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{{Coexpression_clusters
{{Coexpression_clusters|coexpression_dpi_cluster_scores_median=0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.670030963153865,0.398986195304492,0.454657394945217,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.267491812392555,1.24938385966151,1.35228862127085,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1.21120845495636,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.405873209650902,0.70681945923757,0.109512603169101,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0549313087713622,0,0,0,0,0,0,0,0,0,0,0,0,0.757340012776534,0.740052265719991,0.256292328107296,0.305022922250855,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0674361974989848,0.453788509586933,0,0,0,0,0,0.081825314342242,0.109996748514441,0.0516318862226721,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.341840505197881,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.587859933893789,0.835724946875151,0,0,0,0,0,0,0,0,0,0.395774304676761,0.197713313938225,0.246911081527629,0.30353683589945,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.387982427981154,0.369328045138462,0,0,0,1.1607001146988,1.4410004821859,0.51814976977019,0,0,0,0,0,0,0,0,0,0,0.173209711509263,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0873862460237173,0,0.498131334169749,0,0.348040468312977,0,0,0,0,0,0,0.105947296040957,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1.42576188741717,1.08759466444249,0,0,0,0,0.120245177400006,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0368115019473605,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.861624810839228,0,0,0,0,0,0,1.52618814686408,0,0.161955095312168,0,0,0,0.143359213980427,0.0645768949458293,0,0.203964919649634,0,0,0,0,0,0.699560121123555,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.59380210434493,1.64672623386859,0,1.22441470491498,0,0.152177219618649,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.214404368077712,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.727237367378932,0.351052756729229,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.251682437892981,0.0484300422256687,0.505305099909452,0,0,0,0,0,0,0,0,0,0.0598874413026267,0,0,0,0,0,0,0.900200835645675,0,0.052217621604872,0,0,0,0,0.0369091684033041,0,0,0,0,0,0,0.032817368032432,0,0,0,0,0,0,0,0,0,0,0.457116361360864,0.551544795137297,0.96825481127376,0.155405081403798,0,0,0,0,0,0,0,0,0,0,0,0,1.02996055406958,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.97275970762482,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1.1529150767267,0.092743246865863,0.162003215453563,0.156707515791389,0,0,0,1.61571442096086,1.02458960805244,1.36597774060054,0.626083538468696,0.124719478691449,0.0655074646802949,0,0,0,0.524579074618365,0.322255070366512,0.941065350542453,0.221611588102807,0.0796420028184954,0|full_id=C3869_tongue_epidermoid_esophagus_Urothelial_Corneal_cervical_throat|gostat_on_coexpression_clusters=GO:0048503!GPI 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A0159.1;0.565904,MA0160.1;0.871361,MA0161.1;0,MA0162.1;0.455568,MA0163.1;0.776149,MA0164.1;1.01792,MA0080.2;0.643061,MA0018.2;0.987913,MA0099.2;0.902716,MA0079.2;0.181755,MA0102.2;1.88331,MA0258.1;1.29138,MA0259.1;0.575594,MA0442.1;0}}
|full_id=C3869_tongue_epidermoid_esophagus_Urothelial_Corneal_cervical_throat
|gostat_on_coexpression_clusters=GO:0048503!GPI anchor binding!0.0393265041799129!8581$GO:0035091!phosphoinositide binding!0.0393265041799129!8581$GO:0005543!phospholipid binding!0.0393265041799129!8581$GO:0008289!lipid binding!0.0423878488166725!8581$GO:0005624!membrane fraction!0.0423878488166725!8581$GO:0000267!cell fraction!0.0423878488166725!8581$GO:0022610!biological adhesion!0.0423878488166725!8581$GO:0007155!cell adhesion!0.0423878488166725!8581
|id=C3869
}}

Latest revision as of 12:34, 17 September 2013


Full id: C3869_tongue_epidermoid_esophagus_Urothelial_Corneal_cervical_throat



Phase1 CAGE Peaks

Hg19::chr1:153285395..153285434,-p@chr1:153285395..153285434
-
Hg19::chr2:241831424..241831455,-p5@C2orf54
Hg19::chr8:143867946..143867962,-p1@LY6D


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:0048503GPI anchor binding0.0393265041799129
GO:0035091phosphoinositide binding0.0393265041799129
GO:0005543phospholipid binding0.0393265041799129
GO:0008289lipid binding0.0423878488166725
GO:0005624membrane fraction0.0423878488166725
GO:0000267cell fraction0.0423878488166725
GO:0022610biological adhesion0.0423878488166725
GO:0007155cell adhesion0.0423878488166725



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>

Cell Type
Ontology termp-valuen
endo-epithelial cell7.94e-2542
epithelial cell of alimentary canal7.33e-1820
endodermal cell3.21e-1658
respiratory epithelial cell7.23e-1413
general ecto-epithelial cell1.69e-1314
acinar cell3.20e-135
protein secreting cell6.11e-116
epithelial cell1.99e-09253
acinar cell of salivary gland1.43e-083
bronchial epithelial cell2.36e-083
gingival epithelial cell4.73e-083
glandular epithelial cell3.90e-079
epidermal cell4.56e-079
stratified squamous epithelial cell5.38e-076
keratin accumulating cell5.38e-076
stratified epithelial cell5.38e-076
keratinizing barrier epithelial cell5.38e-076
epithelial fate stem cell5.38e-076
stratified epithelial stem cell5.38e-076
surface ectodermal cell5.38e-076
ecto-epithelial cell7.43e-0734
epithelial cell of tracheobronchial tree7.87e-079
epithelial cell of lower respiratory tract7.87e-079
transitional epithelial cell8.50e-074
urothelial cell8.50e-074
Uber Anatomy
Ontology termp-valuen
endoderm-derived structure1.36e-18160
endoderm1.36e-18160
presumptive endoderm1.36e-18160
respiratory system5.88e-1774
oral opening1.40e-1622
orifice1.56e-1536
mouth8.83e-1429
stomodeum8.83e-1429
anterior region of body1.06e-1362
craniocervical region1.06e-1362
surface structure1.72e-1399
digestive system1.06e-12145
digestive tract1.06e-12145
primitive gut1.06e-12145
neck8.13e-1110
head4.88e-1056
subdivision of head2.21e-0949
respiratory tract5.35e-0954
subdivision of digestive tract1.37e-08118
urothelium1.37e-085
lower respiratory tract epithelium2.36e-083
epithelium of bronchus2.36e-083
gland of gut2.44e-0810
mucosa3.23e-0820
mouth mucosa3.45e-0813
gingival epithelium4.73e-083
pharynx9.46e-0811
foregut2.80e-0787
tracheobronchial tree3.03e-0715
lower respiratory tract3.03e-0715
transitional epithelium3.84e-076
saliva-secreting gland5.55e-076
gland of oral region5.55e-076
gland of foregut5.55e-076
oral gland5.55e-076
oral cavity5.55e-076
Disease
Ontology termp-valuen
squamous cell carcinoma1.12e-0714


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)
MA0003.10.401049
MA0004.10.826076
MA0006.10.639288
MA0007.10.804807
MA0009.11.3275
MA0014.10.118426
MA0017.11.64148
MA0019.10.990656
MA0024.11.21731
MA0025.11.46617
MA0027.12.95767
MA0028.10.658629
MA0029.11.23771
MA0030.11.22561
MA0031.11.15713
MA0038.10.94098
MA0040.11.24388
MA0041.10.847069
MA0042.10.810843
MA0043.11.32783
MA0046.11.31611
MA0048.10.341392
MA0050.10.81185
MA0051.10.936307
MA0052.11.24796
MA0055.11.06172
MA0056.10
MA0057.10.333427
MA0058.10.716037
MA0059.10.714521
MA0060.10.492218
MA0061.10.456531
MA0063.10
MA0066.10.941452
MA0067.11.65513
MA0068.10.405474
MA0069.11.31207
MA0070.11.30033
MA0071.10.897953
MA0072.11.29561
MA0073.12.26659
MA0074.12.15449
MA0076.10.734647
MA0077.11.28751
MA0078.11.04495
MA0081.10.714712
MA0083.11.33535
MA0084.11.84562
MA0087.11.29304
MA0088.10.715722
MA0089.10
MA0090.10.751469
MA0091.10.829044
MA0092.10.785956
MA0093.10.642957
MA0095.10
MA0098.10
MA0100.10.956299
MA0101.10.646932
MA0103.10.628063
MA0105.10.31555
MA0106.10.986396
MA0107.10.556367
MA0108.21.15387
MA0109.10
MA0111.10.767139
MA0113.11.00436
MA0114.11.35563
MA0115.11.57693
MA0116.10.560723
MA0117.11.36676
MA0119.10.695578
MA0122.11.39371
MA0124.11.53432
MA0125.11.44766
MA0130.10
MA0131.11.06461
MA0132.10
MA0133.10
MA0135.11.35921
MA0136.10.948776
MA0139.10.440097
MA0140.10.894983
MA0141.10.712476
MA0142.11.12317
MA0143.11.00455
MA0144.10.531867
MA0145.10.752137
MA0146.10.348055
MA0147.10.565108
MA0148.10.854239
MA0149.10.884158
MA0062.20.449458
MA0035.20.894194
MA0039.22.15877
MA0138.21.04628
MA0002.21.20011
MA0137.20.666381
MA0104.20.491226
MA0047.20.973066
MA0112.21.34467
MA0065.21.39232
MA0150.10.744617
MA0151.10
MA0152.10.902317
MA0153.11.43021
MA0154.10.838867
MA0155.10.711948
MA0156.10.669101
MA0157.11.09377
MA0158.10
MA0159.10.565904
MA0160.10.871361
MA0161.10
MA0162.10.455568
MA0163.10.776149
MA0164.11.01792
MA0080.20.643061
MA0018.20.987913
MA0099.20.902716
MA0079.20.181755
MA0102.21.88331
MA0258.11.29138
MA0259.10.575594
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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