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Coexpression cluster:C523: Difference between revisions

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{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=0,0

Latest revision as of 11:24, 17 September 2013


Full id: C523_diffuse_acute_testicular_medulloblastoma_acantholytic_mesenchymal_chronic



Phase1 CAGE Peaks

Hg19::chr10:129899956..129899970,-p@chr10:129899956..129899970
-
Hg19::chr10:129900980..129901015,-p3@MKI67
Hg19::chr10:129905850..129905864,-p@chr10:129905850..129905864
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Hg19::chr10:129905999..129906012,-p@chr10:129905999..129906012
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Hg19::chr10:129906218..129906232,-p@chr10:129906218..129906232
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Hg19::chr10:129906236..129906271,-p@chr10:129906236..129906271
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Hg19::chr10:129906581..129906598,-p@chr10:129906581..129906598
-
Hg19::chr10:129907093..129907109,-p@chr10:129907093..129907109
-
Hg19::chr10:129907150..129907167,-p@chr10:129907150..129907167
-
Hg19::chr10:129907230..129907245,-p@chr10:129907230..129907245
-
Hg19::chr10:129907365..129907387,-p@chr10:129907365..129907387
-
Hg19::chr10:129907447..129907485,-p@chr10:129907447..129907485
-
Hg19::chr10:129907676..129907689,-p@chr10:129907676..129907689
-
Hg19::chr1:214814697..214814711,+p@chr1:214814697..214814711
+
Hg19::chr1:214816318..214816335,+p@chr1:214816318..214816335
+
Hg19::chr1:214819419..214819434,+p4@CENPF
Hg19::chr1:214819709..214819731,+p@chr1:214819709..214819731
+


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:0051382kinetochore assembly0.00413045802224499
GO:0000940outer kinetochore of condensed chromosome0.00413045802224499
GO:0045502dynein binding0.00413045802224499
GO:0051310metaphase plate congression0.00413045802224499
GO:0051319G2 phase0.00413045802224499
GO:0051383kinetochore organization and biogenesis0.00413045802224499
GO:0000085G2 phase of mitotic cell cycle0.00413045802224499
GO:0050000chromosome localization0.00413045802224499
GO:0007094mitotic cell cycle spindle assembly checkpoint0.00413045802224499
GO:0051303establishment of chromosome localization0.00413045802224499
GO:0031981nuclear lumen0.00413045802224499
GO:0031577spindle checkpoint0.00413045802224499
GO:0000777condensed chromosome kinetochore0.00413045802224499
GO:0000779condensed chromosome, pericentric region0.00413045802224499
GO:0008283cell proliferation0.00413045802224499
GO:0007049cell cycle0.00491186317248736
GO:0016202regulation of striated muscle development0.00554112090993136
GO:0031974membrane-enclosed lumen0.00554112090993136
GO:0043233organelle lumen0.00554112090993136
GO:0044428nuclear part0.00685516084370633
GO:0051656establishment of organelle localization0.0083150809596365
GO:0007093mitotic cell cycle checkpoint0.00931694317203566
GO:0000776kinetochore0.00980521760370183
GO:0000922spindle pole0.00980521760370183
GO:0051640organelle localization0.0100200046997096
GO:0016363nuclear matrix0.0137192055392882
GO:0000793condensed chromosome0.0146154451927507
GO:0000075cell cycle checkpoint0.0151766834680746
GO:0007059chromosome segregation0.0154376681870074
GO:0042493response to drug0.0159338744900135
GO:0007088regulation of mitosis0.0163592285586099
GO:0043623cellular protein complex assembly0.0163592285586099
GO:0008022protein C-terminus binding0.0169056812134763
GO:0000775chromosome, pericentric region0.0169056812134763
GO:0005819spindle0.0169056812134763
GO:0051329interphase of mitotic cell cycle0.0179092642258482
GO:0014706striated muscle development0.0179633871655014
GO:0051325interphase0.0179633871655014
GO:0046982protein heterodimerization activity0.0204154045913138
GO:0003682chromatin binding0.0223651637342596
GO:0043232intracellular non-membrane-bound organelle0.0226844325350292
GO:0043228non-membrane-bound organelle0.0226844325350292
GO:0042803protein homodimerization activity0.0278408503124006
GO:0005730nucleolus0.0284105918318076
GO:0007517muscle development0.0289547680760609
GO:0005635nuclear envelope0.0319379510590241
GO:0007067mitosis0.0373753288038742
GO:0000087M phase of mitotic cell cycle0.0373753288038742
GO:0051301cell division0.0373753288038742
GO:0044446intracellular organelle part0.0373753288038742
GO:0044422organelle part0.0373753288038742
GO:0016481negative regulation of transcription0.042318527633139
GO:0000279M phase0.0436505938916569
GO:0045934negative regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process0.0439992967273111
GO:0000785chromatin0.0439992967273111
GO:0000278mitotic cell cycle0.0439992967273111
GO:0006461protein complex assembly0.0449546445064837
GO:0000074regulation of progression through cell cycle0.0449546445064837
GO:0051726regulation of cell cycle0.0449546445064837
GO:0042802identical protein binding0.0449546445064837
GO:0046983protein dimerization activity0.0449546445064837
GO:0022403cell cycle phase0.0449546445064837
GO:0031324negative regulation of cellular metabolic process0.0456717010254775



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><br>disease_data<br>

Cell Type
Ontology termp-valuen
epithelial cell6.22e-10253
animal cell8.58e-09679
eukaryotic cell8.58e-09679
Disease
Ontology termp-valuen
cancer1.53e-63235
disease of cellular proliferation2.06e-62239
cell type cancer6.04e-31143
organ system cancer4.75e-26137
carcinoma3.94e-23106
hematologic cancer1.52e-2251
immune system cancer1.52e-2251
leukemia3.04e-1639
myeloid leukemia1.08e-1031
disease of anatomical entity4.27e-0839
lymphoma9.76e-0810


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)
MA0003.11.09804e-06
MA0004.10.631966
MA0006.10.112549
MA0007.10.208008
MA0009.12.55773
MA0014.10.000129423
MA0017.10.137108
MA0019.10.340029
MA0024.10.525161
MA0025.10.747404
MA0027.12.20546
MA0028.10.122394
MA0029.10.542771
MA0030.10.532314
MA0031.10.474026
MA0038.10.302644
MA0040.10.548121
MA0041.10.664972
MA0042.11.14502
MA0043.10.621991
MA0046.10.611559
MA0048.10.174542
MA0050.10.609862
MA0051.10.299199
MA0052.11.35924
MA0055.10.157354
MA0056.10
MA0057.10.0128587
MA0058.11.46022
MA0059.12.08941
MA0060.10.0509127
MA0061.10.155208
MA0063.10
MA0066.10.302992
MA0067.10.924196
MA0068.10.0264141
MA0069.10.607975
MA0070.10.597583
MA0071.12.93184
MA0072.10.593415
MA0073.10.000143211
MA0074.10.298586
MA0076.10.493997
MA0077.10.586275
MA0078.10.382364
MA0081.10.465308
MA0083.10.628701
MA0084.11.10674
MA0087.10.591148
MA0088.10.0797435
MA0089.10
MA0090.10.174619
MA0091.10.223914
MA0092.10.570207
MA0093.10.740148
MA0095.10
MA0098.10
MA0100.10.314026
MA0101.10.116395
MA0103.10.10701
MA0105.10.0103933
MA0106.10.33677
MA0107.10.551112
MA0108.20.471286
MA0109.10
MA0111.10.184188
MA0113.10.350573
MA0114.10.072201
MA0115.13.28088
MA0116.10.0765991
MA0117.10.656858
MA0119.10.862312
MA0122.10.681203
MA0124.10.810546
MA0125.10.730403
MA0130.10
MA0131.10.398042
MA0132.10
MA0133.10
MA0135.10.650071
MA0136.10.830767
MA0139.10.140313
MA0140.10.269307
MA0141.10.462123
MA0142.10.445733
MA0143.10.350722
MA0144.10.0651126
MA0145.10.094973
MA0146.10.0313344
MA0147.10.569428
MA0148.11.25586
MA0149.10.261654
MA0062.20.148712
MA0035.20.268747
MA0039.21.99256e-06
MA0138.20.38342
MA0002.20.174654
MA0137.20.126444
MA0104.20.420925
MA0047.20.87164
MA0112.20.00512484
MA0065.20.211898
MA0150.10.170499
MA0151.10
MA0152.10.274535
MA0153.10.714423
MA0154.10.137179
MA0155.10.00448085
MA0156.10.4018
MA0157.10.421609
MA0158.10
MA0159.10.0787617
MA0160.10.252705
MA0161.10
MA0162.10.000394937
MA0163.10.00136657
MA0164.10.361105
MA0080.20.11444
MA0018.20.337929
MA0099.20.27482
MA0079.22.33512e-13
MA0102.21.14323
MA0258.10.218609
MA0259.10.28219
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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