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{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=0,0

Latest revision as of 11:31, 17 September 2013


Full id: C825_bile_papillotubular_mucinous_Neutrophils_Gingival_squamous_giant



Phase1 CAGE Peaks

Hg19::chr13:38307395..38307406,-p@chr13:38307395..38307406
-
Hg19::chr13:38307430..38307446,-p@chr13:38307430..38307446
-
Hg19::chr13:38307471..38307497,-p@chr13:38307471..38307497
-
Hg19::chr14:51145019..51145024,+p@chr14:51145019..51145024
+
Hg19::chr14:51145106..51145119,+p@chr14:51145106..51145119
+
Hg19::chr20:56265718..56265764,-p12@PMEPA1
Hg19::chr2:241679478..241679495,+p@chr2:241679478..241679495
+
Hg19::chr6:136947581..136947582,-p@chr6:136947581..136947582
-
Hg19::chr6:136947642..136947673,-p@chr6:136947642..136947673
-
Hg19::chr7:44426058..44426097,-p11@NUDCD3


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><br>uberon_data<br>disease_data<br>

Uber Anatomy
Ontology termp-valuen
hepatopancreatic ampulla2.55e-981
extrahepatic bile duct2.55e-981
common bile duct2.55e-981
duodenal papilla2.55e-981
bile duct2.83e-666
digestive system duct2.83e-666
biliary system9.75e-459
biliary tree9.75e-459
biliary bud9.75e-459
duodenum5.96e-342
duct5.37e-2219
small intestine5.15e-214
hepatic diverticulum3.41e-1922
liver primordium3.41e-1922
digestive tract diverticulum2.02e-1823
epithelial sac4.64e-1725
epithelium of foregut-midgut junction4.64e-1725
anatomical boundary4.64e-1725
hepatobiliary system4.64e-1725
foregut-midgut junction4.64e-1725
septum transversum4.64e-1725
sac1.86e-1626
gut epithelium1.34e-0854
intestine7.60e-0717
Disease
Ontology termp-valuen
tubular adenocarcinoma4.52e-502
gastrointestinal system cancer2.00e-0814


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)
MA0003.10.000221536
MA0004.10.380329
MA0006.10.236135
MA0007.10.363007
MA0009.10.828613
MA0014.10.0036779
MA0017.10.270554
MA0019.10.520264
MA0024.10.725404
MA0025.10.960689
MA0027.12.43535
MA0028.10.25013
MA0029.10.744375
MA0030.10.733118
MA0031.10.669876
MA0038.10.477043
MA0040.10.750125
MA0041.10.397617
MA0042.10.367902
MA0043.10.828925
MA0046.10.817858
MA0048.10.0613414
MA0050.10.368721
MA0051.10.473017
MA0052.10.753928
MA0055.10.344701
MA0056.10
MA0057.10.0580131
MA0058.10.293055
MA0059.10.291897
MA0060.10.138988
MA0061.10.377096
MA0063.10
MA0066.10.477449
MA0067.11.1435
MA0068.10.304755
MA0069.10.814052
MA0070.10.803003
MA0071.10.440254
MA0072.10.798564
MA0073.10.0447366
MA0074.10.4723
MA0076.10.828432
MA0077.10.790956
MA0078.11.39444
MA0081.10.292043
MA0083.10.836033
MA0084.11.32998
MA0087.10.79615
MA0088.10.0309101
MA0089.10
MA0090.10.320494
MA0091.10.382762
MA0092.10.347826
MA0093.10.238771
MA0095.10
MA0098.10
MA0100.10.49029
MA0101.10.241637
MA0103.11.20737
MA0105.10.422512
MA0106.10.516528
MA0107.10.529721
MA0108.20.666881
MA0109.10
MA0111.10.33284
MA0113.10.532314
MA0114.10.174997
MA0115.11.06753
MA0116.10.182037
MA0117.10.865782
MA0119.10.760742
MA0122.10.891407
MA0124.11.0263
MA0125.10.942948
MA0130.10
MA0131.10.585907
MA0132.10
MA0133.10
MA0135.10.858623
MA0136.10.483775
MA0139.10.353333
MA0140.10.437738
MA0141.10.290336
MA0142.11.54256
MA0143.10.532484
MA0144.10.163394
MA0145.10.332712
MA0146.10.0551603
MA0147.10.184931
MA0148.10.403564
MA0149.10.428597
MA0062.20.114378
MA0035.20.437071
MA0039.20.0317541
MA0138.20.569505
MA0002.20.129981
MA0137.20.255808
MA0104.20.138396
MA0047.20.504873
MA0112.20.133417
MA0065.20.0371828
MA0150.10.315136
MA0151.10
MA0152.10.443956
MA0153.10.926242
MA0154.10.0494985
MA0155.10.030416
MA0156.10.257809
MA0157.10.612166
MA0158.10
MA0159.10.185458
MA0160.10.417847
MA0161.10
MA0162.10.00711618
MA0163.10.0235237
MA0164.11.34364
MA0080.20.671553
MA0018.20.517858
MA0099.21.97502
MA0079.26.56091e-07
MA0102.21.36707
MA0258.10.155735
MA0259.10.191914
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

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.

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