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Coexpression cluster:C182: Difference between revisions

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{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=0,0

Latest revision as of 10:50, 17 September 2013


Full id: C182_renal_mature_mesothelioma_lung_Mammary_Adipocyte_acute



Phase1 CAGE Peaks

Hg19::chr10:26621582..26621588,+p@chr10:26621582..26621588
+
Hg19::chr10:61530889..61530896,-p@chr10:61530889..61530896
-
Hg19::chr10:64280228..64280239,+p11@ZNF365
Hg19::chr11:74751521..74751532,+p@chr11:74751521..74751532
+
Hg19::chr12:110032559..110032564,+p@chr12:110032559..110032564
+
Hg19::chr12:110032567..110032577,+p@chr12:110032567..110032577
+
Hg19::chr12:16109519..16109568,+p6@DERA
Hg19::chr12:16115719..16115725,+p8@DERA
Hg19::chr12:49730970..49731010,-p1@C1QL4
Hg19::chr12:5198337..5198341,+p@chr12:5198337..5198341
+
Hg19::chr12:5198350..5198359,+p@chr12:5198350..5198359
+
Hg19::chr12:5198401..5198415,+p@chr12:5198401..5198415
+
Hg19::chr13:42975929..42975949,+p@chr13:42975929..42975949
+
Hg19::chr13:49164719..49164734,-p@chr13:49164719..49164734
-
Hg19::chr14:74296806..74296828,-p1@ENST00000555539
p1@uc001xov.1
Hg19::chr14:98792210..98792215,-p@chr14:98792210..98792215
-
Hg19::chr15:67351518..67351557,-p1@ENST00000558071
Hg19::chr15:67351586..67351591,-p2@ENST00000558071
Hg19::chr15:85201423..85201439,-p1@NMB
Hg19::chr16:53780145..53780169,+p@chr16:53780145..53780169
+
Hg19::chr16:81516526..81516531,+p@chr16:81516526..81516531
+
Hg19::chr17:38877280..38877286,-p3@KRT223P
Hg19::chr17:38877316..38877317,-p4@KRT223P
Hg19::chr18:57877275..57877283,+p@chr18:57877275..57877283
+
Hg19::chr19:15160130..15160142,+p3@CASP14
Hg19::chr19:15160255..15160260,+p4@CASP14
Hg19::chr19:15160267..15160278,+p2@CASP14
Hg19::chr19:15160280..15160296,+p1@CASP14
Hg19::chr19:15166954..15166967,+p@chr19:15166954..15166967
+
Hg19::chr19:15167325..15167344,+p@chr19:15167325..15167344
+
Hg19::chr19:29492197..29492204,+p@chr19:29492197..29492204
+
Hg19::chr1:105010925..105010935,-p@chr1:105010925..105010935
-
Hg19::chr1:115771931..115771941,+p@chr1:115771931..115771941
+
Hg19::chr1:152140591..152140604,+p@chr1:152140591..152140604
+
Hg19::chr1:152140624..152140650,+p@chr1:152140624..152140650
+
Hg19::chr1:152140653..152140680,+p@chr1:152140653..152140680
+
Hg19::chr1:241790873..241790886,-p@chr1:241790873..241790886
-
Hg19::chr1:25046836..25046839,+p@chr1:25046836..25046839
+
Hg19::chr1:25046846..25046851,+p@chr1:25046846..25046851
+
Hg19::chr1:25046857..25046871,+p@chr1:25046857..25046871
+
Hg19::chr1:25046892..25046903,+p@chr1:25046892..25046903
+
Hg19::chr1:69983683..69983707,+p@chr1:69983683..69983707
+
Hg19::chr20:52784969..52785020,+p@chr20:52784969..52785020
+
Hg19::chr22:18404843..18404853,-p@chr22:18404843..18404853
-
Hg19::chr22:30951607..30951613,-p@chr22:30951607..30951613
-
Hg19::chr22:30951996..30952007,-p@chr22:30951996..30952007
-
Hg19::chr22:30956754..30956769,-p2@GAL3ST1
Hg19::chr22:30960863..30960867,-p12@GAL3ST1
Hg19::chr22:30960879..30960895,-p1@GAL3ST1
Hg19::chr22:30961419..30961468,-p10@GAL3ST1
Hg19::chr22:30968796..30968805,-p11@GAL3ST1
Hg19::chr22:30968813..30968829,-p9@GAL3ST1
Hg19::chr22:30968839..30968859,-p6@GAL3ST1
Hg19::chr2:10529417..10529422,+p@chr2:10529417..10529422
+
Hg19::chr2:120234198..120234212,+p1@ENST00000457436
Hg19::chr2:166790331..166790338,+p2@LOC100506134
Hg19::chr2:166790366..166790383,+p1@LOC100506134
Hg19::chr2:166790396..166790405,+p1@ENST00000443032
p1@ENST00000446624
Hg19::chr2:58109118..58109152,-p@chr2:58109118..58109152
-
Hg19::chr2:9519004..9519013,+p@chr2:9519004..9519013
+
Hg19::chr3:122694165..122694189,-p7@SEMA5B
Hg19::chr3:122694215..122694221,-p10@SEMA5B
Hg19::chr3:129375556..129375570,-p16@TMCC1
Hg19::chr3:187225661..187225665,-p@chr3:187225661..187225665
-
Hg19::chr4:69915736..69915762,-p@chr4:69915736..69915762
-
Hg19::chr5:10502761..10502785,-p2@ENST00000515243
Hg19::chr5:10502793..10502819,-p1@ENST00000515243
Hg19::chr5:10502847..10502857,-p3@ENST00000515243
Hg19::chr5:150006500..150006508,-p@chr5:150006500..150006508
-
Hg19::chr5:31911541..31911549,-p@chr5:31911541..31911549
-
Hg19::chr5:31995212..31995260,+p@chr5:31995212..31995260
+
Hg19::chr5:31995297..31995305,+p@chr5:31995297..31995305
+
Hg19::chr5:31995382..31995392,+p@chr5:31995382..31995392
+
Hg19::chr5:31995396..31995404,+p@chr5:31995396..31995404
+
Hg19::chr6:12314642..12314666,+p@chr6:12314642..12314666
+
Hg19::chr6:154799214..154799219,-p@chr6:154799214..154799219
-
Hg19::chr6:25868678..25868683,-p3@SLC17A3
Hg19::chr7:112740700..112740737,+p1@ENST00000441928
Hg19::chr7:125077880..125077889,+p4@ENST00000458437
Hg19::chr7:125077895..125077898,+p5@ENST00000458437
Hg19::chr7:125077915..125077928,+p1@ENST00000458437
Hg19::chr7:125077931..125077940,+p3@ENST00000458437
Hg19::chr7:17414360..17414389,+p1@ENST00000419463
Hg19::chr7:46213508..46213536,+p@chr7:46213508..46213536
+
Hg19::chr7:46213564..46213575,+p@chr7:46213564..46213575
+
Hg19::chr7:46213607..46213616,+p@chr7:46213607..46213616
+
Hg19::chr7:46213930..46213940,+p@chr7:46213930..46213940
+
Hg19::chr7:46214057..46214073,+p@chr7:46214057..46214073
+
Hg19::chr7:46214090..46214099,+p@chr7:46214090..46214099
+
Hg19::chr7:46214112..46214115,+p@chr7:46214112..46214115
+
Hg19::chr7:57639694..57639702,+p@chr7:57639694..57639702
+
Hg19::chr8:39542555..39542568,+p3@ADAM18
Hg19::chrX:144963106..144963110,-p@chrX:144963106..144963110
-
Hg19::chrY:18943864..18943891,+p@chrY:18943864..18943891
+


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:0000267cell fraction0.0154189406315746
GO:0006682galactosylceramide biosynthetic process0.0165822834491149
GO:0019375galactolipid biosynthetic process0.0165822834491149
GO:0005624membrane fraction0.0237674954960085
GO:0046476glycosylceramide biosynthetic process0.0237674954960085
GO:0050694galactose 3-O-sulfotransferase activity0.0237674954960085
GO:0001733galactosylceramide sulfotransferase activity0.0237674954960085
GO:0006681galactosylceramide metabolic process0.0237674954960085
GO:0019374galactolipid metabolic process0.0237674954960085
GO:0004139deoxyribose-phosphate aldolase activity0.0237674954960085
GO:0007283spermatogenesis0.0237674954960085
GO:0048232male gamete generation0.0237674954960085
GO:0005436sodium:phosphate symporter activity0.0248470806030616
GO:0046513ceramide biosynthetic process0.0248470806030616
GO:0009264deoxyribonucleotide catabolic process0.0248470806030616
GO:0006677glycosylceramide metabolic process0.0248470806030616
GO:0007276gamete generation0.0248470806030616
GO:0046520sphingoid biosynthetic process0.0248470806030616
GO:0007275multicellular organismal development0.0280585067008458
GO:0019953sexual reproduction0.0310262213524435
GO:0015114phosphate transmembrane transporter activity0.0316026226003279
GO:0016832aldehyde-lyase activity0.0316026226003279
GO:0009247glycolipid biosynthetic process0.0323834920180048
GO:0030148sphingolipid biosynthetic process0.0434133450508024
GO:0009166nucleotide catabolic process0.0495824162942606
GO:0042552myelination0.0495824162942606



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>

Cell Type
Ontology termp-valuen
kidney cell4.22e-1317
kidney epithelial cell4.22e-1317
Uber Anatomy
Ontology termp-valuen
kidney4.34e-0926
kidney mesenchyme4.34e-0926
upper urinary tract4.34e-0926
kidney rudiment4.34e-0926
kidney field4.34e-0926
cavitated compound organ7.41e-0831


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)
MA0003.13.45709e-11
MA0004.10.0551739
MA0006.10.0842645
MA0007.10.538623
MA0009.10.108434
MA0014.17.51236e-07
MA0017.10.521891
MA0019.10.359885
MA0024.10.23433
MA0025.10.526867
MA0027.11.46891
MA0028.10.00162006
MA0029.10.254275
MA0030.10.242352
MA0031.10.404718
MA0038.10.475561
MA0040.10.0751108
MA0041.10.0664781
MA0042.10.113625
MA0043.10.108579
MA0046.17.93943
MA0048.10.0149303
MA0050.10.22044
MA0051.10.130742
MA0052.10.0765778
MA0055.10.0236614
MA0056.10
MA0057.10.00603111
MA0058.10.0454385
MA0059.10.294644
MA0060.10.352706
MA0061.10.159156
MA0063.10
MA0066.10.476673
MA0067.10.297643
MA0068.10.0117033
MA0069.11.12974
MA0070.10.0968661
MA0071.10.0341691
MA0072.10.315125
MA0073.16.65862e-05
MA0074.10.267996
MA0076.10.055702
MA0077.10.306248
MA0078.10.245667
MA0081.10.848494
MA0083.11.75088
MA0084.10.440614
MA0087.10.312297
MA0088.10.0844147
MA0089.10
MA0090.13.66526
MA0091.10.0566878
MA0092.10.692092
MA0093.10.0176824
MA0095.10
MA0098.10
MA0100.10.780058
MA0101.10.16288
MA0103.11.31834
MA0105.10.0571144
MA0106.10.178734
MA0107.10.355251
MA0108.20.0468855
MA0109.10
MA0111.10.156309
MA0113.10.635754
MA0114.10.230648
MA0115.10.245041
MA0116.10.0122756
MA0117.10.397936
MA0119.11.86693
MA0122.10.431449
MA0124.10.218148
MA0125.10.16775
MA0130.10
MA0131.10.0265884
MA0132.10
MA0133.10
MA0135.10.388757
MA0136.10.141881
MA0139.10.903993
MA0140.10.0976418
MA0141.10.438278
MA0142.10.633643
MA0143.10.385181
MA0144.10.388243
MA0145.10.0270447
MA0146.10.00299504
MA0147.10.110276
MA0148.10.0706608
MA0149.10.0899333
MA0062.20.00284633
MA0035.20.097067
MA0039.23.49936e-08
MA0138.20.100473
MA0002.23.15129
MA0137.20.308775
MA0104.20.110531
MA0047.20.16512
MA0112.20.185536
MA0065.20.0187903
MA0150.10.542411
MA0151.10
MA0152.10.219607
MA0153.17.25743
MA0154.10.0110814
MA0155.10.0239138
MA0156.10.315748
MA0157.10.310089
MA0158.10
MA0159.10.111377
MA0160.10.0813271
MA0161.10
MA0162.11.03686e-09
MA0163.14.00716e-05
MA0164.10.410316
MA0080.20.156686
MA0018.20.0689878
MA0099.21.96161
MA0079.29.64327e-17
MA0102.20.47097
MA0258.10.101519
MA0259.10.573202
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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