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Coexpression cluster:C1783: Difference between revisions

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|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0000489!1.82e-18!32;UBERON:0002113!3.08e-14!27;UBERON:0003918!3.08e-14!27;UBERON:0005095!3.08e-14!27;UBERON:0007687!3.08e-14!27;UBERON:0001008!1.82e-13!45;UBERON:0000080!2.45e-13!18;UBERON:0002120!2.45e-13!18;UBERON:0004875!2.45e-13!18;UBERON:0005721!2.45e-13!18;UBERON:0005754!2.45e-13!18;UBERON:0007297!2.45e-13!18;UBERON:0006554!7.93e-13!44;UBERON:0002417!1.82e-12!61;UBERON:0000916!1.82e-12!61;UBERON:0006555!2.37e-12!17;UBERON:0005103!2.37e-12!17;UBERON:0000083!2.37e-12!17;UBERON:0009201!2.37e-12!17;UBERON:0004819!2.37e-12!17;UBERON:0006553!2.37e-12!17;UBERON:0003074!2.37e-12!17;UBERON:0003060!2.37e-12!17;UBERON:0003886!3.23e-12!63;UBERON:0003887!7.74e-12!21;UBERON:0004876!2.31e-11!20;UBERON:0004211!2.34e-11!16;UBERON:0001285!2.34e-11!16;UBERON:0007684!2.34e-11!16;UBERON:0003220!2.34e-11!16;UBERON:0004208!2.34e-11!16;UBERON:0002553!2.16e-10!70;UBERON:0009773!2.24e-10!12;UBERON:0001231!2.24e-10!12;UBERON:0004810!2.24e-10!12;UBERON:0000058!3.74e-10!26;UBERON:0005177!1.15e-09!107;UBERON:0003064!2.32e-09!37;UBERON:0005172!4.40e-09!55;UBERON:0005173!4.40e-09!55;UBERON:0001225!1.34e-08!13;UBERON:0008987!1.34e-08!13;UBERON:0009569!6.89e-08!113;UBERON:0002100!1.52e-07!216;UBERON:0000464!1.62e-07!104;UBERON:0001473!8.33e-07!8;UBERON:0004536!8.33e-07!8;UBERON:0006558!8.33e-07!8;UBERON:0000353!9.19e-07!17
|ontology_enrichment_uberon=UBERON:0000489!1.82e-18!32;UBERON:0002113!3.08e-14!27;UBERON:0003918!3.08e-14!27;UBERON:0005095!3.08e-14!27;UBERON:0007687!3.08e-14!27;UBERON:0001008!1.82e-13!45;UBERON:0000080!2.45e-13!18;UBERON:0002120!2.45e-13!18;UBERON:0004875!2.45e-13!18;UBERON:0005721!2.45e-13!18;UBERON:0005754!2.45e-13!18;UBERON:0007297!2.45e-13!18;UBERON:0006554!7.93e-13!44;UBERON:0002417!1.82e-12!61;UBERON:0000916!1.82e-12!61;UBERON:0006555!2.37e-12!17;UBERON:0005103!2.37e-12!17;UBERON:0000083!2.37e-12!17;UBERON:0009201!2.37e-12!17;UBERON:0004819!2.37e-12!17;UBERON:0006553!2.37e-12!17;UBERON:0003074!2.37e-12!17;UBERON:0003060!2.37e-12!17;UBERON:0003886!3.23e-12!63;UBERON:0003887!7.74e-12!21;UBERON:0004876!2.31e-11!20;UBERON:0004211!2.34e-11!16;UBERON:0001285!2.34e-11!16;UBERON:0007684!2.34e-11!16;UBERON:0003220!2.34e-11!16;UBERON:0004208!2.34e-11!16;UBERON:0002553!2.16e-10!70;UBERON:0009773!2.24e-10!12;UBERON:0001231!2.24e-10!12;UBERON:0004810!2.24e-10!12;UBERON:0000058!3.74e-10!26;UBERON:0005177!1.15e-09!107;UBERON:0003064!2.32e-09!37;UBERON:0005172!4.40e-09!55;UBERON:0005173!4.40e-09!55;UBERON:0001225!1.34e-08!13;UBERON:0008987!1.34e-08!13;UBERON:0009569!6.89e-08!113;UBERON:0002100!1.52e-07!216;UBERON:0000464!1.62e-07!104;UBERON:0001473!8.33e-07!8;UBERON:0004536!8.33e-07!8;UBERON:0006558!8.33e-07!8;UBERON:0000353!9.19e-07!17
|tf_chipseq_enrich=SUZ12#23512;5:50.1157809110629:3.15480790456198e-09:2.62120113559705e-07
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}}
}}

Revision as of 12:09, 5 September 2012


Full id: C1783_alveolar_nonsmall_ductus_spinal_seminal_epididymis_somatostatinoma



Phase1 CAGE Peaks

Hg19::chr17:46690197..46690210,-p@chr17:46690197..46690210
-
Hg19::chr17:46692457..46692484,-p2@HOXB8
Hg19::chr17:46692582..46692589,-p14@HOXB8
Hg19::chr17:46692603..46692621,-p6@HOXB8
Hg19::chr17:46692624..46692659,-p3@HOXB8


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
cavitated compound organ1.82e-1832
kidney3.08e-1427
kidney mesenchyme3.08e-1427
kidney rudiment3.08e-1427
kidney field3.08e-1427
renal system1.82e-1345
mesonephros2.45e-1318
pronephros2.45e-1318
nephrogenic cord2.45e-1318
pronephric mesoderm2.45e-1318
rostral part of nephrogenic cord2.45e-1318
presumptive pronephric mesoderm2.45e-1318
urinary system structure7.93e-1344
abdominal segment of trunk1.82e-1261
abdomen1.82e-1261
excretory tube2.37e-1217
mesonephric epithelium2.37e-1217
mesonephric tubule2.37e-1217
nephric duct2.37e-1217
kidney epithelium2.37e-1217
renal duct2.37e-1217
mesonephric duct2.37e-1217
pronephric duct2.37e-1217
body cavity precursor3.23e-1263
intraembryonic coelom7.74e-1221
urogenital ridge2.31e-1120
nephron epithelium2.34e-1116
nephron2.34e-1116
uriniferous tubule2.34e-1116
metanephric mesenchyme2.34e-1116
nephrogenic mesenchyme2.34e-1116
anatomical cavity2.16e-1070
renal tubule2.24e-1012
nephron tubule2.24e-1012
nephron tubule epithelium2.24e-1012
duct3.74e-1026
trunk region element1.15e-09107
intermediate mesoderm2.32e-0937
abdomen element4.40e-0955
abdominal segment element4.40e-0955
cortex of kidney1.34e-0813
renal parenchyma1.34e-0813
subdivision of trunk6.89e-08113
trunk1.52e-07216
anatomical space1.62e-07104
lymphatic vessel8.33e-078
lymph vasculature8.33e-078
lymphatic part of lymphoid system8.33e-078
parenchyma9.19e-0717


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
SUZ12#23512550.11578091106293.15480790456198e-092.62120113559705e-07



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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