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{{Coexpression_clusters
{
|full_id=C748_amniotic_keratoacanthoma_salivary_Keratinocyte_maxillary_Corneal_esophagus
 

Latest revision as of 11:30, 17 September 2013


Full id: C748_amniotic_keratoacanthoma_salivary_Keratinocyte_maxillary_Corneal_esophagus



Phase1 CAGE Peaks

Hg19::chr12:52881239..52881250,-p@chr12:52881239..52881250
-
Hg19::chr18:24129045..24129064,-p5@KCTD1
Hg19::chr18:24129073..24129122,-p2@KCTD1
Hg19::chr18:28622699..28622725,-p1@DSC3
Hg19::chr18:28622729..28622751,-p2@DSC3
Hg19::chr18:28622774..28622792,-p3@DSC3
Hg19::chr6:138412531..138412579,-p@chr6:138412531..138412579
-
Hg19::chr6:138412884..138412951,-p@chr6:138412884..138412951
-
Hg19::chr6:138417550..138417583,-p@chr6:138417550..138417583
-
Hg19::chr6:138428549..138428563,-p1@PERP
Hg19::chr6:138428580..138428599,-p2@PERP


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:0044459plasma membrane part0.0156189599557952
GO:0030054cell junction0.0156189599557952
GO:0005886plasma membrane0.0309965043918817
GO:0022610biological adhesion0.0309965043918817
GO:0007155cell adhesion0.0309965043918817



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 structure5.87e-21160
endoderm5.87e-21160
presumptive endoderm5.87e-21160
respiratory system9.53e-1974
digestive system2.83e-14145
digestive tract2.83e-14145
primitive gut2.83e-14145
respiratory tract2.33e-1354
subdivision of digestive tract4.09e-12118
orifice3.47e-1136
anatomical space4.97e-1195
foregut3.44e-1087
female organism5.93e-1041
respiratory primordium6.87e-1038
endoderm of foregut6.87e-1038
segment of respiratory tract7.29e-1047
oral opening1.99e-0922
extraembryonic membrane3.30e-0914
membranous layer3.30e-0914
reproductive structure4.43e-0959
reproductive system4.43e-0959
anterior region of body1.60e-0862
craniocervical region1.60e-0862
immaterial anatomical entity1.63e-08117
organism subdivision2.40e-08264
reproductive organ3.69e-0848
thoracic segment of trunk5.37e-0852
female reproductive organ6.58e-0837
female reproductive system6.58e-0837
head8.83e-0856
epithelial bud1.15e-0737
primordium1.75e-07160
thoracic cavity element2.44e-0734
thoracic cavity2.44e-0734
chorion5.55e-077
thoracic segment organ6.27e-0735
endo-epithelium7.23e-0782
internal genitalia7.24e-0725
mouth8.79e-0729
stomodeum8.79e-0729
Disease
Ontology termp-valuen
carcinoma7.73e-14106
cell type cancer1.49e-10143
squamous cell carcinoma5.31e-0914
cancer7.06e-08235
disease of cellular proliferation1.49e-07239


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)
MA0003.14.66732
MA0004.10.349539
MA0006.10.210781
MA0007.10.332734
MA0009.10.79061
MA0014.15.54861
MA0017.10.24363
MA0019.10.486183
MA0024.10.688373
MA0025.10.921763
MA0027.12.39404
MA0028.10.224112
MA0029.10.707146
MA0030.11.6617
MA0031.10.633489
MA0038.10.443833
MA0040.10.712837
MA0041.10.366339
MA0042.10.337481
MA0043.10.790919
MA0046.10.779945
MA0048.11.57917
MA0050.10.338274
MA0051.10.439895
MA0052.10.716602
MA0055.10.00989454
MA0056.10
MA0057.10.0465155
MA0058.10.265212
MA0059.10.2641
MA0060.10.119532
MA0061.10.100525
MA0063.10
MA0066.10.444231
MA0067.11.1037
MA0068.10.0758327
MA0069.10.776171
MA0070.10.765217
MA0071.10.40788
MA0072.10.760818
MA0073.10.00428338
MA0074.10.439193
MA0076.10.278993
MA0077.10.753278
MA0078.10.533387
MA0081.10.26424
MA0083.10.79797
MA0084.11.28962
MA0087.10.758426
MA0088.10.10094
MA0089.10
MA0090.10.291627
MA0091.10.351901
MA0092.10.318032
MA0093.10.213288
MA0095.10
MA0098.10
MA0100.10.456802
MA0101.10.216017
MA0103.10.203171
MA0105.11.0054
MA0106.13.11277
MA0107.10.156959
MA0108.20.630531
MA0109.10
MA0111.10.303543
MA0113.10.498009
MA0114.10.465415
MA0115.11.02805
MA0116.10.159642
MA0117.10.827487
MA0119.10.250314
MA0122.10.852927
MA0124.10.98702
MA0125.10.904129
MA0130.10
MA0131.10.550695
MA0132.10
MA0133.10
MA0135.10.820382
MA0136.10.450422
MA0139.10.637178
MA0140.10.405425
MA0141.10.2626
MA0142.10.602852
MA0143.10.498176
MA0144.10.438224
MA0145.11.19384
MA0146.12.72284
MA0147.10.162359
MA0148.10.372124
MA0149.10.396509
MA0062.20.0969238
MA0035.20.404774
MA0039.20.396868
MA0138.20.534556
MA0002.20.111226
MA0137.20.229531
MA0104.20.378829
MA0047.20.47109
MA0112.20.106997
MA0065.20.527167
MA0150.10.286461
MA0151.10
MA0152.10.411494
MA0153.10.887528
MA0154.10.0391503
MA0155.11.4993
MA0156.10.231442
MA0157.11.41182
MA0158.10
MA0159.10.948902
MA0160.10.386031
MA0161.10
MA0162.10.519336
MA0163.10.585549
MA0164.10.509774
MA0080.20.21336
MA0018.20.483823
MA0099.21.05945
MA0079.20.0388923
MA0102.21.32663
MA0258.10.135061
MA0259.10.168926
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
TFAP2C#702243.930628585403720.01418989706912680.0497792704310414
ZNF263#1012753.737200744095760.006510908182094970.027877695130773



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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