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{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=0,0

Latest revision as of 11:38, 17 September 2013


Full id: C1136_Gingival_Mallassezderived_Keratinocyte_Sebocyte_Prostate_keratoacanthoma_Urothelial



Phase1 CAGE Peaks

Hg19::chr11:13073062..13073067,+p@chr11:13073062..13073067
+
Hg19::chr20:11137813..11137835,+p@chr20:11137813..11137835
+
Hg19::chr4:143470541..143470551,+p@chr4:143470541..143470551
+
Hg19::chr7:40883504..40883519,+p@chr7:40883504..40883519
+
Hg19::chr7:40883521..40883532,+p@chr7:40883521..40883532
+
Hg19::chr7:40883542..40883550,+p@chr7:40883542..40883550
+
Hg19::chr7:40883552..40883571,+p@chr7:40883552..40883571
+


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

No GOStat results

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
general ecto-epithelial cell8.28e-4414
epithelial cell of alimentary canal3.01e-2420
endo-epithelial cell1.06e-2242
gingival epithelial cell9.78e-213
acinar cell1.83e-205
epithelial cell of Malassez2.00e-203
epithelial cell1.36e-18253
endodermal cell1.97e-1858
epidermal cell1.43e-179
stratified squamous epithelial cell4.32e-176
keratin accumulating cell4.32e-176
stratified epithelial cell4.32e-176
keratinizing barrier epithelial cell4.32e-176
protein secreting cell4.32e-176
epithelial fate stem cell4.32e-176
stratified epithelial stem cell4.32e-176
surface ectodermal cell4.32e-176
ecto-epithelial cell5.07e-1734
mammary gland epithelial cell1.89e-144
sebum secreting cell5.88e-142
epithelial cell of sweat gland5.88e-142
epithelial cell of skin gland5.88e-142
acinar cell of sebaceous gland5.88e-142
corneal epithelial cell2.39e-132
keratinocyte5.84e-125
squamous epithelial cell6.77e-1263
glandular epithelial cell1.89e-119
embryonic cell1.04e-09250
acinar cell of salivary gland3.39e-093
ectodermal cell2.12e-0872
buccal mucosa cell1.07e-071
endothelial cell of viscerocranial mucosa1.07e-071
keratinized cell of the oral mucosa1.07e-071
epithelial cell of esophagus1.30e-071
transitional epithelial cell2.89e-074
urothelial cell2.89e-074
Uber Anatomy
Ontology termp-valuen
surface structure1.24e-2199
gingival epithelium9.78e-213
mouth mucosa2.49e-1713
head1.20e-1656
jaw skeleton1.85e-154
splanchnocranium1.85e-154
anterior region of body8.64e-1562
craniocervical region8.64e-1562
mammary gland1.89e-144
mammary bud1.89e-144
mammary ridge1.89e-144
mammary placode1.89e-144
skin gland5.88e-142
epidermis gland5.88e-142
gland of integumental system5.88e-142
sebaceous gland5.88e-142
skin sebaceous gland5.88e-142
sweat gland5.88e-142
sweat gland placode5.88e-142
sebaceous gland placode5.88e-142
oral opening2.35e-1322
mouth6.86e-1329
stomodeum6.86e-1329
primary subdivision of cranial skeletal system1.80e-125
subdivision of head3.81e-1149
mucosa4.48e-1120
protuberance1.80e-106
pharyngeal arch1.80e-106
embryonic head1.80e-106
skin epidermis1.83e-1015
outer epithelium1.83e-1015
enveloping layer of ectoderm1.83e-1015
orifice3.52e-1036
exocrine gland4.87e-0931
ectodermal placode4.87e-0931
exocrine system4.87e-0931
respiratory system3.34e-0874
epithelium of mucosa4.48e-088
gingiva4.48e-088
ectoderm-derived structure5.03e-08171
ectoderm5.03e-08171
presumptive ectoderm5.03e-08171
ecto-epithelium1.15e-07104
external ectoderm1.80e-078
cornea4.20e-074
eye surface4.20e-074
optic eminence4.20e-074
corneal primordium4.20e-074
mucosa of oral region4.91e-074
respiratory system mucosa4.91e-074
endoderm-derived structure9.97e-07160
endoderm9.97e-07160
presumptive endoderm9.97e-07160
Disease
Ontology termp-valuen
skin squamous cell carcinoma7.76e-081
keratoacanthoma7.76e-081
squamous cell carcinoma4.47e-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)
MA0003.10.213534
MA0004.10.502801
MA0006.10.341337
MA0007.10.483857
MA0009.10.973289
MA0014.10.0156227
MA0017.10.991615
MA0019.10.652951
MA0024.10.867125
MA0025.11.10816
MA0027.12.59001
MA0028.10.35747
MA0029.10.886702
MA0030.10.875089
MA0031.10.809638
MA0038.10.60704
MA0040.10.892629
MA0041.10.521615
MA0042.10.48922
MA0043.10.973609
MA0046.10.962263
MA0048.10.382278
MA0050.10.490116
MA0051.10.602745
MA0052.10.896548
MA0055.11.01052
MA0056.10
MA0057.10.115382
MA0058.10.406232
MA0059.10.404929
MA0060.10.224688
MA0061.10.198335
MA0063.10
MA0066.14.91822
MA0067.11.29359
MA0068.10.162298
MA0069.10.958358
MA0070.10.947018
MA0071.12.38293
MA0072.10.942461
MA0073.10.0022316
MA0074.10.60198
MA0076.10.422297
MA0077.10.934645
MA0078.10.703614
MA0081.11.84202
MA0083.10.980893
MA0084.11.48179
MA0087.10.939982
MA0088.10.538456
MA0089.10
MA0090.11.11391
MA0091.10.505453
MA0092.10.467172
MA0093.10.344385
MA0095.10
MA0098.10
MA0100.10.621149
MA0101.10.347695
MA0103.10.332048
MA0105.10.104569
MA0106.17.96372
MA0107.10.274127
MA0108.20.806528
MA0109.10
MA0111.10.45062
MA0113.10.665691
MA0114.10.741402
MA0115.11.21667
MA0116.10.277571
MA0117.11.01134
MA0119.10.388712
MA0122.11.03753
MA0124.11.17486
MA0125.11.0901
MA0130.10
MA0131.10.722072
MA0132.10
MA0133.10
MA0135.11.00402
MA0136.10.614215
MA0139.10.186511
MA0140.10.564957
MA0141.10.403171
MA0142.10.777365
MA0143.10.66587
MA0144.10.254954
MA0145.10.980834
MA0146.10.0127148
MA0147.10.281049
MA0148.10.528066
MA0149.10.555119
MA0062.20.193221
MA0035.20.564239
MA0039.20.128723
MA0138.20.704862
MA0002.20.213296
MA0137.20.36398
MA0104.20.223944
MA0047.20.636643
MA0112.21.95102
MA0065.20.282161
MA0150.10.430951
MA0151.10
MA0152.10.571637
MA0153.11.07307
MA0154.10.102476
MA0155.10.071478
MA0156.10.36627
MA0157.10.749547
MA0158.10
MA0159.10.281681
MA0160.10.543522
MA0161.10
MA0162.10.25944
MA0163.10.0167306
MA0164.10.678332
MA0080.20.344472
MA0018.20.650405
MA0099.20.572
MA0079.20.00447823
MA0102.21.51913
MA0258.11.97124
MA0259.10.289405
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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