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Coexpression cluster:C4627: Difference between revisions

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|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0003914!3.51e-30!118;UBERON:0000055!4.34e-29!69;UBERON:0002049!2.80e-28!79;UBERON:0007798!2.80e-28!79;UBERON:0004872!1.72e-26!84;UBERON:0001981!5.23e-26!60;UBERON:0007500!5.23e-26!60;UBERON:0004537!5.23e-26!60;UBERON:0006965!5.23e-26!60;UBERON:0000490!3.02e-24!138;UBERON:0004535!2.04e-21!110;UBERON:0001009!2.14e-21!113;UBERON:0001637!2.29e-21!42;UBERON:0003509!2.29e-21!42;UBERON:0004572!2.29e-21!42;UBERON:0002100!5.19e-19!216;UBERON:0005256!2.23e-18!143;UBERON:0003104!1.07e-16!238;UBERON:0009142!1.07e-16!238;UBERON:0004573!2.30e-16!33;UBERON:0004571!2.30e-16!33;UBERON:0004290!8.32e-15!70;UBERON:0000914!6.62e-14!83;UBERON:0002329!6.62e-14!83;UBERON:0003077!6.62e-14!83;UBERON:0003059!6.62e-14!83;UBERON:0007282!6.62e-14!83;UBERON:0009618!6.62e-14!83;UBERON:0007285!6.62e-14!83;UBERON:0001134!1.02e-13!61;UBERON:0002036!1.02e-13!61;UBERON:0003082!1.02e-13!61;UBERON:0002385!1.16e-13!63;UBERON:0001015!1.16e-13!63;UBERON:0000383!1.16e-13!63;UBERON:0000486!3.94e-13!82;UBERON:0006914!4.60e-13!25;UBERON:0001986!6.93e-13!18;UBERON:0004638!6.93e-13!18;UBERON:0004852!6.93e-13!18;UBERON:0000487!1.68e-12!22;UBERON:0000926!1.05e-10!448;UBERON:0004120!1.05e-10!448;UBERON:0006603!1.05e-10!448;UBERON:0000947!1.04e-09!21;UBERON:0010191!1.04e-09!21;UBERON:0009569!1.79e-09!113;UBERON:0000477!6.14e-09!286;UBERON:0002417!2.71e-08!61;UBERON:0000916!2.71e-08!61;UBERON:0000483!3.12e-07!309;UBERON:0003915!3.14e-07!9;UBERON:0004700!3.14e-07!9;UBERON:0001917!3.14e-07!9;UBERON:0004111!3.46e-07!241;UBERON:0000119!3.49e-07!312;UBERON:0000481!7.35e-07!347
|ontology_enrichment_uberon=UBERON:0003914!3.51e-30!118;UBERON:0000055!4.34e-29!69;UBERON:0002049!2.80e-28!79;UBERON:0007798!2.80e-28!79;UBERON:0004872!1.72e-26!84;UBERON:0001981!5.23e-26!60;UBERON:0007500!5.23e-26!60;UBERON:0004537!5.23e-26!60;UBERON:0006965!5.23e-26!60;UBERON:0000490!3.02e-24!138;UBERON:0004535!2.04e-21!110;UBERON:0001009!2.14e-21!113;UBERON:0001637!2.29e-21!42;UBERON:0003509!2.29e-21!42;UBERON:0004572!2.29e-21!42;UBERON:0002100!5.19e-19!216;UBERON:0005256!2.23e-18!143;UBERON:0003104!1.07e-16!238;UBERON:0009142!1.07e-16!238;UBERON:0004573!2.30e-16!33;UBERON:0004571!2.30e-16!33;UBERON:0004290!8.32e-15!70;UBERON:0000914!6.62e-14!83;UBERON:0002329!6.62e-14!83;UBERON:0003077!6.62e-14!83;UBERON:0003059!6.62e-14!83;UBERON:0007282!6.62e-14!83;UBERON:0009618!6.62e-14!83;UBERON:0007285!6.62e-14!83;UBERON:0001134!1.02e-13!61;UBERON:0002036!1.02e-13!61;UBERON:0003082!1.02e-13!61;UBERON:0002385!1.16e-13!63;UBERON:0001015!1.16e-13!63;UBERON:0000383!1.16e-13!63;UBERON:0000486!3.94e-13!82;UBERON:0006914!4.60e-13!25;UBERON:0001986!6.93e-13!18;UBERON:0004638!6.93e-13!18;UBERON:0004852!6.93e-13!18;UBERON:0000487!1.68e-12!22;UBERON:0000926!1.05e-10!448;UBERON:0004120!1.05e-10!448;UBERON:0006603!1.05e-10!448;UBERON:0000947!1.04e-09!21;UBERON:0010191!1.04e-09!21;UBERON:0009569!1.79e-09!113;UBERON:0000477!6.14e-09!286;UBERON:0002417!2.71e-08!61;UBERON:0000916!2.71e-08!61;UBERON:0000483!3.12e-07!309;UBERON:0003915!3.14e-07!9;UBERON:0004700!3.14e-07!9;UBERON:0001917!3.14e-07!9;UBERON:0004111!3.46e-07!241;UBERON:0000119!3.49e-07!312;UBERON:0000481!7.35e-07!347
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}}
}}

Revision as of 20:11, 8 August 2012


Full id: C4627_lymphangiectasia_Endothelial_Smooth_Renal_hepatic_Lymphatic_lymph



Phase1 CAGE Peaks

Hg19::chr6:7904848..7904912,+p@chr6:7904848..7904912
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Hg19::chr6:7910773..7910814,+p@chr6:7910773..7910814
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Hg19::chr6:7911009..7911038,-p1@TXNDC5


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
mesodermal cell4.16e-27119
non-terminally differentiated cell3.42e-21180
embryonic cell1.81e-16248
endothelial cell of vascular tree1.96e-1624
meso-epithelial cell3.05e-1544
muscle precursor cell3.34e-1557
myoblast3.34e-1557
multi-potent skeletal muscle stem cell3.34e-1557
endothelial cell7.68e-1535
muscle cell8.92e-1554
contractile cell1.14e-1459
vascular associated smooth muscle cell7.65e-1432
smooth muscle cell2.30e-1342
smooth muscle myoblast2.30e-1342
blood vessel endothelial cell6.93e-1318
embryonic blood vessel endothelial progenitor cell6.93e-1318
lining cell1.02e-1257
barrier cell1.02e-1257
electrically responsive cell1.62e-1260
electrically active cell1.62e-1260
animal cell1.61e-10679
eukaryotic cell1.61e-10679
somatic cell5.98e-10591
fibroblast1.64e-0975
endothelial cell of artery3.14e-079
Uber Anatomy
Ontology termp-valuen
epithelial tube3.51e-30118
vessel4.34e-2969
vasculature2.80e-2879
vascular system2.80e-2879
splanchnic layer of lateral plate mesoderm1.72e-2684
blood vessel5.23e-2660
epithelial tube open at both ends5.23e-2660
blood vasculature5.23e-2660
vascular cord5.23e-2660
unilaminar epithelium3.02e-24138
cardiovascular system2.04e-21110
circulatory system2.14e-21113
artery2.29e-2142
arterial blood vessel2.29e-2142
arterial system2.29e-2142
trunk5.19e-19216
trunk mesenchyme2.23e-18143
mesenchyme1.07e-16238
entire embryonic mesenchyme1.07e-16238
systemic artery2.30e-1633
systemic arterial system2.30e-1633
dermomyotome8.32e-1570
somite6.62e-1483
paraxial mesoderm6.62e-1483
presomitic mesoderm6.62e-1483
presumptive segmental plate6.62e-1483
trunk paraxial mesoderm6.62e-1483
presumptive paraxial mesoderm6.62e-1483
skeletal muscle tissue1.02e-1361
striated muscle tissue1.02e-1361
myotome1.02e-1361
muscle tissue1.16e-1363
musculature1.16e-1363
musculature of body1.16e-1363
multilaminar epithelium3.94e-1382
squamous epithelium4.60e-1325
endothelium6.93e-1318
blood vessel endothelium6.93e-1318
cardiovascular system endothelium6.93e-1318
simple squamous epithelium1.68e-1222
mesoderm1.05e-10448
mesoderm-derived structure1.05e-10448
presumptive mesoderm1.05e-10448
aorta1.04e-0921
aortic system1.04e-0921
subdivision of trunk1.79e-09113
anatomical cluster6.14e-09286
abdominal segment of trunk2.71e-0861
abdomen2.71e-0861
epithelium3.12e-07309
endothelial tube3.14e-079
arterial system endothelium3.14e-079
endothelium of artery3.14e-079
anatomical conduit3.46e-07241
cell layer3.49e-07312
multi-tissue structure7.35e-07347


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.