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Coexpression cluster:C548: Difference between revisions

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|tf_chipseq_enrich=JUND#3727;7:2.88015574077042:0.00633428905131037:0.0275805392407989!STAT1#6772;5:6.09017279329388:0.000995541757041492:0.00714397317326209
|tf_chipseq_enrich=JUND#3727;7:2.88015574077042:0.00633428905131037:0.0275805392407989!STAT1#6772;5:6.09017279329388:0.000995541757041492:0.00714397317326209
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}}
}}

Revision as of 14:18, 26 November 2012


Full id: C548_Mesothelial_mesenchymal_rhabdomyosarcoma_Renal_mesothelioma_Hepatic_clear



Phase1 CAGE Peaks

Hg19::chr20:6020237..6020248,-p@chr20:6020237..6020248
-
Hg19::chr20:6020266..6020281,-p@chr20:6020266..6020281
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Hg19::chr20:6020518..6020536,-p@chr20:6020518..6020536
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Hg19::chr20:6022771..6022780,-p12@LRRN4
Hg19::chr20:6031540..6031548,-p@chr20:6031540..6031548
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Hg19::chr20:6032946..6032956,-p9@AB527789
Hg19::chr20:6033494..6033509,-p5@AB527789
Hg19::chr20:6033532..6033548,-p2@AB527789
Hg19::chr20:6033667..6033675,-p13@AB527789
Hg19::chr20:6034241..6034256,-p@chr20:6034241..6034256
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Hg19::chr20:6034557..6034560,-p10@LRRN4
Hg19::chr20:6034576..6034592,-p3@LRRN4
Hg19::chr20:6034598..6034603,-p7@LRRN4
Hg19::chr20:6034607..6034616,-p6@LRRN4
Hg19::chr20:6034618..6034669,-p1@LRRN4
Hg19::chr20:6034672..6034714,-p2@LRRN4
Hg19::chr20:6034828..6034857,-p5@LRRN4


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>


Uber Anatomy
Ontology termp-valuen
nephron tubule epithelium1.13e-4310
nephron epithelium3.02e-3515
renal tubule3.02e-3515
nephron tubule3.02e-3515
nephron3.02e-3515
uriniferous tubule3.02e-3515
nephrogenic mesenchyme3.02e-3515
excretory tube6.25e-3316
kidney epithelium6.25e-3316
kidney1.01e-3226
kidney mesenchyme1.01e-3226
upper urinary tract1.01e-3226
kidney rudiment1.01e-3226
kidney field1.01e-3226
cavitated compound organ5.17e-2731
cortex2.17e-2215
abdomen element2.69e-2254
abdominal segment element2.69e-2254
cortex of kidney1.02e-2112
renal parenchyma1.02e-2112
abdominal segment of trunk1.01e-1960
abdomen1.01e-1960
urinary system structure1.07e-1947
renal system3.16e-1948
parenchyma3.38e-1715
trunk region element1.81e-13101
compound organ1.09e-1268
abdomen connective tissue2.53e-122
abdominal segment connective tissue2.53e-122
trunk connective tissue2.53e-122
interstitial tissue2.53e-122
extraglomerular mesangium2.53e-122
kidney interstitium2.53e-122
juxtaglomerular apparatus2.53e-122
mesangium2.53e-122
subdivision of trunk9.09e-12112
renal cortex tubule1.97e-083
region of nephron tubule1.97e-083
proximal tubule1.97e-083
mesenchyme4.42e-08160
entire embryonic mesenchyme4.42e-08160
primitive nephron1.02e-077
renal glomerulus1.02e-077
renal corpuscle1.02e-077
glomerular capsule1.02e-077
metanephric mesenchyme1.02e-077
glomerular tuft1.02e-077
S-shaped body1.02e-077
renal vesicle1.02e-077
comma-shaped body1.02e-077
female gonad7.16e-0713
mesonephric epithelium8.40e-078
mesonephric tubule8.40e-078
nephric duct8.40e-078
renal duct8.40e-078
mesonephric duct8.40e-078
pronephric duct8.40e-078
Disease
Ontology termp-valuen
ovarian cancer8.59e-1414
female reproductive organ cancer3.60e-0927
reproductive organ cancer1.78e-0829


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
JUND#372772.880155740770420.006334289051310370.0275805392407989
STAT1#677256.090172793293880.0009955417570414920.00714397317326209



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.