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Coexpression cluster:C200: Difference between revisions

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{{Coexpression_clusters
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,MA0047.2;0.22076,MA0112.2;0.0601738,MA0065.2;6.42835e-05,MA0150.1;1.27275,MA0151.1;0,MA0152.1;0.504383,MA0153.1;0.550492,MA0154.1;0.0338259,MA0155.1;1.97189e-05,MA0156.1;0.00424386,MA0157.1;0.386779,MA0158.1;0,MA0159.1;0.0109613,MA0160.1;0.118474,MA0161.1;0,MA0162.1;4.93793e-06,MA0163.1;0.195395,MA0164.1;0.114987,MA0080.2;0.00281007,MA0018.2;0.0221366,MA0099.2;0.146186,MA0079.2;0,MA0102.2;0.515212,MA0258.1;0.110258,MA0259.1;0.0326405,MA0442.1;0}}
|full_id=C200_seminal_Cardiac_Smooth_Hair_submaxillary_Neutrophils_mixed
|id=C200
|ontology_enrichment_celltype=CL:0002057!6.44e-07!42;CL:0002009!6.54e-07!65
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0003081!5.07e-13!216;UBERON:0000926!1.09e-10!448;UBERON:0004120!1.09e-10!448;UBERON:0006603!1.09e-10!448;UBERON:0007023!1.34e-09!115;UBERON:0001009!8.48e-09!113;UBERON:0000468!2.28e-08!659;UBERON:0004535!4.34e-08!110;UBERON:0002204!7.55e-08!167;UBERON:0002049!7.91e-08!79;UBERON:0007798!7.91e-08!79;UBERON:0000055!1.37e-07!69;UBERON:0002050!1.38e-07!605;UBERON:0005423!1.38e-07!605;UBERON:0000923!1.58e-07!604;UBERON:0005291!1.58e-07!604;UBERON:0006598!1.58e-07!604;UBERON:0002532!1.58e-07!604;UBERON:0000467!1.84e-07!625;UBERON:0001981!2.41e-07!60;UBERON:0007500!2.41e-07!60;UBERON:0004537!2.41e-07!60;UBERON:0006965!2.41e-07!60;UBERON:0000480!2.46e-07!626;UBERON:0001637!9.11e-07!42;UBERON:0003509!9.11e-07!42;UBERON:0004572!9.11e-07!42;UBERON:0004872!9.73e-07!84
}}

Latest revision as of 10:54, 17 September 2013


Full id: C200_seminal_Cardiac_Smooth_Hair_submaxillary_Neutrophils_mixed



Phase1 CAGE Peaks

Hg19::chr10:50911176..50911180,-p@chr10:50911176..50911180
-
Hg19::chr10:50911313..50911330,-p@chr10:50911313..50911330
-
Hg19::chr11:111691980..111692005,-p@chr11:111691980..111692005
-
Hg19::chr11:13285557..13285582,+p@chr11:13285557..13285582
+
Hg19::chr11:77597678..77597713,+p1@ENST00000516522
Hg19::chr11:85195010..85195053,+p2@ENST00000463796
Hg19::chr12:127650900..127650948,-p1@ENST00000488123
Hg19::chr12:127650961..127650963,-p4@ENST00000488123
Hg19::chr12:127650966..127650970,-p3@ENST00000488123
Hg19::chr12:127650982..127650997,-p2@ENST00000488123
Hg19::chr12:20704366..20704465,+p1@ENST00000459949
Hg19::chr12:34372645..34372687,-p1@ENST00000483424
Hg19::chr12:85562743..85562771,-p@chr12:85562743..85562771
-
Hg19::chr14:43722994..43723027,+p@chr14:43722994..43723027
+
Hg19::chr14:90341521..90341554,-p1@ENST00000471006
Hg19::chr16:33963051..33963078,+p@chr16:33963051..33963078
+
Hg19::chr16:33963085..33963113,+p@chr16:33963085..33963113
+
Hg19::chr16:33963114..33963125,+p@chr16:33963114..33963125
+
Hg19::chr16:33963205..33963248,+p@chr16:33963205..33963248
+
Hg19::chr16:33963307..33963381,+p@chr16:33963307..33963381
+
Hg19::chr16:33963702..33963740,+p@chr16:33963702..33963740
+
Hg19::chr16:33963885..33963944,+p@chr16:33963885..33963944
+
Hg19::chr19:24182441..24182447,-p@chr19:24182441..24182447
-
Hg19::chr19:24183089..24183138,-p@chr19:24183089..24183138
-
Hg19::chr19:24183260..24183291,-p@chr19:24183260..24183291
-
Hg19::chr19:24183404..24183444,-p@chr19:24183404..24183444
-
Hg19::chr19:24186160..24186198,-p@chr19:24186160..24186198
-
Hg19::chr19:42070281..42070329,-p@chr19:42070281..42070329
-
Hg19::chr19:42070456..42070481,-p@chr19:42070456..42070481
-
Hg19::chr19:43911276..43911313,+p@chr19:43911276..43911313
+
Hg19::chr19:43911674..43911688,+p@chr19:43911674..43911688
+
Hg19::chr1:237766403..237766436,+p@chr1:237766403..237766436
+
Hg19::chr1:237766565..237766606,+p@chr1:237766565..237766606
+
Hg19::chr1:237766669..237766688,+p@chr1:237766669..237766688
+
Hg19::chr1:91852815..91852953,-p1@ENST00000516420
Hg19::chr1:91852985..91853011,-p2@ENST00000516420
Hg19::chr1:91853019..91853049,-p@chr1:91853019..91853049
-
Hg19::chr21:15457277..15457318,-p@chr21:15457277..15457318
-
Hg19::chr21:15457426..15457442,-p@chr21:15457426..15457442
-
Hg19::chr2:133012497..133012510,-p@chr2:133012497..133012510
-
Hg19::chr2:133012853..133012916,-p@chr2:133012853..133012916
-
Hg19::chr2:133013392..133013403,-p@chr2:133013392..133013403
-
Hg19::chr2:133013454..133013486,-p@chr2:133013454..133013486
-
Hg19::chr2:133013686..133013716,-p@chr2:133013686..133013716
-
Hg19::chr2:133036537..133036585,-p@chr2:133036537..133036585
-
Hg19::chr2:133036692..133036736,-p@chr2:133036692..133036736
-
Hg19::chr2:133037053..133037081,-p@chr2:133037053..133037081
-
Hg19::chr2:133037423..133037469,-p@chr2:133037423..133037469
-
Hg19::chr2:133037552..133037583,-p@chr2:133037552..133037583
-
Hg19::chr2:133037595..133037612,-p@chr2:133037595..133037612
-
Hg19::chr2:159440737..159440770,-p@chr2:159440737..159440770
-
Hg19::chr2:191402684..191402709,-p@chr2:191402684..191402709
-
Hg19::chr2:191402749..191402790,-p1@ENST00000492032
Hg19::chr2:203211018..203211031,-p@chr2:203211018..203211031
-
Hg19::chr2:203211038..203211057,-p2@ENST00000473498
Hg19::chr2:78928720..78928755,+p@chr2:78928720..78928755
+
Hg19::chr2:78928877..78928888,+p@chr2:78928877..78928888
+
Hg19::chr2:78928923..78928950,+p@chr2:78928923..78928950
+
Hg19::chr4:107924792..107924829,-p@chr4:107924792..107924829
-
Hg19::chr4:76807171..76807211,+p1@ENST00000464639
Hg19::chr5:154788152..154788155,+p1@ENST00000485443
Hg19::chr6:144692233..144692263,-p@chr6:144692233..144692263
-
Hg19::chr7:104966296..104966333,+p1@ENST00000469253
Hg19::chr7:68527622..68527642,+p2@ENST00000517158
Hg19::chr7:80962970..80962986,+p@chr7:80962970..80962986
+
Hg19::chr7:80963063..80963113,+p@chr7:80963063..80963113
+
Hg19::chr8:21456056..21456083,+p@chr8:21456056..21456083
+
Hg19::chr8:46951861..46951876,-p@chr8:46951861..46951876
-
Hg19::chr8:46952011..46952037,-p@chr8:46952011..46952037
-
Hg19::chr8:56755211..56755245,-p@chr8:56755211..56755245
-
Hg19::chr8:56822005..56822038,-p1@ENST00000481252
Hg19::chr8:69218623..69218656,-p@chr8:69218623..69218656
-
Hg19::chr8:70602393..70602439,-p1@ENST00000516388
Hg19::chr8:70602464..70602479,-p2@ENST00000516388
Hg19::chr8:70602485..70602518,-p@chr8:70602485..70602518
-
Hg19::chr8:70602589..70602625,-p@chr8:70602589..70602625
-
Hg19::chr9:19278548..19278559,+p@chr9:19278548..19278559
+
Hg19::chr9:79186644..79186694,+p1@ENST00000463508
Hg19::chrX:108297392..108297444,+p@chrX:108297392..108297444
+
Hg19::chrX:108297652..108297666,+p@chrX:108297652..108297666
+
Hg19::chrX:108297700..108297742,+p@chrX:108297700..108297742
+
Hg19::chrX:108297778..108297814,+p@chrX:108297778..108297814
+
Hg19::chrX:47749756..47749774,-p1@ENST00000487797


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><br>

Cell Type
Ontology termp-valuen
defensive cell4.13e-0848
phagocyte4.13e-0848
macrophage dendritic cell progenitor1.52e-0761
monopoietic cell4.22e-0759
monocyte4.22e-0759
monoblast4.22e-0759
promonocyte4.22e-0759
classical monocyte5.38e-0742
CD14-positive, CD16-negative classical monocyte5.38e-0742
smooth muscle cell9.98e-0743
smooth muscle myoblast9.98e-0743
Uber Anatomy
Ontology termp-valuen
lateral plate mesoderm2.26e-14203
mesoderm1.86e-12315
mesoderm-derived structure1.86e-12315
presumptive mesoderm1.86e-12315
germ layer3.78e-09560
germ layer / neural crest3.78e-09560
embryonic tissue3.78e-09560
presumptive structure3.78e-09560
germ layer / neural crest derived structure3.78e-09560
epiblast (generic)3.78e-09560
circulatory system9.00e-09112
developing anatomical structure9.62e-09581
adult organism1.31e-08114
embryonic structure1.50e-08564
multi-cellular organism1.60e-08656
cardiovascular system4.50e-08109
vasculature8.45e-0878
vascular system8.45e-0878
musculoskeletal system8.70e-08167
embryo1.12e-07592
vessel1.78e-0768
anatomical system2.46e-07624
epithelial tube open at both ends3.18e-0759
blood vessel3.18e-0759
blood vasculature3.18e-0759
vascular cord3.18e-0759
anatomical group3.38e-07625
artery6.65e-0742
arterial blood vessel6.65e-0742
arterial system6.65e-0742


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)
MA0003.10.00972909
MA0004.10.0844656
MA0006.10.0111051
MA0007.10.1593
MA0009.10.132914
MA0014.11.86624e-05
MA0017.10.0209186
MA0019.10.740629
MA0024.10.0847075
MA0025.10.209014
MA0027.11.52208
MA0028.10.00361044
MA0029.10.0927579
MA0030.10.616378
MA0031.10.226789
MA0038.10.602859
MA0040.10.316052
MA0041.10.861352
MA0042.11.00399
MA0043.10.133076
MA0046.10.1274
MA0048.10.00608427
MA0050.10.72929
MA0051.10.179669
MA0052.10.320587
MA0055.12.45995e-05
MA0056.10
MA0057.10.000753909
MA0058.10.00822795
MA0059.10.0292348
MA0060.11.32566
MA0061.10.12577
MA0063.10
MA0066.10.0153188
MA0067.10.335825
MA0068.10.0305062
MA0069.10.125475
MA0070.10.381375
MA0071.10.141756
MA0072.10.117786
MA0073.16.36387e-06
MA0074.10.178792
MA0076.10.0104267
MA0077.11.2122
MA0078.10.314107
MA0081.10.151651
MA0083.10.424525
MA0084.11.2153
MA0087.10.750161
MA0088.10.106987
MA0089.10
MA0090.10.0433271
MA0091.11.42598
MA0092.11.52423
MA0093.10.0336844
MA0095.10
MA0098.10
MA0100.10.0173095
MA0101.10.0353954
MA0103.10.666647
MA0105.10.656376
MA0106.10.236791
MA0107.10.00271118
MA0108.20.223708
MA0109.10
MA0111.10.119067
MA0113.10.106298
MA0114.10.00830659
MA0115.10.280508
MA0116.10.105927
MA0117.10.1528
MA0119.10.229
MA0122.10.500528
MA0124.10.251986
MA0125.10.574999
MA0130.10
MA0131.10.342505
MA0132.10
MA0133.10
MA0135.10.148871
MA0136.10.0162794
MA0139.10.432178
MA0140.10.0506345
MA0141.10.260978
MA0142.13.37609
MA0143.10.259572
MA0144.10.0374491
MA0145.10.208839
MA0146.14.42436e-06
MA0147.10.028007
MA0148.10.0361909
MA0149.10.00914493
MA0062.20.000892037
MA0035.20.0100644
MA0039.21.83865e-08
MA0138.20.134443
MA0002.23.57433
MA0137.20.294584
MA0104.20.000632458
MA0047.20.22076
MA0112.20.0601738
MA0065.26.42835e-05
MA0150.11.27275
MA0151.10
MA0152.10.504383
MA0153.10.550492
MA0154.10.0338259
MA0155.11.97189e-05
MA0156.10.00424386
MA0157.10.386779
MA0158.10
MA0159.10.0109613
MA0160.10.118474
MA0161.10
MA0162.14.93793e-06
MA0163.10.195395
MA0164.10.114987
MA0080.20.00281007
MA0018.20.0221366
MA0099.20.146186
MA0079.20
MA0102.20.515212
MA0258.10.110258
MA0259.10.0326405
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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