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Coexpression cluster:C698: Difference between revisions

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|ontology_enrichment_uberon=UBERON:0003102!5.55e-12!99;UBERON:0002199!3.66e-10!46;UBERON:0002416!3.66e-10!46;UBERON:0002384!6.86e-09!371;UBERON:0002097!2.28e-08!41;UBERON:0003688!2.75e-08!6;UBERON:0002358!2.75e-08!6;UBERON:0003684!2.75e-08!6;UBERON:0001178!2.75e-08!6;UBERON:0004573!8.14e-08!33;UBERON:0004571!8.14e-08!33;UBERON:0007524!1.44e-07!73;UBERON:0002329!2.43e-07!71;UBERON:0003059!2.43e-07!71;UBERON:0007282!2.43e-07!71;UBERON:0004290!2.43e-07!71;UBERON:0009618!2.43e-07!71;UBERON:0003077!4.13e-07!72;UBERON:0007285!4.13e-07!72;UBERON:0000486!5.21e-07!83
|ontology_enrichment_uberon=UBERON:0003102!5.55e-12!99;UBERON:0002199!3.66e-10!46;UBERON:0002416!3.66e-10!46;UBERON:0002384!6.86e-09!371;UBERON:0002097!2.28e-08!41;UBERON:0003688!2.75e-08!6;UBERON:0002358!2.75e-08!6;UBERON:0003684!2.75e-08!6;UBERON:0001178!2.75e-08!6;UBERON:0004573!8.14e-08!33;UBERON:0004571!8.14e-08!33;UBERON:0007524!1.44e-07!73;UBERON:0002329!2.43e-07!71;UBERON:0003059!2.43e-07!71;UBERON:0007282!2.43e-07!71;UBERON:0004290!2.43e-07!71;UBERON:0009618!2.43e-07!71;UBERON:0003077!4.13e-07!72;UBERON:0007285!4.13e-07!72;UBERON:0000486!5.21e-07!83
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|tfbs_overrepresentation_for_novel_motifs=1.21158,0.854134,0.223258,0.345441,0.190185,0.344001,0.411652,0.104517,0.102889,0.0552668,0.317729,0.451026,0.0765797,0.401301,0.189126,0.597712,0.617549,0.148925,0.0839658,0.533397,0.223306,0.891656,0.337221,0.18624,0.260754,0.471832,0.499542,0.335332,0.192587,0.454328,0.298956,0.65246,0.12577,0.0778977,3.69431,0.00238655,0.161511,0.345014,1.40365,0.0916487,1.51412,0.285097,0.0815132,0.187953,0.437801,1.28372,0.412635,0.308385,0.0157812,0.192687,0.484909,0.423285,0.0382824,0.725869,0.873575,0.403938,0.195993,0.374657,0.454008,0.373762,0.691524,0.414771,1.13949,0.591384,0.43102,0.559038,0.959746,1.32257,0.642589,1.16217,0.273995,0.108268,0.0373297,2.0239,0.0739759,0.237079,0.216432,0.575479,1.54395,0.255642,0.293113,0.590372,1.92912,1.70185,0.821696,0.00480132,0.0287315,0.0540708,0.508983,1.42111,1.05129,0.795567,0.66846,0.409242,0.190761,0.140087,1.48453,0.709167,0.51326,0.0463096,0.145361,0.663075,0.703825,0.621018,0.54826,1.52332,0.606045,0.398205,0.260543,0.177931,0.232335,0.701175,0.21882,0.325885,1.00416,0.16034,0.00677971,2.23935,2.3477,0.132787,0.863578,0.506732,0.341589,0.44095,1.11293,0.576194,0.405934,1.61431,0.905059,0.140769,0.796235,0.301402,4.99072,0.437919,1.06395,0.189287,0.293853,0.335825,1.02226,1.87395,1.47317,0.985665,0.407489,0.70579,0.549903,0.367151,0.534339,1.71519,0.282284,0.128495,0.313334,0.0750447,0.796604,1.10243,0.414334,1.19239,0.494,0.179455,2.05068,0.237047,0.984474,0.778717,0.638755,0.239672,0.564971,1.09889,1.82201,0.410452,0.00249101
}}
}}

Revision as of 14:24, 26 November 2012


Full id: C698_Smooth_Adipocyte_Fibroblast_Preadipocyte_Olfactory_Ewing_basal



Phase1 CAGE Peaks

Hg19::chr13:102104716..102104735,+p5@ITGBL1
Hg19::chr13:102104738..102104747,+p11@ITGBL1
Hg19::chr13:102104920..102104936,+p4@ITGBL1
Hg19::chr13:102104952..102104959,+p6@ITGBL1
Hg19::chr13:102104980..102105050,+p1@ITGBL1
Hg19::chr13:102105055..102105060,+p7@ITGBL1
Hg19::chr13:102105062..102105085,+p2@ITGBL1
Hg19::chr13:102105089..102105094,+p8@ITGBL1
Hg19::chr13:102105139..102105150,+p3@ITGBL1
Hg19::chr13:102220045..102220071,+p@chr13:102220045..102220071
+
Hg19::chr13:102235656..102235669,+p@chr13:102235656..102235669
+
Hg19::chr13:102359103..102359116,+p9@ITGBL1


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
fibroblast1.23e-2976
skin fibroblast1.73e-1323
multi fate stem cell7.69e-12427
preadipocyte1.12e-1112
somatic stem cell3.73e-11433
stem cell2.78e-10441
connective tissue cell5.27e-08361
muscle precursor cell1.27e-0758
myoblast1.27e-0758
multi-potent skeletal muscle stem cell1.27e-0758
stromal cell1.45e-0728
non-terminally differentiated cell2.33e-07106
mesenchymal cell5.62e-07354
somatic cell6.96e-07588
Uber Anatomy
Ontology termp-valuen
surface structure5.55e-1299
integument3.66e-1046
integumental system3.66e-1046
connective tissue6.86e-09371
skin of body2.28e-0841
omentum2.75e-086
peritoneum2.75e-086
abdominal cavity2.75e-086
visceral peritoneum2.75e-086
systemic artery8.14e-0833
systemic arterial system8.14e-0833
dense mesenchyme tissue1.44e-0773
somite2.43e-0771
presomitic mesoderm2.43e-0771
presumptive segmental plate2.43e-0771
dermomyotome2.43e-0771
trunk paraxial mesoderm2.43e-0771
paraxial mesoderm4.13e-0772
presumptive paraxial mesoderm4.13e-0772
multilaminar epithelium5.21e-0783


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)

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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.

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