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{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=0,0,

Latest revision as of 11:31, 17 September 2013


Full id: C820_cervical_tongue_esophagus_throat_tonsil_oral_uterus



Phase1 CAGE Peaks

Hg19::chr12:57328113..57328161,-p2@SDR9C7
Hg19::chr17:39661947..39661969,-p2@KRT13
Hg19::chr18:61253887..61253899,+p7@SERPINB13
Hg19::chr18:61254400..61254410,+p8@SERPINB13
Hg19::chr18:61254548..61254562,+p3@SERPINB13
Hg19::chr18:61254570..61254585,+p2@SERPINB13
Hg19::chr18:61254622..61254641,+p1@SERPINB13
Hg19::chr18:61265362..61265366,+p@chr18:61265362..61265366
+
Hg19::chr19:51569044..51569051,-p@chr19:51569044..51569051
-
Hg19::chr4:68995571..68995593,-p1@TMPRSS11F


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>

Uber Anatomy
Ontology termp-valuen
oral opening1.02e-2322
respiratory system5.31e-2274
neck3.36e-2010
mouth4.22e-2029
stomodeum4.22e-2029
anterior region of body7.08e-1962
craniocervical region7.08e-1962
orifice9.47e-1836
mouth mucosa2.63e-1513
mucosa6.72e-1520
pharynx1.89e-1411
subdivision of head3.53e-1449
mucosa of oral region6.24e-144
respiratory system mucosa6.24e-144
surface structure1.11e-1399
head1.44e-1356
endoderm-derived structure2.20e-13160
endoderm2.20e-13160
presumptive endoderm2.20e-13160
respiratory tract4.68e-1254
chordate pharynx7.05e-1210
pharyngeal region of foregut7.05e-1210
tongue2.05e-113
gustatory system2.05e-113
future tongue2.05e-113
gingival epithelium1.59e-103
digestive system4.24e-09145
digestive tract4.24e-09145
primitive gut4.24e-09145
open tracheal system trachea2.82e-082
trachea4.07e-087
respiratory airway4.07e-087
gland of gut5.48e-0810
throat5.50e-082
Disease
Ontology termp-valuen
squamous cell carcinoma6.61e-2314


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)
MA0003.10.000221536
MA0004.10.380329
MA0006.10.665232
MA0007.10.363007
MA0009.10.828613
MA0014.10.0036779
MA0017.10.270554
MA0019.10.520264
MA0024.10.725404
MA0025.10.960689
MA0027.12.43535
MA0028.10.25013
MA0029.10.744375
MA0030.10.733118
MA0031.10.669876
MA0038.10.477043
MA0040.10.750125
MA0041.10.397617
MA0042.10.367902
MA0043.10.828925
MA0046.10.817858
MA0048.10.220931
MA0050.10.965046
MA0051.10.473017
MA0052.10.753928
MA0055.10.0662377
MA0056.10
MA0057.10.211138
MA0058.10.293055
MA0059.10.291897
MA0060.10.138988
MA0061.10.118318
MA0063.10
MA0066.10.477449
MA0067.11.1435
MA0068.14.21299
MA0069.10.814052
MA0070.10.803003
MA0071.10.440254
MA0072.10.798564
MA0073.10.0447366
MA0074.10.4723
MA0076.10.307383
MA0077.10.790956
MA0078.10.568317
MA0081.10.292043
MA0083.10.836033
MA0084.11.32998
MA0087.10.79615
MA0088.10.0309101
MA0089.10
MA0090.10.857892
MA0091.10.382762
MA0092.10.347826
MA0093.10.238771
MA0095.10
MA0098.10
MA0100.10.49029
MA0101.10.678051
MA0103.10.646502
MA0105.10.0508589
MA0106.10.516528
MA0107.10.179177
MA0108.20.666881
MA0109.10
MA0111.10.33284
MA0113.10.532314
MA0114.10.174997
MA0115.11.06753
MA0116.11.62509
MA0117.10.865782
MA0119.10.277531
MA0122.10.891407
MA0124.11.0263
MA0125.10.942948
MA0130.10
MA0131.10.585907
MA0132.10
MA0133.10
MA0135.10.858623
MA0136.10.483775
MA0139.10.109245
MA0140.10.437738
MA0141.10.290336
MA0142.10.638837
MA0143.10.532484
MA0144.11.51733
MA0145.10.0359093
MA0146.10.0169564
MA0147.10.184931
MA0148.10.403564
MA0149.10.428597
MA0062.20.114378
MA0035.20.437071
MA0039.20.360905
MA0138.20.569505
MA0002.20.129981
MA0137.20.255808
MA0104.20.138396
MA0047.20.504873
MA0112.20.0329985
MA0065.20.147044
MA0150.11.52802
MA0151.10
MA0152.11.12912
MA0153.10.926242
MA0154.10.0494985
MA0155.10.545933
MA0156.10.257809
MA0157.10.612166
MA0158.10
MA0159.10.544949
MA0160.10.417847
MA0161.10
MA0162.10.00711618
MA0163.10.00405048
MA0164.10.544294
MA0080.20.238846
MA0018.20.517858
MA0099.21.12985
MA0079.20.000284498
MA0102.21.36707
MA0258.10.155735
MA0259.10.560522
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
STAT3#677444.20778599886170.01071331240583090.0395478451276888



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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