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{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=0,0,

Latest revision as of 12:02, 17 September 2013


Full id: C2294_hepatocellular_small_hepatoblastoma_Hepatocyte_colon_adenocarcinoma_Intestinal



Phase1 CAGE Peaks

Hg19::chr14:39735833..39735859,+p7@CTAGE5
Hg19::chr20:42187542..42187573,-p@chr20:42187542..42187573
-
Hg19::chr6:30131199..30131210,-p@chr6:30131199..30131210
-
Hg19::chr8:145641934..145641949,-p9@SLC39A4


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

GO IDGO nameFDR corrected p-value
GO:0055038recycling endosome membrane0.0123614848790397
GO:0055037recycling endosome0.0123614848790397
GO:0006829zinc ion transport0.018950649628939
GO:0010008endosome membrane0.0419721296764219
GO:0044440endosomal part0.0419721296764219
GO:0000041transition metal ion transport0.0419721296764219



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>

Cell Type
Ontology termp-valuen
metabolising cell1.06e-1712
endopolyploid cell1.06e-1712
parenchymal cell1.06e-1712
polyploid cell1.06e-1712
hepatocyte1.06e-1712
endodermal cell5.51e-1658
epithelial cell of stomach1.53e-103
epithelial cell2.09e-08253
Uber Anatomy
Ontology termp-valuen
epithelium of foregut-midgut junction6.29e-2725
anatomical boundary6.29e-2725
hepatobiliary system6.29e-2725
foregut-midgut junction6.29e-2725
septum transversum6.29e-2725
gastrointestinal system7.44e-2625
digestive tract diverticulum8.09e-2623
sac9.45e-2626
subdivision of digestive tract8.89e-24118
digestive system2.50e-23145
digestive tract2.50e-23145
primitive gut2.50e-23145
epithelial sac2.72e-2325
hepatic diverticulum2.87e-2322
liver primordium2.87e-2322
intestine6.64e-2117
endoderm-derived structure2.95e-20160
endoderm2.95e-20160
presumptive endoderm2.95e-20160
gut epithelium1.15e-1954
endo-epithelium5.63e-1782
liver1.42e-1619
digestive gland1.42e-1619
liver bud1.42e-1619
foregut5.44e-1487
abdomen element6.99e-1454
abdominal segment element6.99e-1454
trunk region element1.36e-12101
abdominal segment of trunk4.52e-1260
abdomen4.52e-1260
endocrine gland1.92e-1135
endocrine system1.92e-1145
small intestine2.97e-114
large intestine1.07e-1011
colon2.06e-099
exocrine gland2.56e-0931
exocrine system2.56e-0931
immaterial anatomical entity6.19e-09117
subdivision of trunk1.03e-08112
biliary system1.49e-089
biliary tree1.49e-089
biliary bud1.49e-089
organ system subdivision1.84e-08223
multi-tissue structure1.84e-07342
gland7.34e-0759
stomach9.59e-078
food storage organ9.59e-078
Disease
Ontology termp-valuen
carcinoma1.50e-19106
adenocarcinoma2.13e-1825
cell type cancer1.31e-13143
gastrointestinal system cancer2.28e-1014
signet ring cell adenocarcinoma8.88e-082
clear cell adenocarcinoma4.97e-072
tubular adenocarcinoma7.23e-072


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)
MA0003.10.233555
MA0004.10.71247
MA0006.11.31813
MA0007.10.6918
MA0009.11.20602
MA0014.10.0695829
MA0017.11.41335
MA0019.10.873355
MA0024.11.09684
MA0025.11.34373
MA0027.12.83281
MA0028.10.550763
MA0029.11.11704
MA0030.11.10506
MA0031.11.03735
MA0038.10.824639
MA0040.11.12314
MA0041.10.732902
MA0042.10.697662
MA0043.11.20635
MA0046.12.68101
MA0048.10.709734
MA0050.10.69864
MA0051.10.820063
MA0052.12.54431
MA0055.10.125954
MA0056.10
MA0057.10.248209
MA0058.10.605914
MA0059.10.604454
MA0060.10.393285
MA0061.10.360128
MA0063.10
MA0066.10.825101
MA0067.11.53181
MA0068.10.313194
MA0069.11.19071
MA0070.11.17908
MA0071.10.782546
MA0072.11.1744
MA0073.10.00636811
MA0074.10.819248
MA0076.10.623864
MA0077.11.16637
MA0078.10.926725
MA0081.10.604638
MA0083.11.21381
MA0084.11.72172
MA0087.11.17185
MA0088.10.536981
MA0089.10
MA0090.10.640115
MA0091.10.715356
MA0092.10.673508
MA0093.10.535768
MA0095.10
MA0098.10
MA0100.10.83965
MA0101.10.539569
MA0103.11.29536
MA0105.10.656404
MA0106.10.869173
MA0107.10.453492
MA0108.21.03412
MA0109.10
MA0111.10.655276
MA0113.10.886811
MA0114.11.13665
MA0115.11.45393
MA0116.10.457606
MA0117.11.24497
MA0119.10.586221
MA0122.11.27173
MA0124.11.41151
MA0125.11.32534
MA0130.10
MA0131.10.94608
MA0132.10
MA0133.10
MA0135.11.23748
MA0136.10.832277
MA0139.10.344952
MA0140.10.779643
MA0141.10.602484
MA0142.11.00381
MA0143.10.887001
MA0144.10.430413
MA0145.11.08195
MA0146.10.481
MA0147.10.46175
MA0148.10.739888
MA0149.10.769072
MA0062.20.353589
MA0035.20.778873
MA0039.20.10559
MA0138.20.928035
MA0002.20.98779
MA0137.21.37305
MA0104.20.392359
MA0047.20.856092
MA0112.21.65877
MA0065.21.09513
MA0150.10.633493
MA0151.10
MA0152.10.78681
MA0153.11.30799
MA0154.10.649108
MA0155.10.533581
MA0156.10.560797
MA0157.10.97481
MA0158.10
MA0159.10.462502
MA0160.10.756582
MA0161.10
MA0162.10.0928415
MA0163.10.253219
MA0164.10.90014
MA0080.20.535868
MA0018.20.870662
MA0099.20.7872
MA0079.20.0270533
MA0102.21.75932
MA0258.11.07498
MA0259.11.1888
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
EP300#203335.08045629466740.01144298405398240.0418787472969781
ESRRA#21011120.9600785340310.008241662461779040.0324811692771978
HEY1#2346244.040111043105710.00375304636917980.0185721113362127
HNF4A#3172211.56614518147680.01057585681762490.0390639048691752
HNF4G#3174321.56506689483510.0001638032421292610.00203587371233343
RXRA#6256210.03730856956660.01391703805920110.0488745935594641
SIN3A#2594245.408884726815140.001168172384885160.00795065204985473
TCF12#693837.975848676639820.003090920396013070.0162748996843564



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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