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Coexpression cluster:C1324: Difference between revisions

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|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0000914!1.20e-12!83;UBERON:0002329!1.20e-12!83;UBERON:0003077!1.20e-12!83;UBERON:0003059!1.20e-12!83;UBERON:0007282!1.20e-12!83;UBERON:0009618!1.20e-12!83;UBERON:0007285!1.20e-12!83;UBERON:0005256!4.92e-12!143;UBERON:0004290!1.66e-11!70;UBERON:0002100!4.14e-11!216;UBERON:0000926!1.38e-10!448;UBERON:0004120!1.38e-10!448;UBERON:0006603!1.38e-10!448;UBERON:0002199!3.53e-10!45;UBERON:0002416!3.53e-10!45;UBERON:0003102!7.22e-10!95;UBERON:0002385!1.18e-09!63;UBERON:0001015!1.18e-09!63;UBERON:0000383!1.18e-09!63;UBERON:0000486!1.83e-09!82;UBERON:0001134!3.23e-09!61;UBERON:0002036!3.23e-09!61;UBERON:0003082!3.23e-09!61;UBERON:0002097!3.56e-09!40;UBERON:0003104!4.77e-09!238;UBERON:0009142!4.77e-09!238;UBERON:0000468!4.03e-08!659;UBERON:0000475!7.56e-08!365;UBERON:0000467!1.47e-07!625;UBERON:0000480!2.26e-07!626;UBERON:0004923!6.30e-07!57
|ontology_enrichment_uberon=UBERON:0000914!1.20e-12!83;UBERON:0002329!1.20e-12!83;UBERON:0003077!1.20e-12!83;UBERON:0003059!1.20e-12!83;UBERON:0007282!1.20e-12!83;UBERON:0009618!1.20e-12!83;UBERON:0007285!1.20e-12!83;UBERON:0005256!4.92e-12!143;UBERON:0004290!1.66e-11!70;UBERON:0002100!4.14e-11!216;UBERON:0000926!1.38e-10!448;UBERON:0004120!1.38e-10!448;UBERON:0006603!1.38e-10!448;UBERON:0002199!3.53e-10!45;UBERON:0002416!3.53e-10!45;UBERON:0003102!7.22e-10!95;UBERON:0002385!1.18e-09!63;UBERON:0001015!1.18e-09!63;UBERON:0000383!1.18e-09!63;UBERON:0000486!1.83e-09!82;UBERON:0001134!3.23e-09!61;UBERON:0002036!3.23e-09!61;UBERON:0003082!3.23e-09!61;UBERON:0002097!3.56e-09!40;UBERON:0003104!4.77e-09!238;UBERON:0009142!4.77e-09!238;UBERON:0000468!4.03e-08!659;UBERON:0000475!7.56e-08!365;UBERON:0000467!1.47e-07!625;UBERON:0000480!2.26e-07!626;UBERON:0004923!6.30e-07!57
|tf_chipseq_enrich=STAT3#6774;5:8.76622083096187:4.28672496720299e-05:0.000765955977501647
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}}
}}

Revision as of 13:02, 5 September 2012


Full id: C1324_Fibroblast_Preadipocyte_basal_migratory_mesenchymal_Smooth_spindle



Phase1 CAGE Peaks

Hg19::chr10:95242223..95242232,-p8@MYOF
Hg19::chr18:56246303..56246344,-p9@ALPK2
Hg19::chr18:56246346..56246375,-p6@ALPK2
Hg19::chr18:56246399..56246415,-p15@ALPK2
Hg19::chr18:56246464..56246503,-p3@ALPK2
Hg19::chr4:77659857..77659874,+p3@SHROOM3


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


GO IDGO nameFDR corrected p-value
GO:0043476pigment accumulation0.00447414122204642
GO:0043482cellular pigment accumulation0.00447414122204642
GO:0033059cellular pigmentation0.00447414122204642
GO:0045176apical protein localization0.00894736048387635
GO:0008105asymmetric protein localization0.00894736048387635
GO:0022603regulation of anatomical structure morphogenesis0.0234757577475775
GO:0008360regulation of cell shape0.0234757577475775
GO:0022604regulation of cell morphogenesis0.0234757577475775
GO:0005912adherens junction0.026824695916118
GO:0016324apical plasma membrane0.030395052708795
GO:0045177apical part of cell0.0349369160994711
GO:0007389pattern specification process0.0461504527999066



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 cell2.50e-25180
fibroblast7.41e-2075
skin fibroblast1.11e-1123
muscle precursor cell1.54e-0857
myoblast1.54e-0857
multi-potent skeletal muscle stem cell1.54e-0857
smooth muscle cell9.98e-0842
smooth muscle myoblast9.98e-0842
preadipocyte1.40e-0712
muscle cell1.56e-0754
mesodermal cell3.29e-07119
contractile cell4.20e-0759
mesothelial cell5.38e-0719
Uber Anatomy
Ontology termp-valuen
somite1.20e-1283
paraxial mesoderm1.20e-1283
presomitic mesoderm1.20e-1283
presumptive segmental plate1.20e-1283
trunk paraxial mesoderm1.20e-1283
presumptive paraxial mesoderm1.20e-1283
trunk mesenchyme4.92e-12143
dermomyotome1.66e-1170
trunk4.14e-11216
mesoderm1.38e-10448
mesoderm-derived structure1.38e-10448
presumptive mesoderm1.38e-10448
integument3.53e-1045
integumental system3.53e-1045
surface structure7.22e-1095
muscle tissue1.18e-0963
musculature1.18e-0963
musculature of body1.18e-0963
multilaminar epithelium1.83e-0982
skeletal muscle tissue3.23e-0961
striated muscle tissue3.23e-0961
myotome3.23e-0961
skin of body3.56e-0940
mesenchyme4.77e-09238
entire embryonic mesenchyme4.77e-09238
multi-cellular organism4.03e-08659
organism subdivision7.56e-08365
anatomical system1.47e-07625
anatomical group2.26e-07626
organ component layer6.30e-0757


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
STAT3#677458.766220830961874.28672496720299e-050.000765955977501647



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.