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

Latest revision as of 11:26, 17 September 2013


Full id: C594_Keratinocyte_Placental_amniotic_Esophageal_tongue_Corneal_Prostate



Phase1 CAGE Peaks

Hg19::chr12:52867616..52867640,-p2@KRT6C
Hg19::chr12:52881014..52881084,-p@chr12:52881014..52881084
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Hg19::chr12:52881094..52881129,-p@chr12:52881094..52881129
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Hg19::chr12:52881151..52881162,-p@chr12:52881151..52881162
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Hg19::chr12:52881340..52881386,-p@chr12:52881340..52881386
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Hg19::chr12:52881401..52881421,-p@chr12:52881401..52881421
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Hg19::chr12:52881422..52881438,-p@chr12:52881422..52881438
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Hg19::chr12:52881440..52881469,-p@chr12:52881440..52881469
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Hg19::chr12:52881475..52881528,-p@chr12:52881475..52881528
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Hg19::chr12:52884399..52884420,-p7@KRT6A
Hg19::chr12:52885340..52885349,-p10@KRT6A
Hg19::chr12:52885355..52885376,-p2@KRT6A
Hg19::chr12:52886485..52886506,-p6@KRT6A
Hg19::chr12:52886515..52886548,-p4@KRT6A
Hg19::chr12:52887034..52887049,-p1@KRT6A


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:0045111intermediate filament cytoskeleton0.00086501357605482
GO:0005882intermediate filament0.00086501357605482
GO:0044430cytoskeletal part0.00875313881962261
GO:0005856cytoskeleton0.0156475434545066
GO:0005200structural constituent of cytoskeleton0.0359851262584485
GO:0043232intracellular non-membrane-bound organelle0.037983235872607
GO:0043228non-membrane-bound organelle0.037983235872607
GO:0007398ectoderm development0.0385963645451909
GO:0008284positive regulation of cell proliferation0.0483587763804884
GO:0044446intracellular organelle part0.0483587763804884
GO:0044422organelle part0.0483587763804884



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 cell3.00e-3242
respiratory epithelial cell4.93e-2213
endodermal cell1.31e-2158
epithelial cell1.27e-20253
general ecto-epithelial cell5.19e-2014
epithelial cell of alimentary canal1.20e-1520
acinar cell6.02e-155
extraembryonic cell3.08e-1419
protein secreting cell2.12e-126
transitional epithelial cell3.79e-124
urothelial cell3.79e-124
epithelial cell of tracheobronchial tree5.02e-129
epithelial cell of lower respiratory tract5.02e-129
bronchial epithelial cell1.55e-103
gingival epithelial cell1.70e-103
ecto-epithelial cell2.96e-1034
chorionic membrane mesenchymal stem cell7.18e-103
placental epithelial cell7.63e-103
duct epithelial cell1.31e-093
branched duct epithelial cell1.31e-093
tracheal epithelial cell1.31e-093
tracheoblast1.31e-093
acinar cell of salivary gland1.66e-093
epithelial cell of Malassez2.03e-093
epidermal cell1.90e-089
stratified squamous epithelial cell2.13e-086
keratin accumulating cell2.13e-086
stratified epithelial cell2.13e-086
keratinizing barrier epithelial cell2.13e-086
epithelial fate stem cell2.13e-086
stratified epithelial stem cell2.13e-086
surface ectodermal cell2.13e-086
glandular epithelial cell3.81e-089
corneal epithelial cell2.23e-072
mammary gland epithelial cell2.39e-074
sebum secreting cell4.01e-072
epithelial cell of sweat gland4.01e-072
epithelial cell of skin gland4.01e-072
acinar cell of sebaceous gland4.01e-072
squamous epithelial cell7.69e-0763
Uber Anatomy
Ontology termp-valuen
extraembryonic membrane5.18e-2414
membranous layer5.18e-2414
chorion3.21e-207
oral opening9.07e-1722
endoderm-derived structure6.94e-16160
endoderm6.94e-16160
presumptive endoderm6.94e-16160
respiratory system2.02e-1574
mouth3.03e-1429
stomodeum3.03e-1429
surface structure1.24e-1399
orifice5.66e-1336
extraembryonic structure5.74e-1324
head1.29e-1256
anterior region of body2.40e-1262
craniocervical region2.40e-1262
placenta4.52e-124
allantois4.52e-124
organ component layer2.10e-1166
lower respiratory tract epithelium1.55e-103
epithelium of bronchus1.55e-103
gingival epithelium1.70e-103
mouth mucosa3.58e-1013
subdivision of head4.51e-1049
acellular anatomical structure7.18e-103
egg chorion7.18e-103
urothelium1.00e-095
tracheobronchial tree4.13e-0915
lower respiratory tract4.13e-0915
transitional epithelium4.18e-086
mucosa4.91e-0820
respiratory tract8.79e-0854
mammary gland2.39e-074
mammary bud2.39e-074
mammary ridge2.39e-074
mammary placode2.39e-074
amnion2.85e-077
jaw skeleton3.69e-074
splanchnocranium3.69e-074
skin gland4.01e-072
epidermis gland4.01e-072
gland of integumental system4.01e-072
sebaceous gland4.01e-072
skin sebaceous gland4.01e-072
sweat gland4.01e-072
sweat gland placode4.01e-072
sebaceous gland placode4.01e-072
trachea7.32e-077
respiratory airway7.32e-077
Disease
Ontology termp-valuen
squamous cell carcinoma1.49e-0814


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)
MA0003.10.0132214
MA0004.10.256222
MA0006.10.137644
MA0007.10.241375
MA0009.11.6063
MA0014.10.0115261
MA0017.10.95676
MA0019.10.38027
MA0024.10.570967
MA0025.10.796882
MA0027.12.25966
MA0028.10.148561
MA0029.11.43794
MA0030.10.578277
MA0031.10.518602
MA0038.10.34128
MA0040.10.594421
MA0041.10.27117
MA0042.10.245557
MA0043.10.669676
MA0046.10.659066
MA0048.10.23222
MA0050.10.246257
MA0051.10.337676
MA0052.10.598036
MA0055.10.229721
MA0056.10
MA0057.10.0196406
MA0058.10.182945
MA0059.10.182001
MA0060.10.0671843
MA0061.10.0537738
MA0063.10
MA0066.12.45455
MA0067.10.975379
MA0068.10.0373092
MA0069.10.655419
MA0070.10.644843
MA0071.10.308534
MA0072.10.640598
MA0073.10.000193423
MA0074.10.337035
MA0076.10.194691
MA0077.10.633326
MA0078.10.424186
MA0081.11.02736
MA0083.10.676499
MA0084.11.15904
MA0087.10.63829
MA0088.10.00789138
MA0089.10
MA0090.13.28205
MA0091.10.258318
MA0092.10.647316
MA0093.10.139688
MA0095.10
MA0098.10
MA0100.10.353174
MA0101.10.141917
MA0103.10.131472
MA0105.10.074747
MA0106.10.37688
MA0107.10.0950422
MA0108.20.515791
MA0109.10
MA0111.10.215855
MA0113.10.39123
MA0114.10.636237
MA0115.10.900969
MA0116.10.320986
MA0117.10.705104
MA0119.10.170362
MA0122.10.729811
MA0124.10.860724
MA0125.10.779672
MA0130.10
MA0131.10.440395
MA0132.10
MA0133.10
MA0135.10.698212
MA0136.10.347318
MA0139.10.181369
MA0140.10.30631
MA0141.10.533493
MA0142.10.489543
MA0143.10.391385
MA0144.12.67151
MA0145.10.7339
MA0146.10.197185
MA0147.10.0991954
MA0148.10.276339
MA0149.10.298252
MA0062.20.0512998
MA0035.20.305721
MA0039.20.00240387
MA0138.22.85059
MA0002.20.0612545
MA0137.20.908044
MA0104.20.0667907
MA0047.20.959769
MA0112.20.00868143
MA0065.20.140846
MA0150.10.201098
MA0151.10
MA0152.10.311809
MA0153.10.763487
MA0154.10.0723831
MA0155.10.0403226
MA0156.10.154615
MA0157.10.46471
MA0158.10
MA0159.10.0995776
MA0160.10.786431
MA0161.10
MA0162.10.0065085
MA0163.10.0128736
MA0164.10.402162
MA0080.20.432036
MA0018.20.378086
MA0099.20.312108
MA0079.25.17282e-08
MA0102.21.1957
MA0258.10.569952
MA0259.10.104286
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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