBERON:0003059!9.78e-08!83;UBERON:0007282!9.78e-08!83;UBERON:0009618!9.78e-08!83;UBERON:0007285!9.78e-08!83;UBERON:0000464!1.89e-07!104;UBERON:0001444!2.26e-07!48;UBERON:0000064!2.86e-07!219;UBERON:0000466!3.39e-07!126;UBERON:0000467!5.95e-07!625
|tf_chipseq_enrich=E2F1#1869;3:4.90738921487932:0.00846098534723939:0.0327437969644768!EGR1#1958;3:4.98817909481014:0.00805648813738344:0.0322281126313846!SP1#6667;3:5.6983813781409:0.00540396270171217:0.024776524895918!ZBTB7A#51341;3:7.3519093078759:0.00251625586028227:0.0140841012804555
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}}
}}

Revision as of 14:18, 5 September 2012


Full id: C4604_Placental_Amniotic_osteosarcoma_Fibroblast_Mesenchymal_Pericytes_Osteoblast



Phase1 CAGE Peaks

Hg19::chr6:43044003..43044086,+p1@PTK7
Hg19::chr6:43044168..43044181,+p3@PTK7
Hg19::chr6:43044196..43044216,+p2@PTK7


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 cell8.28e-26180
embryonic cell9.73e-17248
fibroblast3.66e-1575
animal cell1.93e-10679
eukaryotic cell1.93e-10679
ectodermal cell2.66e-1071
epithelial cell2.00e-09254
somatic cell7.78e-09591
skin fibroblast1.30e-0723
contractile cell1.94e-0759
ecto-epithelial cell2.06e-0733
neurectodermal cell4.70e-0759
single fate stem cell9.72e-0720
Uber Anatomy
Ontology termp-valuen
organism subdivision2.60e-19365
surface structure4.20e-1495
trunk3.25e-12216
skin of body1.98e-1140
multi-cellular organism2.61e-11659
integument2.72e-1145
integumental system2.72e-1145
trunk mesenchyme7.59e-11143
ectodermal placode3.23e-0929
multi-tissue structure6.67e-09347
cell layer1.99e-08312
multilaminar epithelium3.42e-0882
epithelium4.60e-08309
mesenchyme6.31e-08238
entire embryonic mesenchyme6.31e-08238
organ component layer9.59e-0857
somite9.78e-0883
paraxial mesoderm9.78e-0883
presomitic mesoderm9.78e-0883
presumptive segmental plate9.78e-0883
trunk paraxial mesoderm9.78e-0883
presumptive paraxial mesoderm9.78e-0883
anatomical space1.89e-07104
subdivision of head2.26e-0748
organ part2.86e-07219
immaterial anatomical entity3.39e-07126
anatomical system5.95e-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
E2F1#186934.907389214879320.008460985347239390.0327437969644768
EGR1#195834.988179094810140.008056488137383440.0322281126313846
SP1#666735.69838137814090.005403962701712170.024776524895918
ZBTB7A#5134137.35190930787590.002516255860282270.0140841012804555



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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