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{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=0,0,

Latest revision as of 11:22, 17 September 2013


Full id: C406_Mallassezderived_Mesothelial_mesenchymal_chorionic_Gingival_Placental_Prostate



Phase1 CAGE Peaks

Hg19::chr10:106205466..106205487,+p@chr10:106205466..106205487
+
Hg19::chr10:106205489..106205498,+p@chr10:106205489..106205498
+
Hg19::chr10:106205503..106205518,+p@chr10:106205503..106205518
+
Hg19::chr10:106205565..106205599,+p@chr10:106205565..106205599
+
Hg19::chr10:118187325..118187332,+p5@PNLIPRP3
Hg19::chr12:122380361..122380372,+p@chr12:122380361..122380372
+
Hg19::chr12:56915776..56915787,+p3@RBMS2
Hg19::chr14:81221483..81221489,+p@chr14:81221483..81221489
+
Hg19::chr16:57954525..57954533,-p@chr16:57954525..57954533
-
Hg19::chr16:57954541..57954548,-p@chr16:57954541..57954548
-
Hg19::chr16:79679414..79679446,+p@chr16:79679414..79679446
+
Hg19::chr16:80068152..80068165,-p@chr16:80068152..80068165
-
Hg19::chr17:18343257..18343267,+p2@KRT16P1
Hg19::chr21:44168074..44168079,+p@chr21:44168074..44168079
+
Hg19::chr2:29149934..29149959,+p1@SNORD53
Hg19::chr4:155387574..155387588,-p@chr4:155387574..155387588
-
Hg19::chr4:76481268..76481289,+p1@C4orf26
Hg19::chr5:64454308..64454313,+p@chr5:64454308..64454313
+
Hg19::chr7:137570475..137570486,-p@chr7:137570475..137570486
-
Hg19::chr7:137570496..137570504,-p@chr7:137570496..137570504
-
Hg19::chr9:16094653..16094654,+p@chr9:16094653..16094654
+
Hg19::chr9:27524417..27524425,+p4@IFNK
Hg19::chr9:27524485..27524505,+p2@IFNK
Hg19::chr9:27524537..27524559,+p1@IFNK
Hg19::chr9:27524670..27524673,+p5@IFNK


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:0004420hydroxymethylglutaryl-CoA reductase (NADPH) activity0.0217494896268424
GO:0005132interferon-alpha/beta receptor binding0.0217494896268424
GO:0045089positive regulation of innate immune response0.0217494896268424
GO:0015936coenzyme A metabolic process0.0217494896268424
GO:0045088regulation of innate immune response0.0217494896268424
GO:0004806triacylglycerol lipase activity0.0254136244685966
GO:0030101natural killer cell activation0.0254136244685966



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><br>

Uber Anatomy
Ontology termp-valuen
gingival epithelium1.49e-593
jaw skeleton1.07e-454
splanchnocranium1.07e-454
primary subdivision of cranial skeletal system9.70e-375
protuberance9.21e-316
pharyngeal arch9.21e-316
embryonic head9.21e-316
epithelium of mucosa6.93e-238
gingiva6.93e-238
cranial skeletal system3.90e-1711
surface structure7.63e-1699
mouth mucosa2.28e-1413
axial skeletal system1.30e-1314
head8.92e-1356
skin epidermis1.78e-1215
outer epithelium1.78e-1215
enveloping layer of ectoderm1.78e-1215
subdivision of skeletal system5.39e-1216
anterior region of body1.56e-1162
craniocervical region1.56e-1162
skin gland2.47e-112
epidermis gland2.47e-112
gland of integumental system2.47e-112
sebaceous gland2.47e-112
skin sebaceous gland2.47e-112
sweat gland2.47e-112
sweat gland placode2.47e-112
sebaceous gland placode2.47e-112
pharyngeal arch system9.85e-1118
mucosa1.44e-0920
oral opening9.43e-0922
respiratory system epithelium5.36e-0728
mouth8.95e-0729
stomodeum8.95e-0729


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)
MA0003.10.000233361
MA0004.10.130779
MA0006.10.0525289
MA0007.10.381641
MA0009.10.480543
MA0014.12.83616e-06
MA0017.11.85711
MA0019.10.227177
MA0024.10.391254
MA0025.10.599238
MA0027.12.03861
MA0028.10.213776
MA0029.10.407394
MA0030.10.397801
MA0031.10.344829
MA0038.10.569682
MA0040.10.412311
MA0041.10.437147
MA0042.10.389397
MA0043.10.480818
MA0046.10.47108
MA0048.10.00274349
MA0050.10.781212
MA0051.10.192868
MA0052.10.41557
MA0055.10.200759
MA0056.10
MA0057.10.118248
MA0058.10.0802423
MA0059.10.0796335
MA0060.10.2021
MA0061.10.0122325
MA0063.10
MA0066.11.08273
MA0067.10.769322
MA0068.10.223662
MA0069.10.467738
MA0070.10.458064
MA0071.10.170069
MA0072.10.454189
MA0073.13.93678e-11
MA0074.10.19236
MA0076.10.0879186
MA0077.10.44756
MA0078.11.34069
MA0081.10.27336
MA0083.11.22186
MA0084.10.947429
MA0087.10.452083
MA0088.10.00415386
MA0089.10
MA0090.11.08415
MA0091.10.132307
MA0092.10.357807
MA0093.10.053707
MA0095.10
MA0098.10
MA0100.10.205224
MA0101.10.0550002
MA0103.10.725698
MA0105.10.00176673
MA0106.11.19314
MA0107.10.122976
MA0108.20.906703
MA0109.10
MA0111.10.334615
MA0113.10.236174
MA0114.10.118114
MA0115.10.697973
MA0116.10.030864
MA0117.10.513502
MA0119.10.0722294
MA0122.10.53644
MA0124.10.659634
MA0125.10.583056
MA0130.10
MA0131.10.277285
MA0132.10
MA0133.10
MA0135.10.507125
MA0136.10.581198
MA0139.10.0102505
MA0140.10.168354
MA0141.10.270862
MA0142.10.319458
MA0143.10.236302
MA0144.10.25656
MA0145.10.00568815
MA0146.10.000594916
MA0147.10.031895
MA0148.10.446835
MA0149.10.162171
MA0062.20.0113502
MA0035.20.50217
MA0039.27.1495e-06
MA0138.20.264522
MA0002.22.09636
MA0137.20.221623
MA0104.20.0172311
MA0047.20.215827
MA0112.20.196276
MA0065.20.0230378
MA0150.10.636869
MA0151.10
MA0152.11.57098
MA0153.10.567879
MA0154.10.951837
MA0155.10.177814
MA0156.10.840015
MA0157.10.298026
MA0158.10
MA0159.10.130397
MA0160.10.154993
MA0161.10
MA0162.11.4624e-05
MA0163.14.57949e-05
MA0164.10.68636
MA0080.20.0537406
MA0018.20.225392
MA0099.22.24257
MA0079.22.39411e-07
MA0102.20.983247
MA0258.10.452847
MA0259.10.0344451
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
MAFF#2376436.757842778793420.009609650445008780.0361678720972385
STAT3#6774114.628564598747877.15373012922101e-060.000206161264063387



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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