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{{Coexpression_clusters
{
|full_id=C819_Alveolar_MCF7_mesothelioma_endometrioid_signet_Renal_gastric
 

Latest revision as of 11:31, 17 September 2013


Full id: C819_Alveolar_MCF7_mesothelioma_endometrioid_signet_Renal_gastric



Phase1 CAGE Peaks

Hg19::chr12:53298570..53298600,-p5@KRT8
Hg19::chr12:53298672..53298713,-p7@KRT8
Hg19::chr12:53342893..53342911,+p1@KRT18
Hg19::chr12:53343121..53343150,+p6@KRT18
Hg19::chr12:53344588..53344613,+p4@KRT18
Hg19::chr12:53344624..53344654,-p@chr12:53344624..53344654
-
Hg19::chr12:53345928..53345949,+p3@KRT18
Hg19::chr2:203706578..203706583,-p1@KRT8P15
Hg19::chr2:236715167..236715174,+p@chr2:236715167..236715174
+
Hg19::chr3:170213152..170213154,+p1@KRT8P13


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:0005882intermediate filament0.00163391453254799
GO:0045111intermediate filament cytoskeleton0.00163391453254799
GO:0043000Golgi to plasma membrane CFTR protein transport0.00266882527361085
GO:0043001Golgi to plasma membrane protein transport0.0030023842411101
GO:0006893Golgi to plasma membrane transport0.00560412061869646
GO:0044430cytoskeletal part0.00756000214426228
GO:0030018Z disc0.00756000214426228
GO:0042383sarcolemma0.00756000214426228
GO:0031674I band0.00756000214426228
GO:0006892post-Golgi vesicle-mediated transport0.00840444861332212
GO:0005856cytoskeleton0.0107478076253176
GO:0030017sarcomere0.0160021099440816
GO:0030016myofibril0.0163086417198209
GO:0044449contractile fiber part0.0170648948467576
GO:0043292contractile fiber0.0170648948467576
GO:0005200structural constituent of cytoskeleton0.0197684410496945
GO:0045095keratin filament0.0197684410496945
GO:0048193Golgi vesicle transport0.0197684410496945
GO:0043232intracellular non-membrane-bound organelle0.0251111392713346
GO:0043228non-membrane-bound organelle0.0251111392713346
GO:0016043cellular component organization and biogenesis0.0301217712229689
GO:0051707response to other organism0.0372143670088532
GO:0043066negative regulation of apoptosis0.0372143670088532
GO:0043069negative regulation of programmed cell death0.0372143670088532
GO:0045045secretory pathway0.0372143670088532
GO:0044446intracellular organelle part0.0372143670088532
GO:0044422organelle part0.0372143670088532
GO:0009607response to biotic stimulus0.0408206615432263
GO:0032940secretion by cell0.0408206615432263
GO:0051704multi-organism process0.0442194544953417
GO:0046903secretion0.0493096828301634



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
epithelial cell1.17e-55253
endodermal cell4.97e-1858
endo-epithelial cell2.46e-1342
mesothelial cell2.01e-1219
embryonic cell2.91e-08250
extraembryonic cell8.00e-0819
kidney tubule cell8.58e-0810
nephron tubule epithelial cell8.58e-0810
epithelial cell of nephron3.42e-0715
kidney cell7.93e-0717
kidney epithelial cell7.93e-0717
Uber Anatomy
Ontology termp-valuen
endoderm-derived structure8.28e-23160
endoderm8.28e-23160
presumptive endoderm8.28e-23160
trunk region element1.48e-18101
digestive system1.73e-18145
digestive tract1.73e-18145
primitive gut1.73e-18145
subdivision of digestive tract2.09e-18118
endo-epithelium2.30e-1682
urinary system structure2.25e-1447
primordium3.38e-14160
immaterial anatomical entity4.27e-14117
abdomen element8.50e-1454
abdominal segment element8.50e-1454
renal system8.64e-1448
foregut1.47e-1387
subdivision of trunk3.54e-13112
abdominal segment of trunk1.28e-1160
abdomen1.28e-1160
respiratory primordium3.42e-1138
endoderm of foregut3.42e-1138
gut epithelium2.15e-1054
kidney5.04e-1026
kidney mesenchyme5.04e-1026
upper urinary tract5.04e-1026
kidney rudiment5.04e-1026
kidney field5.04e-1026
extraembryonic membrane9.61e-1014
membranous layer9.61e-1014
trunk1.05e-09199
anatomical space2.10e-0995
organism subdivision2.34e-09264
respiratory tract9.42e-0954
multi-tissue structure1.20e-08342
sac1.71e-0826
epithelial sac3.08e-0825
respiratory system4.36e-0874
cavitated compound organ6.48e-0831
epithelium of foregut-midgut junction7.98e-0825
anatomical boundary7.98e-0825
hepatobiliary system7.98e-0825
foregut-midgut junction7.98e-0825
septum transversum7.98e-0825
nephron tubule epithelium8.58e-0810
segment of respiratory tract1.04e-0747
excretory tube1.47e-0716
kidney epithelium1.47e-0716
larynx1.49e-079
epithelial bud1.55e-0737
nephron epithelium3.42e-0715
renal tubule3.42e-0715
nephron tubule3.42e-0715
nephron3.42e-0715
uriniferous tubule3.42e-0715
nephrogenic mesenchyme3.42e-0715
reproductive structure4.35e-0759
reproductive system4.35e-0759
chorion4.49e-077
Disease
Ontology termp-valuen
carcinoma2.27e-36106
cell type cancer5.53e-29143
cancer1.16e-19235
disease of cellular proliferation2.06e-18239
adenocarcinoma1.01e-1125


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)
MA0003.10.632731
MA0004.10.380329
MA0006.10.236135
MA0007.10.363007
MA0009.10.828613
MA0014.10.686562
MA0017.10.270554
MA0019.10.520264
MA0024.10.725404
MA0025.10.960689
MA0027.12.43535
MA0028.10.25013
MA0029.11.76197
MA0030.10.733118
MA0031.10.669876
MA0038.10.477043
MA0040.10.750125
MA0041.10.397617
MA0042.10.367902
MA0043.10.828925
MA0046.10.817858
MA0048.10.830349
MA0050.10.368721
MA0051.10.473017
MA0052.10.753928
MA0055.10.867653
MA0056.10
MA0057.10.0580131
MA0058.10.293055
MA0059.10.291897
MA0060.10.138988
MA0061.10.377096
MA0063.10
MA0066.12.08608
MA0067.11.1435
MA0068.10.304755
MA0069.11.90569
MA0070.10.803003
MA0071.11.9614
MA0072.10.798564
MA0073.10.00294698
MA0074.11.19015
MA0076.10.307383
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
MA0100.10.49029
MA0101.10.678051
MA0103.11.20737
MA0105.10.0508589
MA0106.10.516528
MA0107.10.529721
MA0108.20.666881
MA0109.10
MA0111.10.33284
MA0113.10.532314
MA0114.11.5848
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
MA0141.11.43869
MA0142.10.638837
MA0143.10.532484
MA0144.10.491079
MA0145.10.332712
MA0146.10.606611
MA0147.10.184931
MA0148.10.403564
MA0149.10.428597
MA0062.20.114378
MA0035.20.437071
MA0039.20.138005
MA0138.20.569505
MA0002.20.129981
MA0137.20.255808
MA0104.20.138396
MA0047.20.504873
MA0112.20.904106
MA0065.20.963081
MA0150.10.315136
MA0151.10
MA0152.10.443956
MA0153.10.926242
MA0154.10.414714
MA0155.10.030416
MA0156.10.257809
MA0157.10.612166
MA0158.10
MA0159.11.04074
MA0160.10.417847
MA0161.10
MA0162.10.403951
MA0163.10.990939
MA0164.10.544294
MA0080.20.238846
MA0018.20.517858
MA0099.20.444294
MA0079.20.0513543
MA0102.21.36707
MA0258.10.919347
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
GTF2F1#296245.095864350703060.00541638888230090.02456817539538
TAF7#687944.573227761969570.007980040641138020.0322633735103675
TFAP2A#702046.607453749217980.002096541917954080.0121254148504378
TFAP2C#702244.323691443944090.009735325145753660.0366118477151477



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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