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{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=0,0,

Latest revision as of 11:23, 17 September 2013


Full id: C442_diffuse_xeroderma_lymphoma_Burkitt_plasma_b_lymphangiectasia



Phase1 CAGE Peaks

Hg19::chr11:111224162..111224190,-p@chr11:111224162..111224190
-
Hg19::chr11:111224819..111224845,+p2@CU689419
Hg19::chr11:111224843..111224854,-p@chr11:111224843..111224854
-
Hg19::chr11:111224975..111224995,-p@chr11:111224975..111224995
-
Hg19::chr11:111225012..111225024,-p@chr11:111225012..111225024
-
Hg19::chr11:111225030..111225046,-p@chr11:111225030..111225046
-
Hg19::chr11:111225132..111225169,-p@chr11:111225132..111225169
-
Hg19::chr11:111225158..111225201,+p1@CU689419
Hg19::chr11:111225198..111225226,-p@chr11:111225198..111225226
-
Hg19::chr11:111225243..111225260,-p@chr11:111225243..111225260
-
Hg19::chr11:111228213..111228235,-p@chr11:111228213..111228235
-
Hg19::chr11:111228281..111228290,-p@chr11:111228281..111228290
-
Hg19::chr11:111228348..111228370,-p@chr11:111228348..111228370
-
Hg19::chr11:111228555..111228566,-p@chr11:111228555..111228566
-
Hg19::chr11:111249993..111250006,-p1@POU2AF1
Hg19::chr12:6554021..6554040,+p4@CD27
Hg19::chr19:19258534..19258541,-p@chr19:19258534..19258541
-
Hg19::chr22:39843178..39843224,+p@chr22:39843178..39843224
+
Hg19::chr22:39843234..39843241,+p@chr22:39843234..39843241
+
Hg19::chr5:133880112..133880133,+p20@PHF15
Hg19::chr6:107078354..107078388,-p4@RTN4IP1
Hg19::chr9:37034469..37034474,-p1@PAX5


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:0006959humoral immune response0.00861922938102902
GO:0007283spermatogenesis0.0141234610606639
GO:0048232male gamete generation0.0141234610606639
GO:0006955immune response0.0141234610606639
GO:0045579positive regulation of B cell differentiation0.0141234610606639
GO:0008588release of cytoplasmic sequestered NF-kappaB0.0141234610606639
GO:0007276gamete generation0.0141234610606639
GO:0002376immune system process0.0141234610606639
GO:0019953sexual reproduction0.0141234610606639
GO:0043027caspase inhibitor activity0.0141234610606639
GO:0042346positive regulation of NF-kappaB import into nucleus0.0141234610606639
GO:0045621positive regulation of lymphocyte differentiation0.0141234610606639
GO:0042993positive regulation of transcription factor import into nucleus0.0141234610606639
GO:0045577regulation of B cell differentiation0.0141234610606639
GO:0042307positive regulation of protein import into nucleus0.0141234610606639
GO:0046824positive regulation of nucleocytoplasmic transport0.0165489821573171
GO:0051222positive regulation of protein transport0.0167212129148552
GO:0042345regulation of NF-kappaB import into nucleus0.0167212129148552
GO:0042348NF-kappaB import into nucleus0.0167212129148552
GO:0046330positive regulation of JNK cascade0.0172079018049975
GO:0045619regulation of lymphocyte differentiation0.0201668720331968
GO:0050871positive regulation of B cell activation0.0207897414522421
GO:0046328regulation of JNK cascade0.0207897414522421
GO:0043028caspase regulator activity0.0207897414522421
GO:0042990regulation of transcription factor import into nucleus0.0207897414522421
GO:0042991transcription factor import into nucleus0.0207897414522421
GO:0042306regulation of protein import into nucleus0.0207897414522421
GO:0033157regulation of intracellular protein transport0.0207897414522421
GO:0006366transcription from RNA polymerase II promoter0.0211804672829906
GO:0050864regulation of B cell activation0.0213346757061976
GO:0032386regulation of intracellular transport0.0213346757061976
GO:0051223regulation of protein transport0.0225592436426157
GO:0046822regulation of nucleocytoplasmic transport0.0225592436426157
GO:0030183B cell differentiation0.0225592436426157
GO:0051050positive regulation of transport0.0287005938275852
GO:0051251positive regulation of lymphocyte activation0.0361440743964373
GO:0016064immunoglobulin mediated immune response0.0361440743964373
GO:0019724B cell mediated immunity0.0361440743964373
GO:0042113B cell activation0.0412907208792365
GO:0030098lymphocyte differentiation0.0418421950910473
GO:0007254JNK cascade0.0418421950910473
GO:0031098stress-activated protein kinase signaling pathway0.0426500390204998
GO:0048513organ development0.0426500390204998
GO:0002449lymphocyte mediated immunity0.0426500390204998
GO:0002250adaptive immune response0.0426500390204998
GO:0002460adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains0.0426500390204998
GO:0051249regulation of lymphocyte activation0.0426500390204998
GO:0002443leukocyte mediated immunity0.0428554367391758
GO:0050865regulation of cell activation0.0430521979591859
GO:0002521leukocyte differentiation0.0474371112883045
GO:0006606protein import into nucleus0.0495899158326127
GO:0051170nuclear import0.049643673186528



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>

Uber Anatomy
Ontology termp-valuen
hemopoietic organ4.71e-147
immune organ4.71e-147
spleen4.91e-133
gastrointestinal system mesentery4.91e-133
stomach region4.91e-133
mesentery4.91e-133
gastrointestinal system serosa4.91e-133
mesentery of stomach4.91e-133
gut mesentery4.91e-133
dorsal mesentery4.91e-133
dorsal mesogastrium4.91e-133
peritoneal cavity4.91e-133
spleen primordium4.91e-133
Disease
Ontology termp-valuen
lymphoma2.36e-1510


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)
MA0003.10.762126
MA0004.10.930499
MA0006.10.0694838
MA0007.10.146569
MA0009.10.526253
MA0014.10.0463889
MA0017.12.10758
MA0019.10.262545
MA0024.10.434294
MA0025.10.647545
MA0027.12.09389
MA0028.10.265828
MA0029.10.450974
MA0030.10.441064
MA0031.10.386141
MA0038.10.22896
MA0040.10.456051
MA0041.10.170492
MA0042.10.149889
MA0043.10.526535
MA0046.10.516541
MA0048.10.00505311
MA0050.10.150446
MA0051.10.22589
MA0052.10.459414
MA0055.10.0584391
MA0056.10
MA0057.10.748244
MA0058.11.66036
MA0059.10.331581
MA0060.10.0258987
MA0061.10.0847828
MA0063.10
MA0066.13.48648
MA0067.10.820123
MA0068.10.302785
MA0069.11.27741
MA0070.10.503171
MA0071.10.201311
MA0072.10.499187
MA0073.10.260075
MA0074.10.225345
MA0076.10.110503
MA0077.10.49237
MA0078.10.30111
MA0081.10.101139
MA0083.10.532971
MA0084.10.999884
MA0087.10.497023
MA0088.12.11513
MA0089.10
MA0090.10.378129
MA0091.10.160096
MA0092.10.4236
MA0093.10.906091
MA0095.10
MA0098.10
MA0100.10.239133
MA0101.10.538883
MA0103.10.862267
MA0105.10.928954
MA0106.10.259598
MA0107.10.041912
MA0108.20.997711
MA0109.10
MA0111.10.398557
MA0113.10.272101
MA0114.11.00251
MA0115.10.747865
MA0116.10.377517
MA0117.10.560027
MA0119.10.0925355
MA0122.10.583485
MA0124.10.70896
MA0125.10.631059
MA0130.10
MA0131.10.846727
MA0132.10
MA0133.10
MA0135.10.553498
MA0136.10.660517
MA0139.10.192454
MA0140.10.578606
MA0141.10.100114
MA0142.10.359701
MA0143.10.272236
MA0144.10.140794
MA0145.10.48721
MA0146.10.254076
MA0147.10.0444528
MA0148.10.174705
MA0149.121.2308
MA0062.20.080288
MA0035.20.198962
MA0039.20.0365001
MA0138.20.302079
MA0002.20.24323
MA0137.20.578057
MA0104.20.0256869
MA0047.20.698519
MA0112.21.16768
MA0065.20.0401599
MA0150.10.369323
MA0151.10
MA0152.10.20405
MA0153.10.615584
MA0154.11.20838
MA0155.11.73348
MA0156.11.46668
MA0157.10.89541
MA0158.10
MA0159.10.170777
MA0160.10.18494
MA0161.10
MA0162.10.0235931
MA0163.11.73402
MA0164.10.28168
MA0080.21.36161
MA0018.20.260646
MA0099.20.204301
MA0079.20.0133971
MA0102.21.03595
MA0258.10.032189
MA0259.10.179817
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
POLR2A#5430171.659395636431240.003374401144947360.0172357353732654



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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