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Coexpression cluster:C204: Difference between revisions

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{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=0,

Latest revision as of 10:55, 17 September 2013


Full id: C204_Smooth_nasal_CD4_CD19_CD8_CD14_CD34



Phase1 CAGE Peaks

Hg19::chr10:101875066..101875070,-p1@ENST00000436100
Hg19::chr10:104417630..104417634,+p24@TRIM8
Hg19::chr10:130274151..130274153,-p@chr10:130274151..130274153
-
Hg19::chr10:34953040..34953066,-p1@ENST00000411602
Hg19::chr10:44227705..44227736,+p1@UQCRHP3
Hg19::chr10:79742483..79742488,+p@chr10:79742483..79742488
+
Hg19::chr10:89603559..89603565,+p4@CFL1P1
Hg19::chr11:103342483..103342485,+p@chr11:103342483..103342485
+
Hg19::chr11:111333549..111333552,+p@chr11:111333549..111333552
+
Hg19::chr11:133725042..133725053,-p@chr11:133725042..133725053
-
Hg19::chr11:16632557..16632558,-p@chr11:16632557..16632558
-
Hg19::chr12:104680968..104680975,-p@chr12:104680968..104680975
-
Hg19::chr12:116030828..116030830,-p1@UBA52P7
Hg19::chr12:125420425..125420437,-p1@RPL22P19
Hg19::chr12:131245413..131245416,+p@chr12:131245413..131245416
+
Hg19::chr12:49161116..49161125,+p@chr12:49161116..49161125
+
Hg19::chr12:55852818..55852819,+p@chr12:55852818..55852819
+
Hg19::chr12:6379598..6379608,-p1@ENST00000537967
p1@ENST00000539998
Hg19::chr12:69078351..69078356,+p1@ENST00000481005
Hg19::chr13:110279492..110279493,+p@chr13:110279492..110279493
+
Hg19::chr13:28552375..28552395,-p@chr13:28552375..28552395
-
Hg19::chr13:32728128..32728129,+p@chr13:32728128..32728129
+
Hg19::chr13:45965544..45965564,-p4@RCN1P2
Hg19::chr13:85097171..85097193,+p@chr13:85097171..85097193
+
Hg19::chr13:92000895..92000896,+p@chr13:92000895..92000896
+
Hg19::chr14:100842679..100842681,+p12@WDR25
Hg19::chr14:104583053..104583055,-p@chr14:104583053..104583055
-
Hg19::chr14:55044887..55044888,+p@chr14:55044887..55044888
+
Hg19::chr15:40773537..40773544,-p1@ENST00000489027
Hg19::chr16:69373815..69373823,-p9@COG8
Hg19::chr18:21290255..21290263,-p1@ENST00000487872
Hg19::chr18:34964447..34964448,-p@chr18:34964447..34964448
-
Hg19::chr18:59541901..59541917,-p@chr18:59541901..59541917
-
Hg19::chr18:72057577..72057600,-p1@ENST00000474180
Hg19::chr1:120139867..120139873,-p1@GAPDHP33
Hg19::chr1:149114642..149114653,+p3@PFN1P12
Hg19::chr1:212225387..212225388,-p1@ENST00000327274
Hg19::chr1:247611515..247611534,-p@chr1:247611515..247611534
-
Hg19::chr1:25894569..25894574,+p@chr1:25894569..25894574
+
Hg19::chr1:55838358..55838367,-p1@ENST00000497619
Hg19::chr1:58515044..58515045,-p1@HNRNPA1P6
Hg19::chr1:91172633..91172644,-p@chr1:91172633..91172644
-
Hg19::chr20:13792868..13792873,-p@chr20:13792868..13792873
-
Hg19::chr20:17749112..17749114,+p@chr20:17749112..17749114
+
Hg19::chr20:43954844..43954850,-p@chr20:43954844..43954850
-
Hg19::chr20:47894852..47894860,-p25@ZNFX1
Hg19::chr22:19466669..19466670,+p5@CDC45
Hg19::chr22:31050822..31050824,-p1@ENST00000510957
Hg19::chr22:36571642..36571657,+p1@ENST00000439552
Hg19::chr22:41471250..41471272,-p1@ENST00000423293
Hg19::chr2:106870291..106870293,-p1@ENST00000436597
Hg19::chr2:47387602..47387612,-p@chr2:47387602..47387612
-
Hg19::chr2:71134479..71134487,+p@chr2:71134479..71134487
+
Hg19::chr3:140621021..140621025,+p1@ENST00000484754
Hg19::chr3:179370966..179370998,-p@chr3:179370966..179370998
-
Hg19::chr3:52227409..52227411,+p4@ALDOAP1
Hg19::chr3:89636109..89636112,-p@chr3:89636109..89636112
-
Hg19::chr4:155073946..155073948,-p@chr4:155073946..155073948
-
Hg19::chr4:84423781..84423782,+p1@ENST00000494923
Hg19::chr5:1037457..1037459,+p@chr5:1037457..1037459
+
Hg19::chr5:175843190..175843195,+p@chr5:175843190..175843195
+
Hg19::chr5:180100953..180100958,-p@chr5:180100953..180100958
-
Hg19::chr5:5807221..5807229,+p@chr5:5807221..5807229
+
Hg19::chr6:119590894..119590904,-p1@ENST00000406333
Hg19::chr7:133000192..133000196,-p1@ENST00000419509
Hg19::chr7:1906143..1906144,-p@chr7:1906143..1906144
-
Hg19::chr7:2700849..2700851,+p53@TTYH3
Hg19::chr7:33574446..33574447,+p@chr7:33574446..33574447
+
Hg19::chr7:4462090..4462094,+p@chr7:4462090..4462094
+
Hg19::chr7:49743079..49743080,-p@chr7:49743079..49743080
-
Hg19::chr7:63889330..63889331,-p@chr7:63889330..63889331
-
Hg19::chr8:30209368..30209381,+p2@TUBBP1
Hg19::chr9:130159593..130159600,+p9@SLC2A8
Hg19::chr9:37637329..37637363,-p3@RAB1C
Hg19::chr9:82591919..82591920,-p@chr9:82591919..82591920
-
Hg19::chrX:151214741..151214745,-p1@ENST00000415403
Hg19::chrX:25013587..25013595,+p@chrX:25013587..25013595
+
Hg19::chrX:6340807..6340814,-p1@ENST00000437297


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
aortic smooth muscle cell3.81e-2110
vascular associated smooth muscle cell1.18e-0732
Uber Anatomy
Ontology termp-valuen
blood vessel smooth muscle3.81e-2110
arterial system smooth muscle3.81e-2110
artery smooth muscle tissue3.81e-2110
aorta smooth muscle tissue3.81e-2110
smooth muscle tissue1.22e-1415
aorta6.74e-1121
aortic system6.74e-1121
systemic artery1.82e-0733
systemic arterial system1.82e-0733


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)
MA0003.10.00761122
MA0004.10.218181
MA0006.10.173953
MA0007.10.0289828
MA0009.10.448088
MA0014.10.0450747
MA0017.10.256839
MA0019.10.510647
MA0024.10.315608
MA0025.10.225339
MA0027.11.54867
MA0028.10.113622
MA0029.11.14277
MA0030.10.32489
MA0031.10.0721564
MA0038.10.0840962
MA0040.10.345724
MA0041.12.09807
MA0042.12.26904
MA0043.10.146285
MA0046.10.433494
MA0048.10.148839
MA0050.10.356379
MA0051.10.400746
MA0052.10.711754
MA0055.10.225858
MA0056.10
MA0057.10.0316536
MA0058.10.011178
MA0059.10.184482
MA0060.10.103032
MA0061.10.000452261
MA0063.10
MA0066.10.0843541
MA0067.10.355517
MA0068.10.0114919
MA0069.10.42837
MA0070.10.820402
MA0071.10.556599
MA0072.10.1302
MA0073.13.27373e-08
MA0074.10.0811225
MA0076.10.111339
MA0077.10.793304
MA0078.10.351566
MA0081.10.315809
MA0083.10.150174
MA0084.10.506143
MA0087.10.804956
MA0088.10.0533261
MA0089.10
MA0090.10.401576
MA0091.10.615763
MA0092.10.304763
MA0093.10.0973944
MA0095.10
MA0098.10
MA0100.10.0927156
MA0101.10.00434863
MA0103.10.156866
MA0105.10.0200514
MA0106.10.269208
MA0107.10.00418302
MA0108.20.24885
MA0109.10
MA0111.10.269888
MA0113.10.123062
MA0114.10.121929
MA0115.10.298932
MA0116.10.137521
MA0117.10.499805
MA0119.10.627074
MA0122.10.181991
MA0124.10.742706
MA0125.10.213886
MA0130.10
MA0131.10.0438471
MA0132.10
MA0133.10
MA0135.10.948814
MA0136.10.0884192
MA0139.10.205268
MA0140.10.163149
MA0141.10.691513
MA0142.10.477603
MA0143.10.293584
MA0144.10.0983211
MA0145.10.293607
MA0146.10.210325
MA0147.10.676043
MA0148.10.694302
MA0149.10.0115789
MA0062.20.00498786
MA0035.20.0126731
MA0039.24.59576e-06
MA0138.20.0392351
MA0002.20.314137
MA0137.20.0581719
MA0104.20.253194
MA0047.20.251992
MA0112.20.248239
MA0065.20.0216785
MA0150.10.821774
MA0151.10
MA0152.10.170603
MA0153.10.203319
MA0154.10.420273
MA0155.10.0191672
MA0156.10.125345
MA0157.10.192737
MA0158.10
MA0159.10.145437
MA0160.10.0512352
MA0161.10
MA0162.10.000266376
MA0163.10.165691
MA0164.10.132533
MA0080.20.0448728
MA0018.20.271204
MA0099.20.064771
MA0079.22.17538e-12
MA0102.20.53771
MA0258.10.472388
MA0259.10.044756
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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