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{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=0,0,0

Latest revision as of 11:27, 17 September 2013


Full id: C640_amniotic_salivary_chorionic_Keratinocyte_Urothelial_Prostate_Mammary



Phase1 CAGE Peaks

Hg19::chr10:105791560..105791576,-p7@COL17A1
Hg19::chr10:105819927..105819974,+p@chr10:105819927..105819974
+
Hg19::chr10:105824227..105824253,+p@chr10:105824227..105824253
+
Hg19::chr10:105824310..105824328,-p12@COL17A1
Hg19::chr10:105830210..105830215,-p@chr10:105830210..105830215
-
Hg19::chr10:105830255..105830294,-p@chr10:105830255..105830294
-
Hg19::chr10:105836085..105836093,-p@chr10:105836085..105836093
-
Hg19::chr10:105836134..105836160,-p@chr10:105836134..105836160
-
Hg19::chr10:105836165..105836175,-p@chr10:105836165..105836175
-
Hg19::chr10:105845551..105845581,-p2@COL17A1
Hg19::chr10:105845611..105845645,-p1@COL17A1
Hg19::chr10:105845674..105845722,-p3@COL17A1
Hg19::chr6:7586117..7586135,+p9@DSP


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

p.valueFDRnGenesnPathwayName
5.75814629513173e-060.00364490660481838269Alpha6-Beta4 Integrin Signaling Pathway (Wikipathways):WP244



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:0008544epidermis development0.000567241222222142
GO:0007398ectoderm development0.000567241222222142
GO:0005911intercellular junction0.000567241222222142
GO:0009888tissue development0.00132564708271702
GO:0030054cell junction0.00210012693832474
GO:0005913cell-cell adherens junction0.00841721083028887
GO:0048513organ development0.010626908581125
GO:0001533cornified envelope0.0106819675426817
GO:0018149peptide cross-linking0.0112207999992292
GO:0030216keratinocyte differentiation0.0116516829588302
GO:0048731system development0.0133844707925655
GO:0005912adherens junction0.0174713479979979
GO:0048856anatomical structure development0.017675968976235
GO:0044459plasma membrane part0.0201424468047065
GO:0007275multicellular organismal development0.0201424468047065
GO:0005200structural constituent of cytoskeleton0.0206164785855694
GO:0030674protein binding, bridging0.0207715838525679
GO:0007160cell-matrix adhesion0.0210321636243287
GO:0031589cell-substrate adhesion0.0210321636243287
GO:0006817phosphate transport0.027723638321343
GO:0032502developmental process0.0304983850393752
GO:0005886plasma membrane0.0363123514587199
GO:0032501multicellular organismal process0.0363123514587199
GO:0005882intermediate filament0.0365527498515394
GO:0045111intermediate filament cytoskeleton0.0365527498515394
GO:0015698inorganic anion transport0.0387074078945368
GO:0006820anion transport0.0462624270633432



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
endoderm-derived structure2.96e-23160
endoderm2.96e-23160
presumptive endoderm2.96e-23160
extraembryonic membrane6.60e-2014
membranous layer6.60e-2014
respiratory system8.52e-1874
oral opening7.20e-1722
orifice8.80e-1536
chorion2.11e-147
mouth8.46e-1429
stomodeum8.46e-1429
digestive system1.75e-13145
digestive tract1.75e-13145
primitive gut1.75e-13145
anterior region of body7.51e-1262
craniocervical region7.51e-1262
surface structure6.02e-1199
subdivision of digestive tract6.73e-11118
urothelium1.75e-105
neck2.56e-1010
extraembryonic structure2.98e-1024
foregut7.10e-1087
respiratory tract8.47e-1054
head3.13e-0956
organ component layer4.22e-0966
mouth mucosa7.41e-0913
gland of gut1.01e-0810
subdivision of head1.03e-0849
transitional epithelium1.21e-086
placenta1.22e-084
allantois1.22e-084
tracheobronchial tree1.53e-0815
lower respiratory tract1.53e-0815
saliva-secreting gland2.18e-086
gland of oral region2.18e-086
gland of foregut2.18e-086
oral gland2.18e-086
oral cavity2.18e-086
mucosa7.27e-0820
amnion9.71e-087
mucosa of oral region9.85e-084
respiratory system mucosa9.85e-084
acellular anatomical structure1.94e-073
egg chorion1.94e-073
gingival epithelium2.15e-073
pharynx3.05e-0711
segment of respiratory tract4.54e-0747
Disease
Ontology termp-valuen
squamous cell carcinoma2.45e-2014


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)
MA0003.10.00135586
MA0004.10.297884
MA0006.10.169524
MA0007.10.282081
MA0009.10.724811
MA0014.10.000874969
MA0017.10.199401
MA0019.10.428118
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
MA0041.10.313738
MA0042.10.286538
MA0043.10.725115
MA0046.10.714324
MA0048.10.131159
MA0050.10.287284
MA0051.10.383704
MA0052.12.65542
MA0055.10.00493639
MA0056.10
MA0057.10.123867
MA0058.10.219229
MA0059.10.218203
MA0060.10.0892161
MA0061.10.255087
MA0063.10
MA0066.11.78288
MA0067.11.03434
MA0068.10.196125
MA0069.10.710614
MA0070.10.69985
MA0071.10.35315
MA0072.11.66071
MA0073.10.000945528
MA0074.10.996524
MA0076.10.231962
MA0077.10.688123
MA0078.10.473657
MA0081.10.218332
MA0083.10.732051
MA0084.11.21913
MA0087.10.693179
MA0088.10.337854
MA0089.10
MA0090.10.243681
MA0091.10.812021
MA0092.10.739628
MA0093.10.171791
MA0095.10
MA0098.10
MA0100.10.399896
MA0101.10.517741
MA0103.10.489275
MA0105.10.0255214
MA0106.11.90842
MA0107.10.385539
MA0108.20.568002
MA0109.10
MA0111.10.254772
MA0113.10.439505
MA0114.10.376635
MA0115.10.959312
MA0116.10.123927
MA0117.10.76111
MA0119.10.205526
MA0122.10.786181
MA0124.10.918678
MA0125.10.83671
MA0130.10
MA0131.10.490408
MA0132.10
MA0133.10
MA0135.11.7821
MA0136.10.393782
MA0139.10.0663461
MA0140.10.350813
MA0141.10.216821
MA0142.10.541045
MA0143.10.439666
MA0144.10.108694
MA0145.10.0164225
MA0146.10.000600379
MA0147.10.397782
MA0148.10.319209
MA0149.10.342334
MA0062.20.0702147
MA0035.20.350194
MA0039.20.0426227
MA0138.20.474787
MA0002.20.280231
MA0137.20.186529
MA0104.20.088751
MA0047.20.413608
MA0112.20.180347
MA0065.20.388593
MA0150.10.671641
MA0151.10
MA0152.10.356591
MA0153.10.820317
MA0154.10.105196
MA0155.10.0633432
MA0156.10.18827
MA0157.10.515488
MA0158.10
MA0159.11.29394
MA0160.10.332385
MA0161.10
MA0162.10.00205586
MA0163.10.000991488
MA0164.10.450848
MA0080.20.171855
MA0018.20.425847
MA0099.20.356906
MA0079.23.37691e-08
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

No analysis results for this cluster

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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