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{{Coexpression_clusters
{
|full_id=C665_amniotic_esophagus_tongue_Corneal_tonsil_salivary_Urothelial
|

Latest revision as of 11:28, 17 September 2013


Full id: C665_amniotic_esophagus_tongue_Corneal_tonsil_salivary_Urothelial



Phase1 CAGE Peaks

Hg19::chr17:74023373..74023426,-p1@EVPL
Hg19::chr19:43965722..43965760,+p1@CU691667
Hg19::chr19:43969748..43969768,-p1@LYPD3
Hg19::chr19:43969782..43969794,-p3@LYPD3
Hg19::chr19:43969796..43969813,-p2@LYPD3
Hg19::chr19:43969827..43969834,-p4@LYPD3
Hg19::chr19:49055390..49055410,+p2@SULT2B1
Hg19::chr19:49055416..49055451,+p1@SULT2B1
Hg19::chr1:156254091..156254143,+p2@TMEM79
Hg19::chr1:201368653..201368705,-p2@LAD1
Hg19::chr1:26680570..26680632,-p1@AIM1L
Hg19::chr7:1600419..1600429,-p11@TMEM184A
Hg19::chr7:1600433..1600475,-p2@TMEM184A


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:0050294steroid sulfotransferase activity0.00700576945720005
GO:0004027alcohol sulfotransferase activity0.00700576945720005



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
endoderm-derived structure7.96e-20160
endoderm7.96e-20160
presumptive endoderm7.96e-20160
respiratory system7.46e-1774
orifice4.65e-1536
extraembryonic membrane4.02e-1314
membranous layer4.02e-1314
digestive system1.91e-12145
digestive tract1.91e-12145
primitive gut1.91e-12145
oral opening8.82e-1222
respiratory tract1.43e-1054
anatomical space5.03e-1095
subdivision of digestive tract5.85e-10118
mouth2.91e-0929
stomodeum2.91e-0929
chorion3.54e-097
surface structure3.95e-0999
thoracic cavity element5.45e-0934
thoracic cavity5.45e-0934
epithelial bud5.62e-0937
tracheobronchial tree5.95e-0915
lower respiratory tract5.95e-0915
anterior region of body7.23e-0962
craniocervical region7.23e-0962
thoracic segment organ1.35e-0835
foregut2.33e-0887
endo-epithelium3.50e-0882
urothelium4.07e-085
epithelial fold4.35e-0847
immaterial anatomical entity4.76e-08117
organism subdivision9.84e-08264
segment of respiratory tract1.10e-0747
thoracic segment of trunk1.30e-0752
extraembryonic structure1.36e-0724
neck2.05e-0710
renal system2.29e-0748
female organism2.80e-0741
respiratory system epithelium4.44e-0728
head5.30e-0756
reproductive structure5.65e-0759
reproductive system5.65e-0759
urinary system structure8.60e-0747
Disease
Ontology termp-valuen
squamous cell carcinoma1.29e-1314
carcinoma1.98e-10106
thoracic cancer7.14e-074
breast cancer7.14e-074


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)
MA0003.11.11833
MA0004.10.806989
MA0006.10.169524
MA0007.10.771118
MA0009.10.724811
MA0014.10.756964
MA0017.10.57848
MA0019.10.428118
MA0024.10.6245
MA0025.10.854131
MA0027.12.32165
MA0028.10.535609
MA0029.10.642879
MA0030.10.63197
MA0031.10.570886
MA0038.10.387473
MA0040.10.648455
MA0041.10.313738
MA0042.10.286538
MA0043.10.725115
MA0046.10.714324
MA0048.11.73714
MA0050.10.287284
MA0051.10.383704
MA0052.10.652145
MA0055.10.531463
MA0056.10
MA0057.10.542827
MA0058.10.219229
MA0059.10.623149
MA0060.10.0892161
MA0061.10.255087
MA0063.10
MA0066.10.387854
MA0067.11.03434
MA0068.10.760324
MA0069.10.710614
MA0070.10.69985
MA0071.10.35315
MA0072.10.695528
MA0073.16.36752
MA0074.10.383033
MA0076.10.231962
MA0077.10.688123
MA0078.10.473657
MA0081.10.218332
MA0083.10.732051
MA0084.11.21913
MA0087.10.693179
MA0088.10.854057
MA0089.10
MA0090.11.26632
MA0091.10.30011
MA0092.10.268302
MA0093.10.511707
MA0095.10
MA0098.10
MA0100.10.399896
MA0101.10.17426
MA0103.12.16524
MA0105.12.03557
MA0106.11.0872
MA0107.10.121572
MA0108.20.568002
MA0109.10
MA0111.10.254772
MA0113.10.439505
MA0114.11.80492
MA0115.10.959312
MA0116.11.27593
MA0117.11.79656
MA0119.10.205526
MA0122.10.786181
MA0124.10.918678
MA0125.10.83671
MA0130.10
MA0131.10.490408
MA0132.10
MA0133.10
MA0135.10.754112
MA0136.10.393782
MA0139.10.235473
MA0140.10.350813
MA0141.10.216821
MA0142.10.541045
MA0143.10.439666
MA0144.10.35188
MA0145.12.16533
MA0146.10.886077
MA0147.10.793354
MA0148.10.319209
MA0149.10.342334
MA0062.20.0702147
MA0035.20.350194
MA0039.24.75477
MA0138.20.474787
MA0002.20.280231
MA0137.20.186529
MA0104.21.03881
MA0047.20.413608
MA0112.21.23793
MA0065.22.70536
MA0150.10.238884
MA0151.10
MA0152.10.356591
MA0153.10.820317
MA0154.12.00778
MA0155.10.560882
MA0156.10.551743
MA0157.10.515488
MA0158.10
MA0159.10.126752
MA0160.10.332385
MA0161.10
MA0162.10.0132346
MA0163.11.33571
MA0164.10.450848
MA0080.20.511865
MA0018.20.425847
MA0099.20.356906
MA0079.22.67713
MA0102.21.25596
MA0258.10.335505
MA0259.10.818705
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
E2F1#186972.642440346473480.007795016405580970.0320248502569714
MYC#4609124.82056788148562.59727634246585e-081.80237172047037e-06
TFAP2A#702045.082656730167680.006165214423051180.0272545536139277
TFAP2C#702254.157395619177010.004615369219926170.0218021867094789



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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