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{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=0,0,

Latest revision as of 11:27, 17 September 2013


Full id: C651_splenic_CD19_B_xeroderma_plasma_Burkitt_lymphoma



Phase1 CAGE Peaks

Hg19::chr10:98460583..98460643,-p2@PIK3AP1
Hg19::chr11:60222928..60222933,+p5@MS4A1
Hg19::chr11:60223277..60223297,+p2@MS4A1
Hg19::chr17:29645385..29645411,+p@chr17:29645385..29645411
+
Hg19::chr19:55128576..55128604,+p3@LILRB1
Hg19::chr1:111670644..111670656,-p7@DRAM2
Hg19::chr1:220943820..220943841,+p@chr1:220943820..220943841
+
Hg19::chr1:221220442..221220467,+p@chr1:221220442..221220467
+
Hg19::chr4:38784572..38784589,-p2@TLR10
Hg19::chr4:38784592..38784619,-p1@TLR10
Hg19::chr6:41700616..41700664,-p8@TFEB
Hg19::chr9:37025706..37025716,-p@chr9:37025706..37025716
-
Hg19::chr9:37025731..37025750,-p@chr9:37025731..37025750
-


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:0006955immune response0.0148625519068601
GO:0008157protein phosphatase 1 binding0.0148625519068601
GO:0002376immune system process0.0148625519068601
GO:0019903protein phosphatase binding0.0437448317277681
GO:0019902phosphatase binding0.0452754369404383



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
blood4.07e-2515
haemolymphatic fluid4.07e-2515
organism substance4.07e-2515
hemopoietic organ2.61e-127
immune organ2.61e-127
adult organism5.70e-12114
spleen1.21e-113
gastrointestinal system mesentery1.21e-113
stomach region1.21e-113
mesentery1.21e-113
gastrointestinal system serosa1.21e-113
mesentery of stomach1.21e-113
gut mesentery1.21e-113
dorsal mesentery1.21e-113
dorsal mesogastrium1.21e-113
peritoneal cavity1.21e-113
spleen primordium1.21e-113
hemolymphoid system1.44e-08108
hematopoietic system9.83e-0898
blood island9.83e-0898
Disease
Ontology termp-valuen
lymphoma1.51e-1210


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)
MA0003.10.00501742
MA0004.10.297884
MA0006.10.506155
MA0007.10.771118
MA0009.10.724811
MA0014.10.000874969
MA0017.10.57848
MA0019.11.92038
MA0024.10.6245
MA0025.10.854131
MA0027.12.32165
MA0028.10.181601
MA0029.10.642879
MA0030.10.63197
MA0031.10.570886
MA0038.10.387473
MA0040.10.648455
MA0041.10.84273
MA0042.10.286538
MA0043.10.725115
MA0046.10.714324
MA0048.10.0323146
MA0050.12.18586
MA0051.10.383704
MA0052.11.57036
MA0055.10.0277818
MA0056.10
MA0057.10.0301256
MA0058.10.219229
MA0059.10.218203
MA0060.10.2996
MA0061.10.542967
MA0063.10
MA0066.11.00709
MA0067.11.03434
MA0068.10.196125
MA0069.10.710614
MA0070.10.69985
MA0071.10.35315
MA0072.10.695528
MA0073.10.000252324
MA0074.10.996524
MA0076.10.231962
MA0077.10.688123
MA0078.10.473657
MA0081.10.218332
MA0083.10.732051
MA0084.11.21913
MA0087.10.693179
MA0088.10.0644248
MA0089.10
MA0090.10.243681
MA0091.10.30011
MA0092.10.739628
MA0093.10.171791
MA0095.10
MA0098.10
MA0100.10.399896
MA0101.10.17426
MA0103.10.489275
MA0105.10.26318
MA0106.10.424592
MA0107.10.121572
MA0108.20.568002
MA0109.10
MA0111.10.708492
MA0113.10.439505
MA0114.10.376635
MA0115.10.959312
MA0116.11.27593
MA0117.10.76111
MA0119.10.205526
MA0122.10.786181
MA0124.10.918678
MA0125.10.83671
MA0130.10
MA0131.10.490408
MA0132.10
MA0133.10
MA0135.10.754112
MA0136.11.02008
MA0139.10.0663461
MA0140.10.350813
MA0141.10.216821
MA0142.10.541045
MA0143.10.439666
MA0144.10.35188
MA0145.10.0164225
MA0146.10.0179216
MA0147.10.126316
MA0148.10.319209
MA0149.10.342334
MA0062.20.0702147
MA0035.20.350194
MA0039.20.000373861
MA0138.20.474787
MA0002.20.588143
MA0137.20.186529
MA0104.20.088751
MA0047.20.413608
MA0112.20.355033
MA0065.20.0781722
MA0150.10.671641
MA0151.10
MA0152.10.356591
MA0153.10.820317
MA0154.11.54414
MA0155.10.0132945
MA0156.10.18827
MA0157.10.515488
MA0158.10
MA0159.10.126752
MA0160.10.332385
MA0161.10
MA0162.10.00205586
MA0163.10.139091
MA0164.10.450848
MA0080.20.985821
MA0018.20.425847
MA0099.20.356906
MA0079.24.63921e-06
MA0102.21.25596
MA0258.10.335505
MA0259.10.132107
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
BCL11A#53335613.09359466320332.65123192532282e-069.28856125624925e-05
BCL3#602410.62987778576560.000406486065895170.00387663210994664
EBF1#187985.48090267481171.92247936454994e-050.000434310669163381
MEF2A#4205811.53429594439636.61255911623314e-084.04101264798287e-06
NFKB1#479093.799428524441897.7463744424886e-050.00119395454604349
POU2F2#545264.202826488188860.001513180596708150.00965630382131263
SPI1#668885.048814466783223.53708006891545e-050.000685232990757671
TCF12#693864.908214570239890.0006606804283463160.0054084341790297
YY1#752872.644476557613610.007760697146882240.031919011118152



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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