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Coexpression cluster:C4675: Difference between revisions

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|full_id=C4675_CD14_mesenchymal_Smooth_gall_hepatic_papillary_cholangiocellular
|full_id=C4675_CD14_mesenchymal_Smooth_gall_hepatic_papillary_cholangiocellular
|id=C4675
|id=C4675
|ontology_enrichment_celltype=CL:0000055!2.11e-19!180;CL:0000222!3.64e-17!119;CL:0000192!1.55e-13!42;CL:0000514!1.55e-13!42;CL:0000359!2.21e-13!32;CL:0000057!5.61e-13!75;CL:0000680!9.46e-12!57;CL:0000056!9.46e-12!57;CL:0000355!9.46e-12!57;CL:0000187!4.13e-11!54;CL:0000183!1.99e-10!59;CL:0000144!1.44e-08!625;CL:0000393!1.50e-08!60;CL:0000211!1.50e-08!60;CL:0000012!1.63e-08!682;CL:0000548!1.89e-08!679;CL:0000004!1.89e-08!679;CL:0000255!1.89e-08!679;CL:0000220!2.15e-08!246;CL:0002321!2.98e-08!248;CL:0002371!1.45e-07!591;CL:0002494!3.37e-07!16
|ontology_enrichment_celltype=CL:0000359!3.05e-13!32;CL:0000048!2.88e-12!427;CL:0000723!1.32e-11!433;CL:0000034!9.17e-11!441;CL:0000192!1.67e-10!43;CL:0000514!1.67e-10!43;CL:0000548!1.94e-09!679;CL:0000255!1.94e-09!679;CL:0002334!2.46e-09!12;CL:0002371!3.01e-09!588;CL:0002494!1.29e-08!16;CL:0000057!1.32e-08!76;CL:0000680!2.13e-08!58;CL:0000056!2.13e-08!58;CL:0000355!2.13e-08!58;CL:0000187!6.32e-08!55;CL:0002539!5.07e-07!10;CL:0000183!7.06e-07!59
|ontology_enrichment_disease=DOID:2394!6.27e-09!14
|ontology_enrichment_disease=DOID:2394!2.13e-14!14;DOID:193!1.47e-10!29;DOID:120!1.57e-10!27
|ontology_enrichment_uberon=UBERON:0004872!7.43e-22!84;UBERON:0000055!1.59e-21!69;UBERON:0001981!6.28e-21!60;UBERON:0007500!6.28e-21!60;UBERON:0004537!6.28e-21!60;UBERON:0006965!6.28e-21!60;UBERON:0002049!1.13e-20!79;UBERON:0007798!1.13e-20!79;UBERON:0003914!6.31e-20!118;UBERON:0001009!7.03e-20!113;UBERON:0004535!1.18e-19!110;UBERON:0001637!1.29e-19!42;UBERON:0003509!1.29e-19!42;UBERON:0004572!1.29e-19!42;UBERON:0004573!6.30e-16!33;UBERON:0004571!6.30e-16!33;UBERON:0001134!3.10e-11!61;UBERON:0002036!3.10e-11!61;UBERON:0003082!3.10e-11!61;UBERON:0002385!5.75e-11!63;UBERON:0001015!5.75e-11!63;UBERON:0000383!5.75e-11!63;UBERON:0000490!1.12e-10!138;UBERON:0004111!1.17e-10!241;UBERON:0000477!1.52e-10!286;UBERON:0000914!3.15e-10!83;UBERON:0002329!3.15e-10!83;UBERON:0003077!3.15e-10!83;UBERON:0003059!3.15e-10!83;UBERON:0007282!3.15e-10!83;UBERON:0009618!3.15e-10!83;UBERON:0007285!3.15e-10!83;UBERON:0005256!3.28e-10!143;UBERON:0004290!4.64e-10!70;UBERON:0000947!1.41e-09!21;UBERON:0010191!1.41e-09!21;UBERON:0000486!2.84e-09!82;UBERON:0000025!3.98e-09!194;UBERON:0002100!5.45e-08!216;UBERON:0000926!6.00e-08!448;UBERON:0004120!6.00e-08!448;UBERON:0006603!6.00e-08!448;UBERON:0007100!8.14e-08!27;UBERON:0000948!9.13e-08!24;UBERON:0005498!9.13e-08!24;UBERON:0004140!9.13e-08!24;UBERON:0009881!9.13e-08!24;UBERON:0004141!9.13e-08!24;UBERON:0003084!9.13e-08!24;UBERON:0007005!9.13e-08!24;UBERON:0004139!9.13e-08!24;UBERON:0004291!9.13e-08!24;UBERON:0000483!9.78e-08!309;UBERON:0000119!1.18e-07!312;UBERON:0003081!2.99e-07!216
|ontology_enrichment_uberon=UBERON:0004573!5.77e-15!33;UBERON:0004571!5.77e-15!33;UBERON:0001637!6.62e-15!42;UBERON:0003509!6.62e-15!42;UBERON:0004572!6.62e-15!42;UBERON:0004872!2.87e-14!83;UBERON:0001009!6.05e-12!112;UBERON:0004535!2.14e-11!109;UBERON:0003914!1.73e-10!117;UBERON:0007500!2.61e-10!59;UBERON:0001981!2.61e-10!59;UBERON:0004537!2.61e-10!59;UBERON:0006965!2.61e-10!59;UBERON:0000055!5.33e-10!68;UBERON:0002049!1.06e-08!78;UBERON:0007798!1.06e-08!78;UBERON:0000926!1.10e-08!315;UBERON:0004120!1.10e-08!315;UBERON:0006603!1.10e-08!315;UBERON:0007100!4.39e-08!27;UBERON:0000947!1.03e-07!21;UBERON:0010191!1.03e-07!21;UBERON:0000992!1.20e-07!13;UBERON:0003081!1.39e-07!203;UBERON:0000948!1.45e-07!24;UBERON:0005498!1.45e-07!24;UBERON:0004140!1.45e-07!24;UBERON:0009881!1.45e-07!24;UBERON:0004141!1.45e-07!24;UBERON:0003084!1.45e-07!24;UBERON:0007005!1.45e-07!24;UBERON:0004139!1.45e-07!24;UBERON:0004291!1.45e-07!24;UBERON:0001134!2.46e-07!62;UBERON:0002036!2.46e-07!62;UBERON:0003082!2.46e-07!62;UBERON:0004237!5.07e-07!10;UBERON:0004695!5.07e-07!10;UBERON:0002111!5.07e-07!10;UBERON:0004178!5.07e-07!10;UBERON:0002385!7.33e-07!64;UBERON:0001015!7.33e-07!64;UBERON:0000383!7.33e-07!64
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}}
}}

Revision as of 16:09, 19 October 2012


Full id: C4675_CD14_mesenchymal_Smooth_gall_hepatic_papillary_cholangiocellular



Phase1 CAGE Peaks

Hg19::chr7:22767022..22767133,+p2@IL6
Hg19::chr7:22769140..22769153,+p@chr7:22769140..22769153
+
Hg19::chr7:22771052..22771099,-p@chr7:22771052..22771099
-


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>disease_data<br>

Cell Type
Ontology termp-valuen
vascular associated smooth muscle cell3.05e-1332
multi fate stem cell2.88e-12427
somatic stem cell1.32e-11433
stem cell9.17e-11441
smooth muscle cell1.67e-1043
smooth muscle myoblast1.67e-1043
animal cell1.94e-09679
eukaryotic cell1.94e-09679
preadipocyte2.46e-0912
somatic cell3.01e-09588
cardiocyte1.29e-0816
fibroblast1.32e-0876
muscle precursor cell2.13e-0858
myoblast2.13e-0858
multi-potent skeletal muscle stem cell2.13e-0858
muscle cell6.32e-0855
aortic smooth muscle cell5.07e-0710
contractile cell7.06e-0759
Uber Anatomy
Ontology termp-valuen
systemic artery5.77e-1533
systemic arterial system5.77e-1533
artery6.62e-1542
arterial blood vessel6.62e-1542
arterial system6.62e-1542
splanchnic layer of lateral plate mesoderm2.87e-1483
circulatory system6.05e-12112
cardiovascular system2.14e-11109
epithelial tube1.73e-10117
epithelial tube open at both ends2.61e-1059
blood vessel2.61e-1059
blood vasculature2.61e-1059
vascular cord2.61e-1059
vessel5.33e-1068
vasculature1.06e-0878
vascular system1.06e-0878
mesoderm1.10e-08315
mesoderm-derived structure1.10e-08315
presumptive mesoderm1.10e-08315
primary circulatory organ4.39e-0827
aorta1.03e-0721
aortic system1.03e-0721
female gonad1.20e-0713
lateral plate mesoderm1.39e-07203
heart1.45e-0724
primitive heart tube1.45e-0724
primary heart field1.45e-0724
anterior lateral plate mesoderm1.45e-0724
heart tube1.45e-0724
heart primordium1.45e-0724
cardiac mesoderm1.45e-0724
cardiogenic plate1.45e-0724
heart rudiment1.45e-0724
skeletal muscle tissue2.46e-0762
striated muscle tissue2.46e-0762
myotome2.46e-0762
blood vessel smooth muscle5.07e-0710
arterial system smooth muscle5.07e-0710
artery smooth muscle tissue5.07e-0710
aorta smooth muscle tissue5.07e-0710
muscle tissue7.33e-0764
musculature7.33e-0764
musculature of body7.33e-0764
Disease
Ontology termp-valuen
ovarian cancer2.13e-1414
reproductive organ cancer1.47e-1029
female reproductive organ cancer1.57e-1027


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

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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