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Coexpression cluster:C1556: Difference between revisions

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|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0000489!2.36e-31!32;UBERON:0002113!1.11e-29!27;UBERON:0003918!1.11e-29!27;UBERON:0005095!1.11e-29!27;UBERON:0007687!1.11e-29!27;UBERON:0000080!1.13e-21!18;UBERON:0002120!1.13e-21!18;UBERON:0004875!1.13e-21!18;UBERON:0005721!1.13e-21!18;UBERON:0005754!1.13e-21!18;UBERON:0007297!1.13e-21!18;UBERON:0006555!6.38e-20!17;UBERON:0005103!6.38e-20!17;UBERON:0000083!6.38e-20!17;UBERON:0009201!6.38e-20!17;UBERON:0004819!6.38e-20!17;UBERON:0006553!6.38e-20!17;UBERON:0003074!6.38e-20!17;UBERON:0003060!6.38e-20!17;UBERON:0000058!6.54e-20!26;UBERON:0004876!5.02e-19!20;UBERON:0006554!1.25e-18!44;UBERON:0009773!3.38e-18!12;UBERON:0001231!3.38e-18!12;UBERON:0004810!3.38e-18!12;UBERON:0004211!3.60e-18!16;UBERON:0001285!3.60e-18!16;UBERON:0007684!3.60e-18!16;UBERON:0003220!3.60e-18!16;UBERON:0004208!3.60e-18!16;UBERON:0001008!4.83e-18!45;UBERON:0003887!6.82e-18!21;UBERON:0005172!1.42e-14!55;UBERON:0005173!1.42e-14!55;UBERON:0003076!2.43e-14!15;UBERON:0003057!2.43e-14!15;UBERON:0003103!1.95e-13!69;UBERON:0001225!3.22e-13!13;UBERON:0008987!3.22e-13!13;UBERON:0004733!1.22e-12!12;UBERON:0002028!1.22e-12!12;UBERON:0007277!1.22e-12!12;UBERON:0001851!1.44e-12!16;UBERON:0002417!2.12e-12!61;UBERON:0000916!2.12e-12!61;UBERON:0003886!2.30e-12!63;UBERON:0003064!2.57e-12!37;UBERON:0005177!1.06e-11!107;UBERON:0004732!1.75e-11!13;UBERON:0002553!2.66e-11!70;UBERON:0000353!3.35e-11!17;UBERON:0003135!1.04e-09!11;UBERON:0000464!1.42e-08!104;UBERON:0002680!2.27e-08!9;UBERON:0001895!2.27e-08!9;UBERON:0010092!2.27e-08!9;UBERON:0000473!1.49e-07!8;UBERON:0002298!2.28e-07!8;UBERON:0006947!3.52e-07!3;UBERON:0004054!3.52e-07!3;UBERON:0009569!5.49e-07!113;UBERON:0006853!7.81e-07!3;UBERON:0007685!7.81e-07!3;UBERON:0004134!7.81e-07!3;UBERON:0000466!9.66e-07!126
|ontology_enrichment_uberon=UBERON:0000489!2.36e-31!32;UBERON:0002113!1.11e-29!27;UBERON:0003918!1.11e-29!27;UBERON:0005095!1.11e-29!27;UBERON:0007687!1.11e-29!27;UBERON:0000080!1.13e-21!18;UBERON:0002120!1.13e-21!18;UBERON:0004875!1.13e-21!18;UBERON:0005721!1.13e-21!18;UBERON:0005754!1.13e-21!18;UBERON:0007297!1.13e-21!18;UBERON:0006555!6.38e-20!17;UBERON:0005103!6.38e-20!17;UBERON:0000083!6.38e-20!17;UBERON:0009201!6.38e-20!17;UBERON:0004819!6.38e-20!17;UBERON:0006553!6.38e-20!17;UBERON:0003074!6.38e-20!17;UBERON:0003060!6.38e-20!17;UBERON:0000058!6.54e-20!26;UBERON:0004876!5.02e-19!20;UBERON:0006554!1.25e-18!44;UBERON:0009773!3.38e-18!12;UBERON:0001231!3.38e-18!12;UBERON:0004810!3.38e-18!12;UBERON:0004211!3.60e-18!16;UBERON:0001285!3.60e-18!16;UBERON:0007684!3.60e-18!16;UBERON:0003220!3.60e-18!16;UBERON:0004208!3.60e-18!16;UBERON:0001008!4.83e-18!45;UBERON:0003887!6.82e-18!21;UBERON:0005172!1.42e-14!55;UBERON:0005173!1.42e-14!55;UBERON:0003076!2.43e-14!15;UBERON:0003057!2.43e-14!15;UBERON:0003103!1.95e-13!69;UBERON:0001225!3.22e-13!13;UBERON:0008987!3.22e-13!13;UBERON:0004733!1.22e-12!12;UBERON:0002028!1.22e-12!12;UBERON:0007277!1.22e-12!12;UBERON:0001851!1.44e-12!16;UBERON:0002417!2.12e-12!61;UBERON:0000916!2.12e-12!61;UBERON:0003886!2.30e-12!63;UBERON:0003064!2.57e-12!37;UBERON:0005177!1.06e-11!107;UBERON:0004732!1.75e-11!13;UBERON:0002553!2.66e-11!70;UBERON:0000353!3.35e-11!17;UBERON:0003135!1.04e-09!11;UBERON:0000464!1.42e-08!104;UBERON:0002680!2.27e-08!9;UBERON:0001895!2.27e-08!9;UBERON:0010092!2.27e-08!9;UBERON:0000473!1.49e-07!8;UBERON:0002298!2.28e-07!8;UBERON:0006947!3.52e-07!3;UBERON:0004054!3.52e-07!3;UBERON:0009569!5.49e-07!113;UBERON:0006853!7.81e-07!3;UBERON:0007685!7.81e-07!3;UBERON:0004134!7.81e-07!3;UBERON:0000466!9.66e-07!126
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}}
}}

Revision as of 13:54, 5 September 2012


Full id: C1556_epididymis_seminal_Renal_ductus_kidney_rhabdomyosarcoma_renal



Phase1 CAGE Peaks

Hg19::chr10:102505147..102505162,+p9@PAX2
Hg19::chr10:102505297..102505302,+p11@PAX2
Hg19::chr10:102505493..102505546,+p2@PAX2
Hg19::chr10:102505946..102505949,+p14@PAX2
Hg19::chr10:102505954..102505973,+p3@PAX2


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 organ2.36e-3132
kidney1.11e-2927
kidney mesenchyme1.11e-2927
kidney rudiment1.11e-2927
kidney field1.11e-2927
mesonephros1.13e-2118
pronephros1.13e-2118
nephrogenic cord1.13e-2118
pronephric mesoderm1.13e-2118
rostral part of nephrogenic cord1.13e-2118
presumptive pronephric mesoderm1.13e-2118
excretory tube6.38e-2017
mesonephric epithelium6.38e-2017
mesonephric tubule6.38e-2017
nephric duct6.38e-2017
kidney epithelium6.38e-2017
renal duct6.38e-2017
mesonephric duct6.38e-2017
pronephric duct6.38e-2017
duct6.54e-2026
urogenital ridge5.02e-1920
urinary system structure1.25e-1844
renal tubule3.38e-1812
nephron tubule3.38e-1812
nephron tubule epithelium3.38e-1812
nephron epithelium3.60e-1816
nephron3.60e-1816
uriniferous tubule3.60e-1816
metanephric mesenchyme3.60e-1816
nephrogenic mesenchyme3.60e-1816
renal system4.83e-1845
intraembryonic coelom6.82e-1821
abdomen element1.42e-1455
abdominal segment element1.42e-1455
posterior neural tube2.43e-1415
chordal neural plate2.43e-1415
compound organ1.95e-1369
cortex of kidney3.22e-1313
renal parenchyma3.22e-1313
segmental subdivision of hindbrain1.22e-1212
hindbrain1.22e-1212
presumptive hindbrain1.22e-1212
cortex1.44e-1216
abdominal segment of trunk2.12e-1261
abdomen2.12e-1261
body cavity precursor2.30e-1263
intermediate mesoderm2.57e-1237
trunk region element1.06e-11107
segmental subdivision of nervous system1.75e-1113
anatomical cavity2.66e-1170
parenchyma3.35e-1117
male reproductive organ1.04e-0911
anatomical space1.42e-08104
regional part of metencephalon2.27e-089
metencephalon2.27e-089
future metencephalon2.27e-089
testis1.49e-078
brainstem2.28e-078
male genital duct3.52e-073
internal male genitalia3.52e-073
subdivision of trunk5.49e-07113
renal cortex tubule7.81e-073
region of nephron tubule7.81e-073
proximal tubule7.81e-073
immaterial anatomical entity9.66e-07126


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
CTBP2#1488337.63020020359693.95343056005017e-050.000737439425363601
SUZ12#23512220.04631236442520.003824075654154750.0188717401712549



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.