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{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=0,0

Latest revision as of 11:52, 17 September 2013


Full id: C1778_tongue_Corneal_Urothelial_salivary_Esophageal_Sebocyte_Keratinocyte



Phase1 CAGE Peaks

Hg19::chr17:39767475..39767486,-p@chr17:39767475..39767486
-
Hg19::chr17:39768786..39768828,-p2@KRT16
Hg19::chr17:39769009..39769026,-p1@KRT16
Hg19::chr1:153003671..153003687,+p1@SPRR1B
Hg19::chr1:153005015..153005047,+p3@SPRR1B


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:0008544epidermis development0.000458597222349455
GO:0007398ectoderm development0.000458597222349455
GO:0045111intermediate filament cytoskeleton0.000600703872260292
GO:0005882intermediate filament0.000600703872260292
GO:0009888tissue development0.000803422474373953
GO:0044430cytoskeletal part0.00607856862473792
GO:0048513organ development0.00802457504051665
GO:0001533cornified envelope0.00802457504051665
GO:0018149peptide cross-linking0.00802457504051665
GO:0005856cytoskeleton0.00802457504051665
GO:0030216keratinocyte differentiation0.00802457504051665
GO:0048731system development0.00859968523366381
GO:0031424keratinization0.00859968523366381
GO:0009913epidermal cell differentiation0.0102953235096531
GO:0048730epidermis morphogenesis0.0107846238557537
GO:0048856anatomical structure development0.0108800945402962
GO:0048729tissue morphogenesis0.012453986215909
GO:0007275multicellular organismal development0.0127161911645875
GO:0005200structural constituent of cytoskeleton0.0131524584277955
GO:0030674protein binding, bridging0.0133756411171839
GO:0043232intracellular non-membrane-bound organelle0.0167855209032985
GO:0043228non-membrane-bound organelle0.0167855209032985
GO:0032502developmental process0.0210957208770382
GO:0032501multicellular organismal process0.0263631339504596
GO:0044446intracellular organelle part0.028415947659475
GO:0044422organelle part0.028415947659475



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 cell1.23e-3142
endodermal cell4.60e-2158
respiratory epithelial cell1.70e-1913
epithelial cell of alimentary canal2.28e-1720
general ecto-epithelial cell1.34e-1514
acinar cell4.78e-155
epithelial cell6.19e-15253
protein secreting cell1.82e-126
epithelial cell of tracheobronchial tree7.82e-119
epithelial cell of lower respiratory tract7.82e-119
ecto-epithelial cell9.21e-1034
acinar cell of salivary gland1.09e-093
bronchial epithelial cell1.16e-093
gingival epithelial cell1.68e-093
duct epithelial cell1.10e-083
branched duct epithelial cell1.10e-083
tracheal epithelial cell1.10e-083
tracheoblast1.10e-083
epidermal cell3.02e-089
glandular epithelial cell3.73e-089
stratified squamous epithelial cell4.91e-086
keratin accumulating cell4.91e-086
stratified epithelial cell4.91e-086
keratinizing barrier epithelial cell4.91e-086
epithelial fate stem cell4.91e-086
stratified epithelial stem cell4.91e-086
surface ectodermal cell4.91e-086
corneal epithelial cell3.82e-072
transitional epithelial cell4.25e-074
urothelial cell4.25e-074
sebum secreting cell4.82e-072
epithelial cell of sweat gland4.82e-072
epithelial cell of skin gland4.82e-072
acinar cell of sebaceous gland4.82e-072
Uber Anatomy
Ontology termp-valuen
respiratory system4.04e-1874
oral opening5.25e-1622
endoderm-derived structure1.06e-15160
endoderm1.06e-15160
presumptive endoderm1.06e-15160
orifice7.40e-1436
surface structure9.80e-1499
mouth1.83e-1329
stomodeum1.83e-1329
respiratory tract1.05e-1154
anterior region of body2.16e-1162
craniocervical region2.16e-1162
tracheobronchial tree2.07e-1015
lower respiratory tract2.07e-1015
head2.61e-1056
lower respiratory tract epithelium1.16e-093
epithelium of bronchus1.16e-093
gingival epithelium1.68e-093
subdivision of head2.02e-0949
tongue2.05e-093
gustatory system2.05e-093
future tongue2.05e-093
mouth mucosa3.40e-0913
trachea4.23e-097
respiratory airway4.23e-097
digestive system5.30e-09145
digestive tract5.30e-09145
primitive gut5.30e-09145
segment of respiratory tract4.52e-0847
foregut1.16e-0787
thoracic cavity element1.78e-0734
thoracic cavity1.78e-0734
mucosa2.60e-0720
thoracic segment organ3.38e-0735
skin gland4.82e-072
epidermis gland4.82e-072
gland of integumental system4.82e-072
sebaceous gland4.82e-072
skin sebaceous gland4.82e-072
sweat gland4.82e-072
sweat gland placode4.82e-072
sebaceous gland placode4.82e-072
Disease
Ontology termp-valuen
squamous cell carcinoma5.66e-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)
MA0003.10.280184
MA0004.10.626788
MA0006.10.452993
MA0007.10.606704
MA0009.11.11255
MA0014.10.0418333
MA0017.12.14806
MA0019.10.784036
MA0024.11.00439
MA0025.11.24931
MA0027.12.73598
MA0028.10.470679
MA0029.11.02437
MA0030.11.01252
MA0031.10.945567
MA0038.10.736268
MA0040.11.03042
MA0041.10.64667
MA0042.10.612397
MA0043.11.11288
MA0046.11.10134
MA0048.10.569896
MA0050.10.613347
MA0051.10.731787
MA0052.11.03442
MA0055.14.0988
MA0056.10
MA0057.10.189508
MA0058.10.523638
MA0059.10.522232
MA0060.10.321781
MA0061.10.291022
MA0063.10
MA0066.10.736721
MA0067.11.43651
MA0068.10.247962
MA0069.11.09737
MA0070.11.08584
MA0071.10.695094
MA0072.11.0812
MA0073.10.215829
MA0074.10.730989
MA0076.11.33654
MA0077.11.07324
MA0078.10.836493
MA0081.10.522409
MA0083.11.12028
MA0084.11.62584
MA0087.11.07867
MA0088.10.412364
MA0089.10
MA0090.10.556637
MA0091.10.629594
MA0092.10.588959
MA0093.10.456342
MA0095.10
MA0098.10
MA0100.10.750974
MA0101.10.459973
MA0103.11.96988
MA0105.10.175503
MA0106.10.779931
MA0107.10.378225
MA0108.20.94238
MA0109.10
MA0111.10.5713
MA0113.10.797251
MA0114.10.372523
MA0115.11.35895
MA0116.14.68138
MA0117.11.1512
MA0119.11.25946
MA0122.11.17777
MA0124.11.31673
MA0125.11.23103
MA0130.10
MA0131.10.855546
MA0132.10
MA0133.10
MA0135.11.14377
MA0136.10.743749
MA0139.10.277033
MA0140.10.692258
MA0141.11.29278
MA0142.10.912455
MA0143.10.797437
MA0144.10.938075
MA0145.11.39943
MA0146.10.0359558
MA0147.10.386018
MA0148.10.653474
MA0149.10.681935
MA0062.20.284987
MA0035.20.691506
MA0039.20.15493
MA0138.20.837782
MA0002.20.30855
MA0137.21.20193
MA0104.20.320919
MA0047.20.767096
MA0112.20.425004
MA0065.20.449243
MA0150.10.550239
MA0151.10
MA0152.10.69926
MA0153.11.21379
MA0154.10.514087
MA0155.10.813062
MA0156.10.480289
MA0157.10.883854
MA0158.10
MA0159.10.386729
MA0160.10.669748
MA0161.10
MA0162.10.21472
MA0163.10.680296
MA0164.10.810347
MA0080.20.456437
MA0018.20.781393
MA0099.20.699641
MA0079.20.0198381
MA0102.21.66336
MA0258.10.345771
MA0259.10.395396
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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