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{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=0,0

Latest revision as of 11:08, 17 September 2013


Full id: C263_cervical_keratoacanthoma_tongue_skin_esophagus_throat_tonsil



Phase1 CAGE Peaks

Hg19::chr10:62029969..62029974,-p@chr10:62029969..62029974
-
Hg19::chr10:62029985..62029992,-p@chr10:62029985..62029992
-
Hg19::chr10:62030063..62030071,-p@chr10:62030063..62030071
-
Hg19::chr10:62030084..62030091,-p@chr10:62030084..62030091
-
Hg19::chr11:20075386..20075404,+p@chr11:20075386..20075404
+
Hg19::chr11:20075419..20075431,+p@chr11:20075419..20075431
+
Hg19::chr12:52779433..52779437,-p1@KRT84
Hg19::chr12:966066..966072,+p@chr12:966066..966072
+
Hg19::chr12:966094..966103,+p@chr12:966094..966103
+
Hg19::chr13:20805611..20805619,-p6@GJB6
Hg19::chr14:23607321..23607333,-p29@SLC7A8
Hg19::chr17:26833250..26833262,+p2@FOXN1
Hg19::chr17:26833339..26833378,+p1@FOXN1
Hg19::chr17:39150341..39150346,-p2@KRTAP3-3
Hg19::chr17:39150411..39150417,-p1@KRTAP3-3
Hg19::chr17:39659057..39659078,-p3@KRT13
Hg19::chr17:39659081..39659098,-p9@KRT13
Hg19::chr17:39659118..39659129,-p10@KRT13
Hg19::chr17:39659818..39659840,-p@chr17:39659818..39659840
-
Hg19::chr17:39661984..39661995,-p7@KRT13
Hg19::chr17:39662068..39662109,-p12@KRT13
Hg19::chr17:39728303..39728318,-p1@KRT9
Hg19::chr17:72931876..72931881,+p3@OTOP3
Hg19::chr17:7990855..7990862,-p3@ALOX12B
Hg19::chr17:7990883..7990893,-p5@ALOX12B
Hg19::chr17:7990909..7990918,-p6@ALOX12B
Hg19::chr18:45553476..45553478,-p@chr18:45553476..45553478
-
Hg19::chr19:36640447..36640459,+p@chr19:36640447..36640459
+
Hg19::chr19:46753477..46753483,-p@chr19:46753477..46753483
-
Hg19::chr19:46753484..46753496,-p@chr19:46753484..46753496
-
Hg19::chr1:153371709..153371712,-p@chr1:153371709..153371712
-
Hg19::chr1:17767804..17767822,-p@chr1:17767804..17767822
-
Hg19::chr1:90320845..90320886,-p@chr1:90320845..90320886
-
Hg19::chr20:2361545..2361557,+p1@TGM6
Hg19::chr21:31744583..31744589,-p1@KRTAP13-2
Hg19::chr2:165706192..165706200,+p@chr2:165706192..165706200
+
Hg19::chr2:56150507..56150564,-p4@EFEMP1
Hg19::chr3:185016843..185016846,+p@chr3:185016843..185016846
+
Hg19::chr5:134907473..134907482,+p@chr5:134907473..134907482
+
Hg19::chr5:160356310..160356324,-p@chr5:160356310..160356324
-
Hg19::chr5:160356347..160356372,-p@chr5:160356347..160356372
-
Hg19::chr5:160356399..160356409,-p@chr5:160356399..160356409
-
Hg19::chr5:160356414..160356417,-p@chr5:160356414..160356417
-
Hg19::chr5:160356450..160356459,-p@chr5:160356450..160356459
-
Hg19::chr7:101448101..101448113,+p@chr7:101448101..101448113
+
Hg19::chr7:101448176..101448184,+p@chr7:101448176..101448184
+
Hg19::chr7:101448204..101448229,+p@chr7:101448204..101448229
+
Hg19::chr7:101448249..101448254,+p@chr7:101448249..101448254
+
Hg19::chr7:101448277..101448287,+p@chr7:101448277..101448287
+
Hg19::chr9:139090625..139090662,-p@chr9:139090625..139090662
-


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:0005882intermediate filament1.12724880080687e-06
GO:0045111intermediate filament cytoskeleton1.12724880080687e-06
GO:0008544epidermis development7.33232629180967e-06
GO:0007398ectoderm development7.53279374665983e-06
GO:0009888tissue development0.000113812529658966
GO:0044430cytoskeletal part0.000306808810804164
GO:0048513organ development0.000751760056303848
GO:0005856cytoskeleton0.0018540601394571
GO:0048731system development0.00297438690637043
GO:0048856anatomical structure development0.00697556275241885
GO:0005200structural constituent of cytoskeleton0.00697556275241885
GO:0004052arachidonate 12-lipoxygenase activity0.0109894317719929
GO:0007275multicellular organismal development0.0109894317719929
GO:0032501multicellular organismal process0.0139250229803728
GO:0045109intermediate filament organization0.0224745487659294
GO:0043588skin development0.0234652206207304
GO:0043232intracellular non-membrane-bound organelle0.0234652206207304
GO:0043228non-membrane-bound organelle0.0234652206207304
GO:0030280structural constituent of epidermis0.0354574183313179
GO:0032502developmental process0.0384841652726446
GO:0016165lipoxygenase activity0.0384841652726446
GO:0045104intermediate filament cytoskeleton organization and biogenesis0.0403887581209315
GO:0003810protein-glutamine gamma-glutamyltransferase activity0.0403887581209315
GO:0045103intermediate filament-based process0.0403887581209315
GO:0015804neutral amino acid transport0.0403887581209315
GO:0015175neutral amino acid transmembrane transporter activity0.0439991467351504
GO:0042605peptide antigen binding0.0448546158351321
GO:0009887organ morphogenesis0.0475044895154243
GO:0043450alkene biosynthetic process0.0493081523095328
GO:0019370leukotriene biosynthetic process0.0493081523095328



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><br>uberon_data<br>disease_data<br>

Uber Anatomy
Ontology termp-valuen
chordate pharynx7.88e-5310
pharyngeal region of foregut7.88e-5310
pharynx4.13e-4811
tongue7.81e-453
gustatory system7.81e-453
future tongue7.81e-453
tonsil5.05e-341
mucosa-associated lymphoid tissue5.05e-341
lymphoid tissue5.05e-341
tonsillar ring5.05e-341
upper respiratory tract3.30e-2819
pharyngeal arch system3.12e-1718
oral opening2.73e-1422
esophagus2.89e-123
esophageal region2.89e-123
segment of respiratory tract8.39e-1247
mouth4.97e-1129
stomodeum4.97e-1129
respiratory tract2.40e-1054
foregut6.36e-1087
thymus1.70e-094
hemolymphoid system gland1.70e-094
thymic region1.70e-094
pharyngeal gland1.70e-094
thymus primordium1.70e-094
anterior region of body4.43e-0962
craniocervical region4.43e-0962
orifice5.00e-0936
respiratory system1.09e-0774
subdivision of digestive tract2.35e-07118
uterine cervix7.17e-076
neck of organ7.17e-076
subdivision of head8.23e-0749
pharyngeal epithelium9.49e-076
Disease
Ontology termp-valuen
cervical cancer5.35e-085


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)
MA0003.10.000882497
MA0004.10.124793
MA0006.10.092505
MA0007.10.110204
MA0009.10.715971
MA0014.10.00117659
MA0017.10.131947
MA0019.10.270778
MA0024.11.05418
MA0025.10.356605
MA0027.11.73957
MA0028.10.00704394
MA0029.10.200942
MA0030.10.564853
MA0031.10.155068
MA0038.10.061294
MA0040.11.11674
MA0041.10.327327
MA0042.10.114241
MA0043.10.258233
MA0046.10.250449
MA0048.10.0278607
MA0050.10.276908
MA0051.10.0597778
MA0052.10.596967
MA0055.10.00203493
MA0056.10
MA0057.10.00336743
MA0058.10.0125392
MA0059.11.95209
MA0060.10.00503132
MA0061.10.0331301
MA0063.10
MA0066.10.481212
MA0067.10.506892
MA0068.11.93574
MA0069.10.247791
MA0070.10.240129
MA0071.10.407053
MA0072.10.667425
MA0073.10.00257418
MA0074.10.215555
MA0076.10.0148368
MA0077.10.231873
MA0078.11.12266
MA0081.10.059749
MA0083.10.728088
MA0084.10.671627
MA0087.11.91785
MA0088.10.00902219
MA0089.10
MA0090.10.388412
MA0091.13.95655
MA0092.10.242464
MA0093.10.0323365
MA0095.10
MA0098.10
MA0100.10.0664206
MA0101.10.00618892
MA0103.11.40775
MA0105.10.0666838
MA0106.10.266303
MA0107.10.0124929
MA0108.20.909263
MA0109.10
MA0111.10.685974
MA0113.10.285402
MA0114.10.0396474
MA0115.10.442812
MA0116.10.106908
MA0117.10.284729
MA0119.10.0103172
MA0122.10.303641
MA0124.11.05321
MA0125.12.46016
MA0130.10
MA0131.10.109406
MA0132.10
MA0133.10
MA0135.10.279516
MA0136.10.0638731
MA0139.10.000236371
MA0140.10.0473363
MA0141.10.810294
MA0142.10.137394
MA0143.10.28561
MA0144.10.032249
MA0145.10.535291
MA0146.10.0804745
MA0147.10.111238
MA0148.10.0367566
MA0149.10.0443634
MA0062.20.00240972
MA0035.20.178284
MA0039.20.331627
MA0138.20.680098
MA0002.20.4368
MA0137.20.114245
MA0104.20.0517305
MA0047.20.252526
MA0112.20.263506
MA0065.20.00067466
MA0150.10.927598
MA0151.10
MA0152.11.57917
MA0153.10.879049
MA0154.10.170949
MA0155.10.0363113
MA0156.10.116578
MA0157.10.122941
MA0158.10
MA0159.10.362746
MA0160.10.652211
MA0161.10
MA0162.18.32282e-07
MA0163.19.85404e-05
MA0164.11.04376
MA0080.20.0323686
MA0018.20.0777542
MA0099.20.0495326
MA0079.25.16514e-07
MA0102.20.705393
MA0258.10.405269
MA0259.10.122012
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

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