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Coexpression cluster:C195: Difference between revisions

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{{Coexpression_clusters
{
|full_id=C195_Small_Gingival_Bronchial_Smooth_mesenchymal_Urothelial_Tracheal
|

Latest revision as of 10:53, 17 September 2013


Full id: C195_Small_Gingival_Bronchial_Smooth_mesenchymal_Urothelial_Tracheal



Phase1 CAGE Peaks

Hg19::chr10:3941138..3941145,-p@chr10:3941138..3941145
-
Hg19::chr11:127965642..127965659,+p@chr11:127965642..127965659
+
Hg19::chr11:127965706..127965714,+p@chr11:127965706..127965714
+
Hg19::chr11:127965736..127965745,+p@chr11:127965736..127965745
+
Hg19::chr11:127965839..127965844,+p@chr11:127965839..127965844
+
Hg19::chr11:127965855..127965866,+p@chr11:127965855..127965866
+
Hg19::chr11:127965869..127965894,+p@chr11:127965869..127965894
+
Hg19::chr11:127965904..127965913,+p@chr11:127965904..127965913
+
Hg19::chr11:127965924..127965935,+p@chr11:127965924..127965935
+
Hg19::chr11:73663222..73663226,+p@chr11:73663222..73663226
+
Hg19::chr11:7927293..7927308,-p4@LOC283299
Hg19::chr11:7927797..7927817,-p1@LOC283299
Hg19::chr12:10513712..10513716,-p1@ENST00000535911
Hg19::chr12:28186158..28186183,-p@chr12:28186158..28186183
-
Hg19::chr14:51963969..51963974,+p@chr14:51963969..51963974
+
Hg19::chr14:51972517..51972536,+p@chr14:51972517..51972536
+
Hg19::chr14:52026212..52026215,+p@chr14:52026212..52026215
+
Hg19::chr14:87730650..87730656,-p@chr14:87730650..87730656
-
Hg19::chr15:71740021..71740037,+p@chr15:71740021..71740037
+
Hg19::chr16:85750444..85750466,-p@chr16:85750444..85750466
-
Hg19::chr17:38653561..38653607,-p@chr17:38653561..38653607
-
Hg19::chr17:56603082..56603097,+p@chr17:56603082..56603097
+
Hg19::chr17:56603128..56603137,+p@chr17:56603128..56603137
+
Hg19::chr17:60858418..60858439,-p@chr17:60858418..60858439
-
Hg19::chr1:107541218..107541228,-p@chr1:107541218..107541228
-
Hg19::chr1:209591333..209591335,-p@chr1:209591333..209591335
-
Hg19::chr1:232854914..232854917,-p@chr1:232854914..232854917
-
Hg19::chr1:8135925..8135929,-p@chr1:8135925..8135929
-
Hg19::chr1:94160495..94160512,-p@chr1:94160495..94160512
-
Hg19::chr21:38233478..38233483,+p@chr21:38233478..38233483
+
Hg19::chr21:44939980..44939983,+p@chr21:44939980..44939983
+
Hg19::chr2:163101439..163101452,+p@chr2:163101439..163101452
+
Hg19::chr2:213770576..213770587,+p@chr2:213770576..213770587
+
Hg19::chr2:231649545..231649550,-p@chr2:231649545..231649550
-
Hg19::chr2:56007040..56007060,+p@chr2:56007040..56007060
+
Hg19::chr2:73299315..73299328,-p11@SFXN5
Hg19::chr3:101909113..101909129,+p@chr3:101909113..101909129
+
Hg19::chr3:101909187..101909198,+p@chr3:101909187..101909198
+
Hg19::chr3:156502182..156502186,+p@chr3:156502182..156502186
+
Hg19::chr3:189655696..189655699,+p@chr3:189655696..189655699
+
Hg19::chr3:45476797..45476808,+p@chr3:45476797..45476808
+
Hg19::chr3:45476828..45476831,+p@chr3:45476828..45476831
+
Hg19::chr3:45476837..45476843,+p@chr3:45476837..45476843
+
Hg19::chr3:48602467..48602469,-p14@COL7A1
Hg19::chr4:108783895..108783898,-p@chr4:108783895..108783898
-
Hg19::chr4:108909370..108909373,+p@chr4:108909370..108909373
+
Hg19::chr4:157695866..157695871,+p@chr4:157695866..157695871
+
Hg19::chr4:166604070..166604073,+p@chr4:166604070..166604073
+
Hg19::chr5:111445067..111445085,-p@chr5:111445067..111445085
-
Hg19::chr5:148293809..148293816,+p@chr5:148293809..148293816
+
Hg19::chr5:52584337..52584344,-p@chr5:52584337..52584344
-
Hg19::chr5:59064137..59064148,-p58@PDE4D
Hg19::chr5:59064162..59064173,-p72@PDE4D
Hg19::chr5:59064199..59064230,-p28@PDE4D
Hg19::chr6:10355646..10355663,-p@chr6:10355646..10355663
-
Hg19::chr6:11791877..11791883,+p@chr6:11791877..11791883
+
Hg19::chr6:12324677..12324683,+p@chr6:12324677..12324683
+
Hg19::chr6:128922463..128922497,+p@chr6:128922463..128922497
+
Hg19::chr6:22222867..22222878,-p@chr6:22222867..22222878
-
Hg19::chr7:106060323..106060328,-p@chr7:106060323..106060328
-
Hg19::chr7:134328418..134328421,+p@chr7:134328418..134328421
+
Hg19::chr7:158196067..158196075,-p@chr7:158196067..158196075
-
Hg19::chr7:55163202..55163244,+p@chr7:55163202..55163244
+
Hg19::chr7:55263885..55263894,+p@chr7:55263885..55263894
+
Hg19::chr8:113686674..113686685,-p@chr8:113686674..113686685
-
Hg19::chr8:113686693..113686717,-p@chr8:113686693..113686717
-
Hg19::chr8:113686738..113686743,-p@chr8:113686738..113686743
-
Hg19::chr8:113686752..113686753,-p@chr8:113686752..113686753
-
Hg19::chr8:113686755..113686782,-p@chr8:113686755..113686782
-
Hg19::chr8:113686792..113686795,-p@chr8:113686792..113686795
-
Hg19::chr8:29414184..29414190,+p@chr8:29414184..29414190
+
Hg19::chr8:29448825..29448836,-p@chr8:29448825..29448836
-
Hg19::chr8:29449835..29449837,+p@chr8:29449835..29449837
+
Hg19::chr9:20224892..20224905,-p@chr9:20224892..20224905
-
Hg19::chr9:21468453..21468457,-p@chr9:21468453..21468457
-
Hg19::chr9:21499276..21499289,-p@chr9:21499276..21499289
-
Hg19::chr9:21499446..21499456,-p@chr9:21499446..21499456
-
Hg19::chr9:21505384..21505411,-p@chr9:21505384..21505411
-
Hg19::chr9:21543873..21543886,-p@chr9:21543873..21543886
-
Hg19::chr9:21549553..21549570,-p@chr9:21549553..21549570
-
Hg19::chr9:21549612..21549619,-p@chr9:21549612..21549619
-
Hg19::chr9:21559689..21559703,-p3@MIR31HG
Hg19::chr9:21559717..21559731,-p4@MIR31HG
Hg19::chr9:21559788..21559806,-p2@MIR31HG
Hg19::chr9:21559809..21559877,-p1@MIR31HG
Hg19::chrX:48369279..48369286,+p9@PORCN
Hg19::chrY:7671916..7671924,-p@chrY:7671916..7671924
-


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:0005590collagen type VII0.0114211703756034
GO:00041153',5'-cyclic-AMP phosphodiesterase activity0.0342514094620916
GO:0030934anchoring collagen0.0342514094620916
GO:0005737cytoplasm0.0456463678366286
GO:0005626insoluble fraction0.0456463678366286



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><br>

Uber Anatomy
Ontology termp-valuen
gingival epithelium1.49e-403
mouth mucosa1.26e-1613
epithelium of mucosa1.16e-158
gingiva1.16e-158
jaw skeleton2.95e-144
splanchnocranium2.95e-144
primary subdivision of cranial skeletal system1.35e-115
mucosa6.57e-1120
respiratory system8.01e-1174
endoderm-derived structure1.66e-10160
endoderm1.66e-10160
presumptive endoderm1.66e-10160
protuberance8.11e-106
pharyngeal arch8.11e-106
embryonic head8.11e-106
orifice3.42e-0936
head3.08e-0856
surface structure8.74e-0899
mouth1.36e-0729
stomodeum1.36e-0729
anterior region of body2.09e-0762
craniocervical region2.09e-0762


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)
MA0003.11.37373e-10
MA0004.10.0233642
MA0006.10.00022642
MA0007.10.0187951
MA0009.10.780226
MA0014.12.35346e-06
MA0017.10.450067
MA0019.10.0867983
MA0024.10.0772874
MA0025.10.572768
MA0027.11.50196
MA0028.10.07403
MA0029.10.0849308
MA0030.10.579045
MA0031.11.21134
MA0038.10.552973
MA0040.10.294414
MA0041.12.21123
MA0042.12.79302
MA0043.10.390523
MA0046.10.756614
MA0048.10.0289491
MA0050.10.444842
MA0051.10.320418
MA0052.10.298798
MA0055.17.28342e-05
MA0056.10
MA0057.10.00291861
MA0058.10.0628759
MA0059.10.129027
MA0060.10.101886
MA0061.10.228336
MA0063.10
MA0066.10.0621543
MA0067.10.321182
MA0068.10.0106221
MA0069.10.116197
MA0070.10.357725
MA0071.11.33152
MA0072.10.714827
MA0073.10
MA0074.10.0123251
MA0076.10.0756636
MA0077.10.105288
MA0078.10.530438
MA0081.10.755348
MA0083.11.29593
MA0084.10.467465
MA0087.10.349243
MA0088.10.00660877
MA0089.10
MA0090.11.52245
MA0091.10.490263
MA0092.10.576399
MA0093.10.00207058
MA0095.10
MA0098.10
MA0100.10.0147624
MA0101.10.0649137
MA0103.10.18056
MA0105.10.00152539
MA0106.13.94073
MA0107.10.0808847
MA0108.20.452222
MA0109.10
MA0111.11.29621
MA0113.12.39843
MA0114.10.0379744
MA0115.11.35275
MA0116.10.0444846
MA0117.10.142504
MA0119.10.674131
MA0122.10.922354
MA0124.10.671777
MA0125.10.546863
MA0130.10
MA0131.10.314316
MA0132.10
MA0133.10
MA0135.10.847274
MA0136.13.58151
MA0139.11.27776e-05
MA0140.10.683623
MA0141.10.0230539
MA0142.12.05709
MA0143.10.724853
MA0144.10.0577741
MA0145.10.0531973
MA0146.15.45815e-08
MA0147.10.00228433
MA0148.11.4618
MA0149.10.00757491
MA0062.20.000122056
MA0035.20.253105
MA0039.27.87365e-09
MA0138.23.87742
MA0002.20.531836
MA0137.20.0805142
MA0104.20.00170629
MA0047.20.385808
MA0112.20.00860371
MA0065.20.00177799
MA0150.10.45016
MA0151.10
MA0152.11.00644
MA0153.11.00406
MA0154.10.132633
MA0155.13.10101e-05
MA0156.13.02382
MA0157.10.155276
MA0158.10
MA0159.10.665048
MA0160.10.389484
MA0161.10
MA0162.10.000161397
MA0163.12.32182e-05
MA0164.10.0239427
MA0080.21.99615
MA0018.20.215507
MA0099.22.64941
MA0079.20
MA0102.20.498347
MA0258.10.225285
MA0259.10.00961053
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
FOS#2353282.895893662632681.2138110998422e-076.98838023464274e-06
JUN#3725213.020338080908773.74013144524048e-060.000122334979019565
NR3C1#2908152.581555746753970.0006172269906107990.00511648302820869
SMARCA4#659747.20762773829370.002410605745787930.0135903510652818
STAT3#6774323.869228504700416.10156636443326e-127.85747829266394e-10



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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