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{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=0,0,

Latest revision as of 11:30, 17 September 2013


Full id: C783_argyrophil_Hepatocyte_liver_gastrointestinal_hepatocellular_adenocarcinoma_Intestinal



Phase1 CAGE Peaks

Hg19::chr10:52645416..52645444,-p2@A1CF
Hg19::chr16:21244912..21244929,-p@chr16:21244912..21244929
-
Hg19::chr17:73553885..73553901,+p3@LLGL2
Hg19::chr1:155274590..155274615,+p@chr1:155274590..155274615
+
Hg19::chr1:94057518..94057547,+p1@LOC100129046
Hg19::chr1:94057553..94057579,+p2@LOC100129046
Hg19::chr1:94057594..94057608,+p3@LOC100129046
Hg19::chr22:37475107..37475111,-p@chr22:37475107..37475111
-
Hg19::chr22:37505724..37505729,-p4@TMPRSS6
Hg19::chr9:683055..683082,+p@chr9:683055..683082
+


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:0042730fibrinolysis0.0111125819727046
GO:0030195negative regulation of blood coagulation0.0111125819727046
GO:0030193regulation of blood coagulation0.0111125819727046
GO:0050819negative regulation of coagulation0.0111125819727046
GO:0050818regulation of coagulation0.0111125819727046
GO:0030198extracellular matrix organization and biogenesis0.0266121358508287
GO:0043062extracellular structure organization and biogenesis0.0338348358154235
GO:0007596blood coagulation0.0338348358154235
GO:0050817coagulation0.0338348358154235
GO:0007599hemostasis0.0338348358154235
GO:0050878regulation of body fluid levels0.0338348358154235
GO:0001525angiogenesis0.0338348358154235
GO:0042060wound healing0.0338348358154235
GO:0048514blood vessel morphogenesis0.0338348358154235
GO:0048646anatomical structure formation0.0338348358154235
GO:0001568blood vessel development0.0338348358154235
GO:0001944vasculature development0.0338348358154235
GO:0051301cell division0.0471077088999902



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 cell1.11e-2212
endopolyploid cell1.11e-2212
parenchymal cell1.11e-2212
polyploid cell1.11e-2212
hepatocyte1.11e-2212
endodermal cell2.22e-1158
Uber Anatomy
Ontology termp-valuen
liver5.96e-2319
digestive gland5.96e-2319
liver bud5.96e-2319
hepatic diverticulum1.32e-1922
liver primordium1.32e-1922
digestive tract diverticulum1.10e-1823
intestine4.32e-1817
epithelial sac4.61e-1725
epithelium of foregut-midgut junction4.61e-1725
anatomical boundary4.61e-1725
hepatobiliary system4.61e-1725
foregut-midgut junction4.61e-1725
septum transversum4.61e-1725
sac2.40e-1626
subdivision of digestive tract7.44e-16118
gastrointestinal system2.45e-1525
exocrine gland1.87e-1331
exocrine system1.87e-1331
gut epithelium1.46e-1254
abdomen element1.62e-1254
abdominal segment element1.62e-1254
digestive system4.45e-12145
digestive tract4.45e-12145
primitive gut4.45e-12145
endocrine gland9.80e-1235
abdominal segment of trunk5.03e-1160
abdomen5.03e-1160
endocrine system8.39e-1145
endoderm-derived structure1.56e-10160
endoderm1.56e-10160
presumptive endoderm1.56e-10160
small intestine1.91e-104
endo-epithelium2.22e-1082
colon9.69e-109
trunk region element3.73e-09101
large intestine5.49e-0811
gland8.54e-0859
immaterial anatomical entity1.96e-07117
organ system subdivision5.20e-07223
foregut6.32e-0787
subdivision of trunk8.03e-07112
Disease
Ontology termp-valuen
adenocarcinoma1.78e-0925
carcinoma3.24e-07106


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)
MA0003.10.00834483
MA0004.10.380329
MA0006.10.236135
MA0007.10.363007
MA0009.10.828613
MA0014.10.0679667
MA0017.12.10084
MA0019.10.520264
MA0024.10.725404
MA0025.10.960689
MA0027.12.43535
MA0028.10.697761
MA0029.10.744375
MA0030.10.733118
MA0031.10.669876
MA0038.10.477043
MA0040.10.750125
MA0041.10.397617
MA0042.10.367902
MA0043.10.828925
MA0046.14.56747
MA0048.10.0613414
MA0050.10.368721
MA0051.10.473017
MA0052.10.753928
MA0055.10.0662377
MA0056.10
MA0057.10.211138
MA0058.10.293055
MA0059.10.291897
MA0060.10.138988
MA0061.10.118318
MA0063.10
MA0066.10.477449
MA0067.11.1435
MA0068.10.0911063
MA0069.10.814052
MA0070.10.803003
MA0071.10.440254
MA0072.11.87381
MA0073.10.213551
MA0074.11.19015
MA0076.11.50024
MA0077.10.790956
MA0078.10.568317
MA0081.10.292043
MA0083.10.836033
MA0084.11.32998
MA0087.10.79615
MA0088.10.300184
MA0089.10
MA0090.10.320494
MA0091.10.382762
MA0092.10.918839
MA0093.10.238771
MA0095.10
MA0098.10
MA0100.11.2287
MA0101.10.241637
MA0103.10.646502
MA0105.10.0508589
MA0106.10.516528
MA0107.10.179177
MA0108.20.666881
MA0109.10
MA0111.10.33284
MA0113.10.532314
MA0114.13.00684
MA0115.12.42332
MA0116.10.536665
MA0117.10.865782
MA0119.15.89181
MA0122.10.891407
MA0124.11.0263
MA0125.10.942948
MA0130.10
MA0131.10.585907
MA0132.10
MA0133.10
MA0135.10.858623
MA0136.11.21476
MA0139.10.109245
MA0140.10.437738
MA0141.10.290336
MA0142.10.638837
MA0143.10.532484
MA0144.10.163394
MA0145.11.35344
MA0146.10.0551603
MA0147.10.184931
MA0148.10.403564
MA0149.10.428597
MA0062.20.740103
MA0035.20.437071
MA0039.20.0721026
MA0138.20.569505
MA0002.23.29372
MA0137.20.255808
MA0104.20.138396
MA0047.20.504873
MA0112.20.573053
MA0065.22.94255
MA0150.10.315136
MA0151.10
MA0152.10.443956
MA0153.13.51652
MA0154.10.729959
MA0155.10.030416
MA0156.11.31919
MA0157.10.612166
MA0158.10
MA0159.10.185458
MA0160.10.417847
MA0161.10
MA0162.10.0377269
MA0163.10.162989
MA0164.11.34364
MA0080.21.24809
MA0018.20.517858
MA0099.20.444294
MA0079.20.00205882
MA0102.21.36707
MA0258.11.47203
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

(#promoters = Number of promoters in this coexpression cluster that have ChIP signal of the TF)

TF#promotersEnrichmentp-valueq-value
BATF#1053837.307340537691090.006678517386486440.0284136254410647
ELF1#199783.406478367046030.0002607995998237460.00279503842031731
EP300#203385.419153380978567.65728824577695e-060.000218144988298063
FOXA1#316988.865135799508361.6719883831087e-079.22942889764744e-06
FOXA2#3170819.70437100213223.07603449086058e-103.10394170232839e-08
HDAC2#306679.390934165638381.25187588461401e-065.03833007758007e-05
HEY1#2346283.232088834484570.0003859230867685430.00377780684778515
HNF4A#3172818.5058322903635.05840698659513e-104.89162006734267e-08
HNF4G#3174514.37671126322341.10559453101475e-050.000286022262136859
MEF2A#420535.622969272893220.01372403878188040.0483268109626354
RXRA#6256816.05969371130661.55412452507963e-091.37203052641413e-07
SP1#666784.558705102512722.88273233272976e-050.000603709007615729
SREBF1#6720314.10175483214650.001032051022814520.00729963272191018
TAF1#687272.34013240002170.01040839844348330.0386325511777294
TRIM28#1015547.436210018105010.001351406221142950.00889908665384294



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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