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Coexpression cluster:C540: Difference between revisions

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|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0007023!1.48e-17!115;UBERON:0000475!1.62e-15!365;UBERON:0000468!5.09e-15!659;UBERON:0000481!6.82e-15!347;UBERON:0000914!7.36e-14!83;UBERON:0002329!7.36e-14!83;UBERON:0003077!7.36e-14!83;UBERON:0003059!7.36e-14!83;UBERON:0007282!7.36e-14!83;UBERON:0009618!7.36e-14!83;UBERON:0007285!7.36e-14!83;UBERON:0004290!5.59e-12!70;UBERON:0000479!5.93e-12!787;UBERON:0003102!4.09e-11!95;UBERON:0002385!6.31e-11!63;UBERON:0001015!6.31e-11!63;UBERON:0000383!6.31e-11!63;UBERON:0000467!2.64e-10!625;UBERON:0001134!3.20e-10!61;UBERON:0002036!3.20e-10!61;UBERON:0003082!3.20e-10!61;UBERON:0000486!3.74e-10!82;UBERON:0000480!4.17e-10!626;UBERON:0007100!5.10e-10!27;UBERON:0000477!7.17e-10!286;UBERON:0005256!1.64e-09!143;UBERON:0000062!5.42e-09!511;UBERON:0000948!9.98e-09!24;UBERON:0005498!9.98e-09!24;UBERON:0004140!9.98e-09!24;UBERON:0009881!9.98e-09!24;UBERON:0004141!9.98e-09!24;UBERON:0003084!9.98e-09!24;UBERON:0007005!9.98e-09!24;UBERON:0004139!9.98e-09!24;UBERON:0004291!9.98e-09!24;UBERON:0003104!5.23e-08!238;UBERON:0009142!5.23e-08!238;UBERON:0000922!9.85e-08!612;UBERON:0002050!1.23e-07!605;UBERON:0005423!1.23e-07!605;UBERON:0000119!1.35e-07!312;UBERON:0000923!2.13e-07!604;UBERON:0005291!2.13e-07!604;UBERON:0006598!2.13e-07!604;UBERON:0002532!2.13e-07!604;UBERON:0002199!2.25e-07!45;UBERON:0002416!2.25e-07!45;UBERON:0002100!2.43e-07!216;UBERON:0000483!3.26e-07!309;UBERON:0001013!4.12e-07!14
|ontology_enrichment_uberon=UBERON:0007023!1.48e-17!115;UBERON:0000475!1.62e-15!365;UBERON:0000468!5.09e-15!659;UBERON:0000481!6.82e-15!347;UBERON:0000914!7.36e-14!83;UBERON:0002329!7.36e-14!83;UBERON:0003077!7.36e-14!83;UBERON:0003059!7.36e-14!83;UBERON:0007282!7.36e-14!83;UBERON:0009618!7.36e-14!83;UBERON:0007285!7.36e-14!83;UBERON:0004290!5.59e-12!70;UBERON:0000479!5.93e-12!787;UBERON:0003102!4.09e-11!95;UBERON:0002385!6.31e-11!63;UBERON:0001015!6.31e-11!63;UBERON:0000383!6.31e-11!63;UBERON:0000467!2.64e-10!625;UBERON:0001134!3.20e-10!61;UBERON:0002036!3.20e-10!61;UBERON:0003082!3.20e-10!61;UBERON:0000486!3.74e-10!82;UBERON:0000480!4.17e-10!626;UBERON:0007100!5.10e-10!27;UBERON:0000477!7.17e-10!286;UBERON:0005256!1.64e-09!143;UBERON:0000062!5.42e-09!511;UBERON:0000948!9.98e-09!24;UBERON:0005498!9.98e-09!24;UBERON:0004140!9.98e-09!24;UBERON:0009881!9.98e-09!24;UBERON:0004141!9.98e-09!24;UBERON:0003084!9.98e-09!24;UBERON:0007005!9.98e-09!24;UBERON:0004139!9.98e-09!24;UBERON:0004291!9.98e-09!24;UBERON:0003104!5.23e-08!238;UBERON:0009142!5.23e-08!238;UBERON:0000922!9.85e-08!612;UBERON:0002050!1.23e-07!605;UBERON:0005423!1.23e-07!605;UBERON:0000119!1.35e-07!312;UBERON:0000923!2.13e-07!604;UBERON:0005291!2.13e-07!604;UBERON:0006598!2.13e-07!604;UBERON:0002532!2.13e-07!604;UBERON:0002199!2.25e-07!45;UBERON:0002416!2.25e-07!45;UBERON:0002100!2.43e-07!216;UBERON:0000483!3.26e-07!309;UBERON:0001013!4.12e-07!14
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}}
}}

Revision as of 20:29, 8 August 2012


Full id: C540_tenocyte_Chondrocyte_Adipocyte_normal_Synoviocyte_Fibroblast_heart



Phase1 CAGE Peaks

Hg19::chr12:91539701..91539744,-p@chr12:91539701..91539744
-
Hg19::chr12:91539859..91539910,-p@chr12:91539859..91539910
-
Hg19::chr12:91539918..91539946,-p@chr12:91539918..91539946
-
Hg19::chr12:91545551..91545568,-p@chr12:91545551..91545568
-
Hg19::chr12:91546941..91546972,-p10@DCN
Hg19::chr12:91550883..91550925,-p@chr12:91550883..91550925
-
Hg19::chr12:91552107..91552118,-p@chr12:91552107..91552118
-
Hg19::chr12:91552211..91552251,-p@chr12:91552211..91552251
-
Hg19::chr12:91558446..91558493,-p@chr12:91558446..91558493
-
Hg19::chr12:91572143..91572274,-p6@DCN
Hg19::chr12:91572278..91572327,-p9@DCN
Hg19::chr12:91572389..91572404,-p14@DCN
Hg19::chr12:91573013..91573042,-p@chr12:91573013..91573042
-
Hg19::chr12:91573228..91573245,-p4@DCN
Hg19::chr12:91573249..91573308,-p2@DCN
Hg19::chr12:91573316..91573365,-p3@DCN
Hg19::chr6:125573037..125573043,+p@chr6:125573037..125573043
+


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 cell9.34e-22180
fibroblast5.14e-1875
muscle precursor cell6.38e-0957
myoblast6.38e-0957
multi-potent skeletal muscle stem cell6.38e-0957
fat cell1.58e-0815
skin fibroblast2.19e-0823
muscle cell4.93e-0854
contractile cell1.53e-0759
Uber Anatomy
Ontology termp-valuen
adult organism1.48e-17115
organism subdivision1.62e-15365
multi-cellular organism5.09e-15659
multi-tissue structure6.82e-15347
somite7.36e-1483
paraxial mesoderm7.36e-1483
presomitic mesoderm7.36e-1483
presumptive segmental plate7.36e-1483
trunk paraxial mesoderm7.36e-1483
presumptive paraxial mesoderm7.36e-1483
dermomyotome5.59e-1270
tissue5.93e-12787
surface structure4.09e-1195
muscle tissue6.31e-1163
musculature6.31e-1163
musculature of body6.31e-1163
anatomical system2.64e-10625
skeletal muscle tissue3.20e-1061
striated muscle tissue3.20e-1061
myotome3.20e-1061
multilaminar epithelium3.74e-1082
anatomical group4.17e-10626
primary circulatory organ5.10e-1027
anatomical cluster7.17e-10286
trunk mesenchyme1.64e-09143
organ5.42e-09511
heart9.98e-0924
primitive heart tube9.98e-0924
primary heart field9.98e-0924
anterior lateral plate mesoderm9.98e-0924
heart tube9.98e-0924
heart primordium9.98e-0924
cardiac mesoderm9.98e-0924
cardiogenic plate9.98e-0924
heart rudiment9.98e-0924
mesenchyme5.23e-08238
entire embryonic mesenchyme5.23e-08238
embryo9.85e-08612
embryonic structure1.23e-07605
developing anatomical structure1.23e-07605
cell layer1.35e-07312
germ layer2.13e-07604
embryonic tissue2.13e-07604
presumptive structure2.13e-07604
epiblast (generic)2.13e-07604
integument2.25e-0745
integumental system2.25e-0745
trunk2.43e-07216
epithelium3.26e-07309
adipose tissue4.12e-0714


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.