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Coexpression cluster:C631: Difference between revisions

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|tfbs_overrepresentation_jaspar=MA0003.1;0.000725818,MA0004.1;0.275994,MA0006.1;0.152601,MA0007.1;0.260673,MA0009.1;0.695988,MA0014.1;0.182178,MA0017.1;0.534321,MA0019.1;0.403106,MA0024.1;0.59663,MA0025.1;0.824398,MA0027.1;2.28954,MA0028.1;0.164086,MA0029.1;0.614815,MA0030.1;0.604021,MA0031.1;0.543644,MA0038.1;0.363295,MA0040.1;0.620334,MA0041.1;0.291389,MA0042.1;0.264992,MA0043.1;0.69629,MA0046.1;0.685589,MA0048.1;2.05724,MA0050.1;0.73369,MA0051.1;0.359609,MA0052.1;0.623986,MA0055.1;1.58506,MA0056.1;0,MA0057.1;0.0243088,MA0058.1;0.200063,MA0059.1;0.199079,MA0060.1;0.0773489,MA0061.1;2.33565,MA0063.1;0,MA0066.1;0.363668,MA0067.1;1.00375,MA0068.1;0.0444239,MA0069.1;0.681911,MA0070.1;0.671241,MA0071.1;0.878639,MA0072.1;0.666958,MA0073.1;0.0183781,MA0074.1;0.358953,MA0076.1;0.212295,MA0077.1;0.65962,MA0078.1;0.447828,MA0081.1;0.578007,MA0083.1;0.703169,MA0084.1;1.18798,MA0087.1;0.664629,MA0088.1;0.752017,MA0089.1;0,MA0090.1;0.635809,MA0091.1;0.278153,MA0092.1;0.247341,MA0093.1;0.154754,MA0095.1;0,MA0098.1;0,MA0100.1;0.375452,MA0101.1;0.92504,MA0103.1;0.878771,MA0105.1;2.3439,MA0106.1;0.399649,MA0107.1;0.708233,MA0108.2;0.540797,MA0109.1;0,MA0111.1;0.660878,MA0113.1;1.06479,MA0114.1;0.339925,MA0115.1;0.929032,MA0116.1;0.354243,MA0117.1;0.732,MA0119.1;0.18693,MA0122.1;0.756889,MA0124.1;0.888592,MA0125.1;0.807083,MA0130.1;0,MA0131.1;0.464307,MA0132.1;0,MA0133.1;0,MA0135.1;0.725055,MA0136.1;0.369468,MA0139.1;0.453946,MA0140.1;0.327488,MA0141.1;0.574537,MA0142.1;1.27972,MA0143.1;1.06513,MA0144.1;1.60185,MA0145.1;0.827687,MA0146.1;0.00293512,MA0147.1;0.111828,MA0148.1;0.296708,MA0149.1;0.319221,MA0062.2;0.0599644,MA0035.2;0.326883,MA0039.2;0.0280647,MA0138.2;0.44894,MA0002.2;0.906125,MA0137.2;0.504333,MA0104.2;0.0769208,MA0047.2;0.388882,MA0112.2;0.0113102,MA0065.2;0.16797,MA0150.1;0.624926,MA0151.1;0,MA0152.1;0.333125,MA0153.1;0.790794,MA0154.1;1.83273,MA0155.1;0.0101184,MA0156.1;0.170442,MA0157.1;0.489002,MA0158.1;0,MA0159.1;0.112236,MA0160.1;0.30953,MA0161.1;0,MA0162.1;0.00929209,MA0163.1;0.106785,MA0164.1;0.425415,MA0080.2;0.154815,MA0018.2;0.400879,MA0099.2;0.333432,MA0079.2;4.50435e-05,MA0102.2;1.22472,MA0258.1;0.089643,MA0259.1;0.117259,MA0442.1;0
}}
}}

Revision as of 19:19, 22 January 2013


Full id: C631_b_plasma_xeroderma_lymphoma_splenic_Burkitt_B



Phase1 CAGE Peaks

Hg19::chr15:31521567..31521649,-p1@ENST00000558109
p1@ENST00000559853
p1@ENST00000560812
Hg19::chr18:10890571..10890584,-p1@PIEZO2
Hg19::chr18:4264542..4264555,+p6@LOC284215
Hg19::chr3:178261188..178261195,-p@chr3:178261188..178261195
-
Hg19::chr3:189838731..189838748,+p1@LEPREL1-AS1
Hg19::chr3:98255434..98255449,-p@chr3:98255434..98255449
-
Hg19::chr7:114556667..114556679,+p@chr7:114556667..114556679
+
Hg19::chr7:119999940..119999943,+p@chr7:119999940..119999943
+
Hg19::chr8:135577784..135577795,-p15@ZFAT
Hg19::chr8:135577814..135577826,-p12@ZFAT
Hg19::chr8:135577829..135577861,-p6@ZFAT
Hg19::chr8:135577914..135577919,-p23@ZFAT
Hg19::chrX:11682587..11682597,-p25@ARHGAP6
Hg19::chrX:11778510..11778522,+p19@MSL3


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:0005100Rho GTPase activator activity0.0137662388633777
GO:0005884actin filament0.0137662388633777
GO:0030041actin filament polymerization0.0137662388633777
GO:0005070SH3/SH2 adaptor activity0.0137662388633777
GO:0060090molecular adaptor activity0.0137662388633777
GO:0008154actin polymerization and/or depolymerization0.0137662388633777
GO:0030674protein binding, bridging0.0164179324149299
GO:0051258protein polymerization0.0164179324149299
GO:0005099Ras GTPase activator activity0.0248243651634679
GO:0007266Rho protein signal transduction0.0254562580949017
GO:0030036actin cytoskeleton organization and biogenesis0.0293378861022803
GO:0030029actin filament-based process0.0293378861022803
GO:0015629actin cytoskeleton0.0308308199512721
GO:0005096GTPase activator activity0.0336579704294293
GO:0007265Ras protein signal transduction0.0376746247774984
GO:0008047enzyme activator activity0.0376746247774984
GO:0005083small GTPase regulator activity0.0376746247774984
GO:0007010cytoskeleton organization and biogenesis0.0498862840605576
GO:0030695GTPase regulator activity0.0498862840605576



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>

Disease
Ontology termp-valuen
genetic disease1.30e-191
monogenic disease1.30e-191
xeroderma pigmentosum1.30e-191
lymphoma3.14e-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)
MA0003.10.000725818
MA0004.10.275994
MA0006.10.152601
MA0007.10.260673
MA0009.10.695988
MA0014.10.182178
MA0017.10.534321
MA0019.10.403106
MA0024.10.59663
MA0025.10.824398
MA0027.12.28954
MA0028.10.164086
MA0029.10.614815
MA0030.10.604021
MA0031.10.543644
MA0038.10.363295
MA0040.10.620334
MA0041.10.291389
MA0042.10.264992
MA0043.10.69629
MA0046.10.685589
MA0048.12.05724
MA0050.10.73369
MA0051.10.359609
MA0052.10.623986
MA0055.11.58506
MA0056.10
MA0057.10.0243088
MA0058.10.200063
MA0059.10.199079
MA0060.10.0773489
MA0061.12.33565
MA0063.10
MA0066.10.363668
MA0067.11.00375
MA0068.10.0444239
MA0069.10.681911
MA0070.10.671241
MA0071.10.878639
MA0072.10.666958
MA0073.10.0183781
MA0074.10.358953
MA0076.10.212295
MA0077.10.65962
MA0078.10.447828
MA0081.10.578007
MA0083.10.703169
MA0084.11.18798
MA0087.10.664629
MA0088.10.752017
MA0089.10
MA0090.10.635809
MA0091.10.278153
MA0092.10.247341
MA0093.10.154754
MA0095.10
MA0098.10
MA0100.10.375452
MA0101.10.92504
MA0103.10.878771
MA0105.12.3439
MA0106.10.399649
MA0107.10.708233
MA0108.20.540797
MA0109.10
MA0111.10.660878
MA0113.11.06479
MA0114.10.339925
MA0115.10.929032
MA0116.10.354243
MA0117.10.732
MA0119.10.18693
MA0122.10.756889
MA0124.10.888592
MA0125.10.807083
MA0130.10
MA0131.10.464307
MA0132.10
MA0133.10
MA0135.10.725055
MA0136.10.369468
MA0139.10.453946
MA0140.10.327488
MA0141.10.574537
MA0142.11.27972
MA0143.11.06513
MA0144.11.60185
MA0145.10.827687
MA0146.10.00293512
MA0147.10.111828
MA0148.10.296708
MA0149.10.319221
MA0062.20.0599644
MA0035.20.326883
MA0039.20.0280647
MA0138.20.44894
MA0002.20.906125
MA0137.20.504333
MA0104.20.0769208
MA0047.20.388882
MA0112.20.0113102
MA0065.20.16797
MA0150.10.624926
MA0151.10
MA0152.10.333125
MA0153.10.790794
MA0154.11.83273
MA0155.10.0101184
MA0156.10.170442
MA0157.10.489002
MA0158.10
MA0159.10.112236
MA0160.10.30953
MA0161.10
MA0162.10.00929209
MA0163.10.106785
MA0164.10.425415
MA0080.20.154815
MA0018.20.400879
MA0099.20.333432
MA0079.24.50435e-05
MA0102.21.22472
MA0258.10.089643
MA0259.10.117259
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
EBF1#187974.45323342328450.0003755857170036150.00373188057255642



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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