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Coexpression cluster:C3685: Difference between revisions

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|tf_chipseq_enrich=E2F6#1876;3:5.01715573169739:0.0079176980688633:0.0321832516779798!GTF2B#2959;3:31.9438299343242:3.06634405746243e-05:0.00062756399572275!GTF2F1#2962;3:12.7396608767577:0.000483552504743859:0.0043349133084072!MXI1#4601;3:9.9615716287593:0.00101147054125902:0.00719794030107325!RFX5#5993;3:12.0479108271951:0.000571724605031258:0.00484229551738379!TCF7L2#6934;3:10.7701765631373:0.000800318129839838:0.00613193640689185!TFAP2C#7022;3:10.8092286098602:0.000791674657575313:0.00615328641530908
|tf_chipseq_enrich=E2F6#1876;3:5.01715573169739:0.0079176980688633:0.0321832516779798!GTF2B#2959;3:31.9438299343242:3.06634405746243e-05:0.00062756399572275!GTF2F1#2962;3:12.7396608767577:0.000483552504743859:0.0043349133084072!MXI1#4601;3:9.9615716287593:0.00101147054125902:0.00719794030107325!RFX5#5993;3:12.0479108271951:0.000571724605031258:0.00484229551738379!TCF7L2#6934;3:10.7701765631373:0.000800318129839838:0.00613193640689185!TFAP2C#7022;3:10.8092286098602:0.000791674657575313:0.00615328641530908
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}}
}}

Revision as of 16:17, 26 November 2012


Full id: C3685_Fibroblast_Pericytes_Mesenchymal_Meningeal_Trabecular_Adipocyte_Saos2



Phase1 CAGE Peaks

Hg19::chr17:75315534..75315612,+p4@SEPT9
Hg19::chr17:75315994..75316022,+p7@SEPT9
Hg19::chr17:75316024..75316071,+p16@SEPT9


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>


Uber Anatomy
Ontology termp-valuen
epithelial vesicle1.22e-2178
dense mesenchyme tissue9.02e-2173
somite9.61e-2171
presomitic mesoderm9.61e-2171
presumptive segmental plate9.61e-2171
dermomyotome9.61e-2171
trunk paraxial mesoderm9.61e-2171
paraxial mesoderm1.62e-2072
presumptive paraxial mesoderm1.62e-2072
skeletal muscle tissue5.61e-1762
striated muscle tissue5.61e-1762
myotome5.61e-1762
muscle tissue7.17e-1764
musculature7.17e-1764
musculature of body7.17e-1764
multilaminar epithelium3.91e-1683
trunk mesenchyme2.04e-13122
mesenchyme3.26e-12160
entire embryonic mesenchyme3.26e-12160
musculoskeletal system7.78e-12167
connective tissue9.64e-12371
mesoderm1.00e-10315
mesoderm-derived structure1.00e-10315
presumptive mesoderm1.00e-10315
integument1.19e-0946
integumental system1.19e-0946
skin of body6.27e-0941
splanchnic layer of lateral plate mesoderm3.68e-0883
tissue1.92e-07773
surface structure3.07e-0799
artery8.82e-0742
arterial blood vessel8.82e-0742
arterial system8.82e-0742


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


(#promoters = Number of promoters in this coexpression cluster that have ChIP signal of the TF)

TF#promotersEnrichmentp-valueq-value
E2F6#187635.017155731697390.00791769806886330.0321832516779798
GTF2B#2959331.94382993432423.06634405746243e-050.00062756399572275
GTF2F1#2962312.73966087675770.0004835525047438590.0043349133084072
MXI1#460139.96157162875930.001011470541259020.00719794030107325
RFX5#5993312.04791082719510.0005717246050312580.00484229551738379
TCF7L2#6934310.77017656313730.0008003181298398380.00613193640689185
TFAP2C#7022310.80922860986020.0007916746575753130.00615328641530908



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.