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{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=0,0

Latest revision as of 11:39, 17 September 2013


Full id: C1196_lymphoma_CD19_diffuse_lymphangiectasia_B_xeroderma_b



Phase1 CAGE Peaks

Hg19::chr14:106725825..106725829,+p@chr14:106725825..106725829
+
Hg19::chr14:22977333..22977378,+p@chr14:22977333..22977378
+
Hg19::chr16:12058994..12059003,+p4@TNFRSF17
Hg19::chr16:12059021..12059048,+p2@TNFRSF17
Hg19::chr16:12059050..12059079,+p1@TNFRSF17
Hg19::chr16:12059091..12059102,+p3@TNFRSF17
Hg19::chr22:24145462..24145501,+p@chr22:24145462..24145501
+


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>

Uber Anatomy
Ontology termp-valuen
adult organism3.65e-15114
hemopoietic organ1.70e-117
immune organ1.70e-117
spleen7.46e-113
gastrointestinal system mesentery7.46e-113
stomach region7.46e-113
mesentery7.46e-113
gastrointestinal system serosa7.46e-113
mesentery of stomach7.46e-113
gut mesentery7.46e-113
dorsal mesentery7.46e-113
dorsal mesogastrium7.46e-113
peritoneal cavity7.46e-113
spleen primordium7.46e-113
gland of gut6.10e-0810
major salivary gland1.07e-072
blood3.29e-0715
haemolymphatic fluid3.29e-0715
organism substance3.29e-0715
Disease
Ontology termp-valuen
lymphoma6.82e-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)
MA0003.10.00215847
MA0004.10.502801
MA0006.10.341337
MA0007.10.483857
MA0009.10.973289
MA0014.10.0156227
MA0017.10.380797
MA0019.10.652951
MA0024.10.867125
MA0025.11.10816
MA0027.12.59001
MA0028.10.35747
MA0029.13.39386
MA0030.10.875089
MA0031.10.809638
MA0038.10.60704
MA0040.10.892629
MA0041.10.521615
MA0042.10.48922
MA0043.10.973609
MA0046.10.962263
MA0048.10.382278
MA0050.10.490116
MA0051.10.602745
MA0052.14.89691
MA0055.10.649431
MA0056.10
MA0057.10.369442
MA0058.10.406232
MA0059.10.404929
MA0060.10.224688
MA0061.10.198335
MA0063.10
MA0066.10.607474
MA0067.11.29359
MA0068.10.488375
MA0069.10.958358
MA0070.10.947018
MA0071.10.567661
MA0072.10.942461
MA0073.10.000265001
MA0074.10.60198
MA0076.10.422297
MA0077.10.934645
MA0078.10.703614
MA0081.10.405093
MA0083.10.980893
MA0084.11.48179
MA0087.10.939982
MA0088.10.0723293
MA0089.10
MA0090.10.436918
MA0091.13.21622
MA0092.10.467172
MA0093.10.344385
MA0095.10
MA0098.10
MA0100.12.55597
MA0101.10.347695
MA0103.10.88373
MA0105.10.104569
MA0106.10.648997
MA0107.10.274127
MA0108.20.806528
MA0109.10
MA0111.11.9963
MA0113.10.665691
MA0114.10.269076
MA0115.11.21667
MA0116.10.277571
MA0117.11.01134
MA0119.10.388712
MA0122.11.03753
MA0124.11.17486
MA0125.11.0901
MA0130.10
MA0131.10.722072
MA0132.10
MA0133.10
MA0135.11.00402
MA0136.10.614215
MA0139.10.186511
MA0140.10.564957
MA0141.10.403171
MA0142.10.777365
MA0143.10.66587
MA0144.10.254954
MA0145.10.0807715
MA0146.10.0127148
MA0147.10.281049
MA0148.10.528066
MA0149.10.555119
MA0062.20.193221
MA0035.20.564239
MA0039.20.00276064
MA0138.20.704862
MA0002.21.15032
MA0137.20.36398
MA0104.20.223944
MA0047.20.636643
MA0112.20.262665
MA0065.20.0828768
MA0150.10.430951
MA0151.10
MA0152.10.571637
MA0153.11.07307
MA0154.10.102476
MA0155.10.250175
MA0156.10.36627
MA0157.10.749547
MA0158.10
MA0159.10.281681
MA0160.10.543522
MA0161.10
MA0162.10.0249953
MA0163.10.0167306
MA0164.10.678332
MA0080.20.344472
MA0018.20.650405
MA0099.20.572
MA0079.29.15802e-07
MA0102.21.51913
MA0258.10.687127
MA0259.10.289405
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
BATF#10538517.39842985164552.2818035468994e-068.1417588190853e-05
BCL11A#53335416.21111720206124.9553880252627e-050.000848836755733002
BCLAF1#9774412.37294149149820.000142162661969680.00185151842542105
CHD2#110645.910870190923920.002402754466874550.0135519400424427
EBF1#187945.089409626610860.004198233162502420.0199935829119284
IRF4#3662412.52257867813950.0001356731131035550.00177630240183305
MEF2A#4205410.71041766265370.0002487360970091120.00268254329156698
MEF2C#4208423.60648828149951.13184591858609e-050.000289231357698097
PAX5#507954.763975379412740.001218821047007470.00819971987428581
POLR2A#543072.147453176558070.004747636447610280.0223380818557449
POU2F2#545267.805249192350731.11144903558223e-050.000284645968188261
TBP#690863.177232017511190.002074112051852660.0120203201034038
TCF12#693846.076837086963670.002165496819676230.0124958463091975



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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