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{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=0,0

Latest revision as of 11:41, 17 September 2013


Full id: C1262_renal_clear_Renal_papillotubular_embryonic_mucinous_serous



Phase1 CAGE Peaks

Hg19::chr22:30653345..30653353,-p@chr22:30653345..30653353
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Hg19::chr22:30653384..30653392,-p@chr22:30653384..30653392
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Hg19::chr22:30653399..30653414,-p@chr22:30653399..30653414
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Hg19::chr22:30653425..30653444,-p@chr22:30653425..30653444
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Hg19::chr22:30653669..30653690,-p@chr22:30653669..30653690
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Hg19::chr22:30653699..30653718,-p@chr22:30653699..30653718
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Hg19::chr22:30653761..30653772,-p@chr22:30653761..30653772
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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 epithelium7.33e-2110
nephron epithelium9.66e-1915
renal tubule9.66e-1915
nephron tubule9.66e-1915
nephron9.66e-1915
uriniferous tubule9.66e-1915
nephrogenic mesenchyme9.66e-1915
trunk region element6.69e-18101
kidney1.58e-1726
kidney mesenchyme1.58e-1726
upper urinary tract1.58e-1726
kidney rudiment1.58e-1726
kidney field1.58e-1726
excretory tube2.31e-1716
kidney epithelium2.31e-1716
cavitated compound organ5.33e-1631
cortex of kidney4.12e-1312
renal parenchyma4.12e-1312
abdomen element1.58e-1254
abdominal segment element1.58e-1254
cortex2.48e-1215
parenchyma3.59e-1215
urinary system structure1.34e-1147
renal system3.02e-1148
abdominal segment of trunk1.12e-1060
abdomen1.12e-1060
viscus4.99e-1018
pancreas6.47e-1010
duct6.79e-0919
trunk9.94e-09199
biliary system1.02e-079
biliary tree1.02e-079
biliary bud1.02e-079
immaterial anatomical entity1.09e-07117
subdivision of trunk1.43e-07112
renal cortex tubule2.97e-073
region of nephron tubule2.97e-073
proximal tubule2.97e-073
body cavity precursor4.84e-0754
organ5.36e-07503
Disease
Ontology termp-valuen
carcinoma5.99e-34106
cell type cancer5.66e-32143
cancer1.28e-21235
disease of cellular proliferation8.57e-21239
adenocarcinoma7.52e-1625
female reproductive endometrioid cancer2.19e-096
organ system cancer3.55e-07137
non-small cell lung carcinoma3.86e-075


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)
MA0003.10.358813
MA0004.10.502801
MA0006.10.904424
MA0007.11.21493
MA0009.10.973289
MA0014.17.74077
MA0017.12.64218
MA0019.10.652951
MA0024.10.867125
MA0025.11.10816
MA0027.12.59001
MA0028.11.67753
MA0029.10.886702
MA0030.10.875089
MA0031.10.809638
MA0038.10.60704
MA0040.10.892629
MA0041.10.521615
MA0042.10.48922
MA0043.10.973609
MA0046.10.962263
MA0048.10.120314
MA0050.10.490116
MA0051.10.602745
MA0052.10.896548
MA0055.10.158296
MA0056.10
MA0057.10.115382
MA0058.10.406232
MA0059.10.404929
MA0060.10.224688
MA0061.10.198335
MA0063.10
MA0066.10.607474
MA0067.11.29359
MA0068.10.162298
MA0069.10.958358
MA0070.10.947018
MA0071.10.567661
MA0072.10.942461
MA0073.111.359
MA0074.13.64367
MA0076.11.08222
MA0077.10.934645
MA0078.10.703614
MA0081.10.405093
MA0083.10.980893
MA0084.11.48179
MA0087.10.939982
MA0088.10.538456
MA0089.10
MA0090.10.436918
MA0091.10.505453
MA0092.11.17914
MA0093.10.344385
MA0095.10
MA0098.10
MA0100.10.621149
MA0101.10.347695
MA0103.10.332048
MA0105.10.104569
MA0106.10.648997
MA0107.10.274127
MA0108.20.806528
MA0109.10
MA0111.11.14351
MA0113.10.665691
MA0114.12.09327
MA0115.11.21667
MA0116.10.277571
MA0117.12.30913
MA0119.10.388712
MA0122.11.03753
MA0124.11.17486
MA0125.11.0901
MA0130.10
MA0131.10.722072
MA0132.10
MA0133.10
MA0135.11.00402
MA0136.10.614215
MA0139.10.547495
MA0140.10.564957
MA0141.10.403171
MA0142.10.777365
MA0143.10.66587
MA0144.10.254954
MA0145.13.29192
MA0146.12.9475
MA0147.10.281049
MA0148.10.528066
MA0149.10.555119
MA0062.21.07166
MA0035.20.564239
MA0039.23.59026
MA0138.20.704862
MA0002.20.213296
MA0137.20.36398
MA0104.20.223944
MA0047.20.636643
MA0112.21.41281
MA0065.20.591589
MA0150.11.10099
MA0151.10
MA0152.10.571637
MA0153.11.07307
MA0154.10.685508
MA0155.13.81102
MA0156.10.959643
MA0157.10.749547
MA0158.10
MA0159.10.770207
MA0160.10.543522
MA0161.10
MA0162.10.0249953
MA0163.11.72058
MA0164.10.678332
MA0080.20.911393
MA0018.20.650405
MA0099.22.39704
MA0079.26.87521
MA0102.21.51913
MA0258.11.27333
MA0259.10.289405
MA0442.10



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
POLR2A#543072.147453176558070.004747636447610280.0223541951648695
TFAP2C#7022710.80922860986025.79365976833206e-083.61244198534228e-06



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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