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{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=0,0,

Latest revision as of 11:21, 17 September 2013


Full id: C374_acute_leukemia_Whole_Smooth_splenic_chronic_liver



Phase1 CAGE Peaks

Hg19::chr10:17462911..17462917,-p@chr10:17462911..17462917
-
Hg19::chr10:6557114..6557128,-p10@PRKCQ
Hg19::chr11:118107842..118107871,-p3@MPZL3
Hg19::chr12:62682366..62682406,+p@chr12:62682366..62682406
+
Hg19::chr16:32757354..32757364,+p@chr16:32757354..32757364
+
Hg19::chr16:76343743..76343763,+p8@CNTNAP4
Hg19::chr18:68919827..68919832,+p@chr18:68919827..68919832
+
Hg19::chr19:10397723..10397732,+p6@ICAM4
Hg19::chr1:68220425..68220451,+p@chr1:68220425..68220451
+
Hg19::chr20:31209143..31209164,-p@chr20:31209143..31209164
-
Hg19::chr21:15954632..15954641,-p@chr21:15954632..15954641
-
Hg19::chr21:21474492..21474518,+p@chr21:21474492..21474518
+
Hg19::chr21:21474584..21474595,+p@chr21:21474584..21474595
+
Hg19::chr21:21474621..21474624,+p@chr21:21474621..21474624
+
Hg19::chr21:21482296..21482301,+p@chr21:21482296..21482301
+
Hg19::chr2:41935103..41935117,-p@chr2:41935103..41935117
-
Hg19::chr2:41935147..41935152,-p@chr2:41935147..41935152
-
Hg19::chr4:127482106..127482117,-p@chr4:127482106..127482117
-
Hg19::chr4:79521364..79521371,+p@chr4:79521364..79521371
+
Hg19::chr4:79521388..79521399,+p@chr4:79521388..79521399
+
Hg19::chr4:79521454..79521465,+p@chr4:79521454..79521465
+
Hg19::chr4:79521477..79521480,+p@chr4:79521477..79521480
+
Hg19::chr5:134812717..134812721,+p@chr5:134812717..134812721
+
Hg19::chr5:91016062..91016069,+p@chr5:91016062..91016069
+
Hg19::chr6:114982634..114982657,+p@chr6:114982634..114982657
+
Hg19::chr6:114995028..114995032,+p@chr6:114995028..114995032
+
Hg19::chr6:311874..311890,+p@chr6:311874..311890
+
Hg19::chr6:49610627..49610651,-p@chr6:49610627..49610651
-
Hg19::chr8:108390956..108390965,+p@chr8:108390956..108390965
+


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:0022610biological adhesion0.00312711544249359
GO:0007155cell adhesion0.00312711544249359
GO:0004697protein kinase C activity0.0313299721032974
GO:0001565phorbol ester receptor activity0.0313299721032974



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><br><br>disease_data<br>

Disease
Ontology termp-valuen
myeloid leukemia5.04e-1431
chronic leukemia1.07e-138
leukemia2.03e-1139
hematologic cancer4.95e-0951
immune system cancer4.95e-0951


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)
MA0003.13.25363e-08
MA0004.10.334532
MA0006.10.14464
MA0007.10.0928194
MA0009.10.429031
MA0014.10.000232451
MA0017.10.185458
MA0019.10.553399
MA0024.10.343215
MA0025.10.544326
MA0027.11.97447
MA0028.10.04151
MA0029.10.358654
MA0030.10.349473
MA0031.10.299024
MA0038.10.160193
MA0040.10.363365
MA0041.10.360103
MA0042.10.316458
MA0043.10.429296
MA0046.10.419892
MA0048.10.00121732
MA0050.11.08896
MA0051.10.927103
MA0052.10.366488
MA0055.10.000216937
MA0056.10
MA0057.10.0271819
MA0058.10.467575
MA0059.10.464811
MA0060.10.0511971
MA0061.10.105673
MA0063.10
MA0066.10.160456
MA0067.10.711124
MA0068.10.451179
MA0069.11.06999
MA0070.11.04968
MA0071.10.42511
MA0072.10.403605
MA0073.11.7954e-05
MA0074.10.157134
MA0076.10.065346
MA0077.11.0276
MA0078.11.18649
MA0081.10.806915
MA0083.11.11054
MA0084.10.887042
MA0087.10.401577
MA0088.10.593752
MA0089.10
MA0090.10.0714597
MA0091.10.103495
MA0092.11.50261
MA0093.10.341935
MA0095.10
MA0098.10
MA0100.10.168841
MA0101.10.348346
MA0103.10.0336762
MA0105.10.0207909
MA0106.10.547251
MA0107.10.0853845
MA0108.20.296685
MA0109.10
MA0111.10.266972
MA0113.10.197248
MA0114.10.0815067
MA0115.10.640975
MA0116.10.0198524
MA0117.10.460927
MA0119.10.430802
MA0122.10.483183
MA0124.11.46826
MA0125.11.31023
MA0130.10
MA0131.10.23543
MA0132.10
MA0133.10
MA0135.10.454747
MA0136.10.955971
MA0139.10.00558827
MA0140.14.99535
MA0141.10.461089
MA0142.12.95551
MA0143.10.573609
MA0144.10.0711193
MA0145.10.00234072
MA0146.10.000118223
MA0147.10.0908362
MA0148.10.369009
MA0149.10.129939
MA0062.20.0340128
MA0035.21.9467
MA0039.20.00122549
MA0138.21.18977
MA0002.20.258808
MA0137.20.167559
MA0104.20.0507482
MA0047.20.178535
MA0112.20.00190071
MA0065.20.357886
MA0150.10.52088
MA0151.10
MA0152.10.430874
MA0153.10.513757
MA0154.10.0528121
MA0155.10.101898
MA0156.10.684207
MA0157.10.254856
MA0158.10
MA0159.10.0913419
MA0160.10.123537
MA0161.10
MA0162.12.81464e-06
MA0163.10.00107556
MA0164.12.48239
MA0080.21.38005
MA0018.20.187315
MA0099.20.431402
MA0079.21.58891e-09
MA0102.20.922526
MA0258.10.170584
MA0259.10.0225104
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
GATA1#262383.740774660358740.0009155736637690570.00666306165914407
GATA2#262493.955323641447790.0002636401749347520.00282316376807244
STAT2#677349.001899473991820.0009620694543644760.00692041957051942
TAL1#688677.209666094554533.82939323176264e-050.00072177946170738



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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