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Coexpression cluster:C516: Difference between revisions

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{{Coexpression_clusters
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1.1;0.343779,MA0103.1;1.09511,MA0105.1;0.121083,MA0106.1;0.319,MA0107.1;0.0664936,MA0108.2;0.451357,MA0109.1;0,MA0111.1;0.170509,MA0113.1;0.884817,MA0114.1;0.495259,MA0115.1;0.827474,MA0116.1;0.0681676,MA0117.1;0.635078,MA0119.1;0.810503,MA0122.1;0.659244,MA0124.1;0.787807,MA0125.1;0.708116,MA0130.1;0,MA0131.1;0.379172,MA0132.1;0,MA0133.1;0,MA0135.1;0.628343,MA0136.1;0.291242,MA0139.1;0.860218,MA0140.1;1.30145,MA0141.1;0.849848,MA0142.1;0.426146,MA0143.1;0.885144,MA0144.1;0.209582,MA0145.1;0.752471,MA0146.1;0.0949152,MA0147.1;0.0698742,MA0148.1;1.19698,MA0149.1;0.245595,MA0062.2;0.0323736,MA0035.2;2.00764,MA0039.2;0.367929,MA0138.2;1.70306,MA0002.2;0.357374,MA0137.2;0.743725,MA0104.2;0.0440964,MA0047.2;0.832232,MA0112.2;0.706966,MA0065.2;0.181893,MA0150.1;0.157331,MA0151.1;0,MA0152.1;0.258148,MA0153.1;0.692238,MA0154.1;0.427971,MA0155.1;0.0644993,MA0156.1;0.116546,MA0157.1;0.402372,MA0158.1;0,MA0159.1;0.246493,MA0160.1;0.666979,MA0161.1;0,MA0162.1;0.0280426,MA0163.1;9.54308e-05,MA0164.1;0.907835,MA0080.2;0.103778,MA0018.2;0.320136,MA0099.2;0.258426,MA0079.2;0.00350186,MA0102.2;1.11935,MA0258.1;0.196984,MA0259.1;0.257452,MA0442.1;0}}
|full_id=C516_endometrioid_clear_serous_anaplastic_malignant_oral_uterus
|id=C516
}}

Latest revision as of 11:24, 17 September 2013


Full id: C516_endometrioid_clear_serous_anaplastic_malignant_oral_uterus



Phase1 CAGE Peaks

Hg19::chr14:33147559..33147570,+p@chr14:33147559..33147570
+
Hg19::chr14:33403217..33403226,+p@chr14:33403217..33403226
+
Hg19::chr14:33403278..33403307,+p@chr14:33403278..33403307
+
Hg19::chr19:28782435..28782439,+p@chr19:28782435..28782439
+
Hg19::chr1:46651830..46651834,-p@chr1:46651830..46651834
-
Hg19::chr4:19457174..19457178,+p3@ENST00000511431
Hg19::chr4:95680517..95680526,-p@chr4:95680517..95680526
-
Hg19::chr4:95680536..95680545,-p@chr4:95680536..95680545
-
Hg19::chr4:95680548..95680553,-p@chr4:95680548..95680553
-
Hg19::chr6:134327986..134327991,-p@chr6:134327986..134327991
-
Hg19::chr6:20541194..20541205,+p@chr6:20541194..20541205
+
Hg19::chr6:31097301..31097322,+p@chr6:31097301..31097322
+
Hg19::chr6:52837931..52837938,-p@chr6:52837931..52837938
-
Hg19::chr6:52837942..52837955,-p@chr6:52837942..52837955
-
Hg19::chr7:27208949..27208981,+p4@ENST00000523790
Hg19::chr7:6312923..6312932,-p@chr7:6312923..6312932
-
Hg19::chr8:145578301..145578317,+p5@GPR172A
Hg19::chr9:124877971..124877982,+p@chr9:124877971..124877982
+


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>

Cell Type
Ontology termp-valuen
epithelial cell of uterus7.67e-186
stromal cell of endometrium7.67e-186
Disease
Ontology termp-valuen
female reproductive endometrioid cancer7.67e-186


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)
MA0003.10.00772785
MA0004.10.207008
MA0006.10.101986
MA0007.10.564363
MA0009.11.46157
MA0014.10.202917
MA0017.10.789059
MA0019.10.322194
MA0024.10.50459
MA0025.10.725013
MA0027.12.18072
MA0028.10.111328
MA0029.10.522011
MA0030.10.511665
MA0031.10.454061
MA0038.10.285594
MA0040.10.527306
MA0041.11.17879
MA0042.10.197306
MA0043.10.60049
MA0046.10.590147
MA0048.10.0114521
MA0050.10.574987
MA0051.10.77145
MA0052.11.31505
MA0055.10.757344
MA0056.10
MA0057.10.141662
MA0058.10.141262
MA0059.10.140431
MA0060.10.0444001
MA0061.10.137405
MA0063.10
MA0066.10.779889
MA0067.10.900956
MA0068.10.239549
MA0069.10.586593
MA0070.10.576293
MA0071.11.30914
MA0072.11.40255
MA0073.10.204429
MA0074.10.281628
MA0076.10.151641
MA0077.11.38762
MA0078.10.363755
MA0081.10.140536
MA0083.10.607144
MA0084.11.08294
MA0087.12.39027
MA0088.10.452761
MA0089.10
MA0090.10.485893
MA0091.10.208918
MA0092.10.53622
MA0093.10.103729
MA0095.10
MA0098.10
MA0100.10.296726
MA0101.10.343779
MA0103.11.09511
MA0105.10.121083
MA0106.10.319
MA0107.10.0664936
MA0108.20.451357
MA0109.10
MA0111.10.170509
MA0113.10.884817
MA0114.10.495259
MA0115.10.827474
MA0116.10.0681676
MA0117.10.635078
MA0119.10.810503
MA0122.10.659244
MA0124.10.787807
MA0125.10.708116
MA0130.10
MA0131.10.379172
MA0132.10
MA0133.10
MA0135.10.628343
MA0136.10.291242
MA0139.10.860218
MA0140.11.30145
MA0141.10.849848
MA0142.10.426146
MA0143.10.885144
MA0144.10.209582
MA0145.10.752471
MA0146.10.0949152
MA0147.10.0698742
MA0148.11.19698
MA0149.10.245595
MA0062.20.0323736
MA0035.22.00764
MA0039.20.367929
MA0138.21.70306
MA0002.20.357374
MA0137.20.743725
MA0104.20.0440964
MA0047.20.832232
MA0112.20.706966
MA0065.20.181893
MA0150.10.157331
MA0151.10
MA0152.10.258148
MA0153.10.692238
MA0154.10.427971
MA0155.10.0644993
MA0156.10.116546
MA0157.10.402372
MA0158.10
MA0159.10.246493
MA0160.10.666979
MA0161.10
MA0162.10.0280426
MA0163.19.54308e-05
MA0164.10.907835
MA0080.20.103778
MA0018.20.320136
MA0099.20.258426
MA0079.20.00350186
MA0102.21.11935
MA0258.10.196984
MA0259.10.257452
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
ESR1#209958.54683424893180.0002175241005708870.00248937097737484



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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