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{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=0,0,

Latest revision as of 11:27, 17 September 2013


Full id: C619_squamous_bile_Small_Mammary_mucinous_Tracheal_giant



Phase1 CAGE Peaks

Hg19::chr11:128376979..128377025,-p@chr11:128376979..128377025
-
Hg19::chr12:31910006..31910040,-p@chr12:31910006..31910040
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Hg19::chr20:10400351..10400358,-p@chr20:10400351..10400358
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Hg19::chr20:10400359..10400384,-p@chr20:10400359..10400384
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Hg19::chr20:10400400..10400411,-p@chr20:10400400..10400411
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Hg19::chr2:20133179..20133195,-p@chr2:20133179..20133195
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Hg19::chr2:20133198..20133223,-p@chr2:20133198..20133223
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Hg19::chr2:29353197..29353206,-p@chr2:29353197..29353206
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Hg19::chr2:29353207..29353220,-p@chr2:29353207..29353220
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Hg19::chr2:29353224..29353251,-p@chr2:29353224..29353251
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Hg19::chr3:101957544..101957547,+p@chr3:101957544..101957547
+
Hg19::chr6:150813975..150813994,+p@chr6:150813975..150813994
+
Hg19::chr6:150813996..150814008,+p@chr6:150813996..150814008
+
Hg19::chr7:101917407..101917443,+p3@CUX1


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>

Disease
Ontology termp-valuen
carcinoma1.43e-39106
cell type cancer3.36e-28143
squamous cell carcinoma4.51e-2614
cancer1.25e-16235
disease of cellular proliferation4.75e-16239
disease of anatomical entity1.16e-1039
adenocarcinoma1.33e-1025
tubular adenocarcinoma1.28e-072
lung cancer4.11e-0715
clear cell adenocarcinoma4.65e-072


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)
MA0003.11.06747e-05
MA0004.10.757232
MA0006.10.464315
MA0007.10.260673
MA0009.10.695988
MA0014.10.00418733
MA0017.11.61959
MA0019.10.403106
MA0024.10.59663
MA0025.10.824398
MA0027.12.28954
MA0028.10.164086
MA0029.10.614815
MA0030.11.4696
MA0031.10.543644
MA0038.10.363295
MA0040.12.55335
MA0041.11.44251
MA0042.10.264992
MA0043.10.69629
MA0046.10.685589
MA0048.10.0262025
MA0050.11.3485
MA0051.10.359609
MA0052.10.623986
MA0055.10.0207496
MA0056.10
MA0057.10.0243088
MA0058.11.09867
MA0059.10.199079
MA0060.10.955356
MA0061.10.224865
MA0063.10
MA0066.10.953901
MA0067.11.00375
MA0068.10.0444239
MA0069.11.6324
MA0070.10.671241
MA0071.10.329767
MA0072.10.666958
MA0073.10.00139087
MA0074.10.943486
MA0076.10.212295
MA0077.10.65962
MA0078.11.13748
MA0081.10.199203
MA0083.10.703169
MA0084.11.18798
MA0087.11.5964
MA0088.10.0103438
MA0089.10
MA0090.11.18995
MA0091.10.278153
MA0092.10.247341
MA0093.10.915249
MA0095.10
MA0098.10
MA0100.10.375452
MA0101.10.1571
MA0103.10.448026
MA0105.10.0203556
MA0106.10.399649
MA0107.10.107387
MA0108.20.540797
MA0109.10
MA0111.10.660878
MA0113.10.414278
MA0114.12.29008
MA0115.10.929032
MA0116.10.10959
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
MA0136.11.71931
MA0139.10.453946
MA0140.10.873545
MA0141.10.574537
MA0142.10.514195
MA0143.10.414436
MA0144.10.316332
MA0145.10.0126924
MA0146.10.000361686
MA0147.10.111828
MA0148.10.804328
MA0149.10.319221
MA0062.20.0599644
MA0035.20.326883
MA0039.20.839657
MA0138.20.44894
MA0002.20.248488
MA0137.20.168782
MA0104.20.265556
MA0047.21.78642
MA0112.20.30305
MA0065.20.846317
MA0150.13.39848
MA0151.10
MA0152.10.333125
MA0153.10.790794
MA0154.10.0196232
MA0155.10.0505475
MA0156.10.980055
MA0157.11.22595
MA0158.10
MA0159.12.37943
MA0160.10.30953
MA0161.10
MA0162.10.00136062
MA0163.10.000620686
MA0164.13.88453
MA0080.20.154815
MA0018.20.400879
MA0099.23.32822
MA0079.21.47279e-05
MA0102.21.22472
MA0258.11.04518
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
BCL3#60237.402950600801070.006944266328473380.0293719516879731
CEBPB#105173.985573812912410.0007472043419239960.00588338919377264
EP300#2033104.838529804445142.76491461776768e-069.56808872647577e-05
FOS#235363.856266560954750.002556261076114450.0141450328774143
FOSL1#8061514.18342132727611.67209788666175e-050.00038550161409507
FOSL2#235556.046500215914890.0009158002195483010.00666424603744461
GATA3#262535.836396362258430.0132868415026020.0469885019534827
JUN#372565.362641082429860.0004446028323499080.004139229382046
JUND#3727104.996188529907882.04570531488249e-067.46771818878058e-05
MAFF#23764312.06757639070250.001758447738855720.0108074220795829
MAFK#797535.807299958106410.01346697296069050.0475723723673787
NFE2#4778316.54377013963480.0007099302705452480.0057051714008522
POLR2A#5430131.994063663946780.0003845688903765380.00377481112237173
STAT3#677486.011122855516711.1795981756812e-050.000298801973975184



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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