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Coexpression cluster:C410: Difference between revisions

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|tfbs_overrepresentation_for_novel_motifs=0.0737355,0.0454283,0.247245,0.44898,0.435938,0.446495,0.193858,0.205635,0.201483,0.111861,0.127781,0.223608,0.0494833,0.18622,0.75795,0.222896,0.359143,0.137813,1.12447,0.173055,0.247319,0.15028,0.14085,0.424971,0.306895,0.239737,0.108901,0.431583,0.200446,0.351258,0.115556,1.00986,0.0251883,0.139529,0.0408246,0.0386354,0.15531,0.146177,0.131632,0.0657489,1.00593,0.346812,0.183842,0.193557,0.0113802,0.0845678,0.566947,0.12165,0.15986,0.442908,0.250009,0.202536,0.121746,0.453481,0.587358,0.551472,0.205541,0.166937,0.195328,0.166299,0.423157,0.196176,0.391942,0.336984,0.208359,0.309988,0.667509,1.01514,0.380596,0.859886,0.328502,0.41347,0.00239942,0.585564,0.046819,0.0398214,0.372449,0.323653,0.985337,0.298626,0.0604183,0.336133,0.208117,0.40535,0.539768,0.000374958,0.00141773,0.00500612,0.269174,1.11136,0.753896,0.516018,1.04021,1.60795,0.437541,0.0307132,0.15207,0.438691,0.272612,0.687221,0.313035,1.81882,0.433978,0.362101,0.301097,0.125207,0.349366,0.541302,0.0917674,0.0472968,0.075464,0.431643,0.516221,0.415422,0.70928,0.635439,0.00350216,0.1149,0.308176,0.116148,0.578146,0.737486,0.442338,0.617696,0.812657,0.324249,1.05739,0.407146,0.616494,0.126749,0.516623,0.373998,0.629526,0.612237,0.765929,0.0774004,0.112299,0.139902,0.726382,1.55835,1.16239,0.691851,0.190777,0.43571,0.302448,0.943753,0.289694,1.40098,0.697322,0.0262058,0.0121652,0.0035534,0.516957,0.188592,0.19585,0.888975,0.714117,0.716828,0.0919218,0.0781127,0.690731,0.500787,0.377296,0.273059,1.52719,1.12809,0.24603,0.192969,0.00108552
|tfbs_overrepresentation_for_novel_motifs=0.0737355,0.0454283,0.247245,0.44898,0.435938,0.446495,0.193858,0.205635,0.201483,0.111861,0.127781,0.223608,0.0494833,0.18622,0.75795,0.222896,0.359143,0.137813,1.12447,0.173055,0.247319,0.15028,0.14085,0.424971,0.306895,0.239737,0.108901,0.431583,0.200446,0.351258,0.115556,1.00986,0.0251883,0.139529,0.0408246,0.0386354,0.15531,0.146177,0.131632,0.0657489,1.00593,0.346812,0.183842,0.193557,0.0113802,0.0845678,0.566947,0.12165,0.15986,0.442908,0.250009,0.202536,0.121746,0.453481,0.587358,0.551472,0.205541,0.166937,0.195328,0.166299,0.423157,0.196176,0.391942,0.336984,0.208359,0.309988,0.667509,1.01514,0.380596,0.859886,0.328502,0.41347,0.00239942,0.585564,0.046819,0.0398214,0.372449,0.323653,0.985337,0.298626,0.0604183,0.336133,0.208117,0.40535,0.539768,0.000374958,0.00141773,0.00500612,0.269174,1.11136,0.753896,0.516018,1.04021,1.60795,0.437541,0.0307132,0.15207,0.438691,0.272612,0.687221,0.313035,1.81882,0.433978,0.362101,0.301097,0.125207,0.349366,0.541302,0.0917674,0.0472968,0.075464,0.431643,0.516221,0.415422,0.70928,0.635439,0.00350216,0.1149,0.308176,0.116148,0.578146,0.737486,0.442338,0.617696,0.812657,0.324249,1.05739,0.407146,0.616494,0.126749,0.516623,0.373998,0.629526,0.612237,0.765929,0.0774004,0.112299,0.139902,0.726382,1.55835,1.16239,0.691851,0.190777,0.43571,0.302448,0.943753,0.289694,1.40098,0.697322,0.0262058,0.0121652,0.0035534,0.516957,0.188592,0.19585,0.888975,0.714117,0.716828,0.0919218,0.0781127,0.690731,0.500787,0.377296,0.273059,1.52719,1.12809,0.24603,0.192969,0.00108552
|tfbs_overrepresentation_jaspar=MA0003.1;0.000233361,MA0004.1;0.130779,MA0006.1;0.0525289,MA0007.1;0.120068,MA0009.1;0.480543,MA0014.1;0.00104451,MA0017.1;0.889393,MA0019.1;0.227177,MA0024.1;0.391254,MA0025.1;0.599238,MA0027.1;2.03861,MA0028.1;0.0589063,MA0029.1;0.407394,MA0030.1;0.397801,MA0031.1;0.344829,MA0038.1;0.569682,MA0040.1;0.412311,MA0041.1;0.437147,MA0042.1;0.123063,MA0043.1;0.480818,MA0046.1;1.18753,MA0048.1;0.055058,MA0050.1;0.390696,MA0051.1;0.562815,MA0052.1;1.87776,MA0055.1;0.121215,MA0056.1;0,MA0057.1;0.015143,MA0058.1;0.0802423,MA0059.1;0.575469,MA0060.1;0.017391,MA0061.1;0.317574,MA0063.1;0,MA0066.1;0.196017,MA0067.1;0.769322,MA0068.1;0.00681877,MA0069.1;0.467738,MA0070.1;1.15955,MA0071.1;0.50749,MA0072.1;1.1512,MA0073.1;1.88547e-07,MA0074.1;0.19236,MA0076.1;0.0879186,MA0077.1;0.44756,MA0078.1;0.72884,MA0081.1;0.27336,MA0083.1;0.487092,MA0084.1;0.947429,MA0087.1;0.452083,MA0088.1;0.0453304,MA0089.1;0,MA0090.1;0.0951695,MA0091.1;1.32898,MA0092.1;0.724515,MA0093.1;0.053707,MA0095.1;0,MA0098.1;0,MA0100.1;0.592379,MA0101.1;0.44587,MA0103.1;0.184112,MA0105.1;0.0974258,MA0106.1;0.224407,MA0107.1;0.293146,MA0108.2;0.342362,MA0109.1;0,MA0111.1;0.684165,MA0113.1;0.236174,MA0114.1;1.21037,MA0115.1;0.697973,MA0116.1;0.030864,MA0117.1;0.513502,MA0119.1;0.25231,MA0122.1;0.53644,MA0124.1;1.58599,MA0125.1;0.583056,MA0130.1;0,MA0131.1;0.277285,MA0132.1;0,MA0133.1;0,MA0135.1;0.507125,MA0136.1;0.581198,MA0139.1;0.0102505,MA0140.1;0.168354,MA0141.1;0.270862,MA0142.1;0.319458,MA0143.1;0.665621,MA0144.1;0.25656,MA0145.1;0.120776,MA0146.1;0.0138947,MA0147.1;0.031895,MA0148.1;0.446835,MA0149.1;0.94608,MA0062.2;0.0113502,MA0035.2;0.167901,MA0039.2;0.00119817,MA0138.2;0.264522,MA0002.2;0.0700986,MA0137.2;0.0615777,MA0104.2;0.0784157,MA0047.2;0.215827,MA0112.2;0.0502653,MA0065.2;0.362574,MA0150.1;0.307678,MA0151.1;0,MA0152.1;0.513688,MA0153.1;0.567879,MA0154.1;0.0110055,MA0155.1;0.00401501,MA0156.1;0.224407,MA0157.1;0.807311,MA0158.1;0,MA0159.1;0.563553,MA0160.1;0.470272,MA0161.1;0,MA0162.1;0.000165262,MA0163.1;0.000292658,MA0164.1;1.27209,MA0080.2;0.438824,MA0018.2;0.225392,MA0099.2;0.172833,MA0079.2;2.60851e-13,MA0102.2;0.983247,MA0258.1;0.452847,MA0259.1;0.138164,MA0442.1;0
}}
}}

Revision as of 19:09, 22 January 2013


Full id: C410_skeletal_left_heart_penis_diaphragm_throat_tongue



Phase1 CAGE Peaks

Hg19::chr10:75408401..75408440,-p@chr10:75408401..75408440
-
Hg19::chr18:8623981..8623992,+p@chr18:8623981..8623992
+
Hg19::chr1:16341491..16341518,-p@chr1:16341491..16341518
-
Hg19::chr1:26380381..26380423,+p@chr1:26380381..26380423
+
Hg19::chr2:179392245..179392258,-p@chr2:179392245..179392258
-
Hg19::chr2:179396497..179396508,-p@chr2:179396497..179396508
-
Hg19::chr2:179415798..179415808,-p@chr2:179415798..179415808
-
Hg19::chr2:179425588..179425600,-p@chr2:179425588..179425600
-
Hg19::chr2:179429330..179429339,-p@chr2:179429330..179429339
-
Hg19::chr2:179440729..179440739,-p@chr2:179440729..179440739
-
Hg19::chr2:179455069..179455078,-p@chr2:179455069..179455078
-
Hg19::chr2:179459301..179459312,-p@chr2:179459301..179459312
-
Hg19::chr2:179466162..179466169,-p@chr2:179466162..179466169
-
Hg19::chr2:179469021..179469032,-p@chr2:179469021..179469032
-
Hg19::chr2:179499143..179499151,-p@chr2:179499143..179499151
-
Hg19::chr2:179585314..179585321,-p@chr2:179585314..179585321
-
Hg19::chr2:179587465..179587474,-p@chr2:179587465..179587474
-
Hg19::chr2:179636186..179636200,-p@chr2:179636186..179636200
-
Hg19::chr2:27995173..27995197,+p5@MRPL33
Hg19::chr4:186066034..186066058,+p@chr4:186066034..186066058
+
Hg19::chr4:186425693..186425704,-p@chr4:186425693..186425704
-
Hg19::chr4:95372874..95372885,+p13@PDLIM5
Hg19::chr8:142441259..142441277,+p@chr8:142441259..142441277
+
Hg19::chr8:22785359..22785366,-p8@PEBP4
Hg19::chrX:21761906..21761916,-p@chrX:21761906..21761916
-


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:0042805actinin binding0.0198640405344692
GO:0005080protein kinase C binding0.0198640405344692



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
primary circulatory organ6.48e-2727
muscle structure1.45e-242
muscle organ1.45e-242
compound organ2.46e-1968
adult organism2.21e-18114
cardiac chamber4.17e-173
tongue1.49e-163
gustatory system1.49e-163
future tongue1.49e-163
valve2.20e-163
cardiac mesenchyme2.20e-163
cardial valve2.20e-163
tunica intima2.20e-163
heart layer2.20e-163
endocardium2.20e-163
endocardial cushion2.20e-163
presumptive endocardium2.20e-163
heart left ventricle1.61e-131
cardiac ventricle1.61e-131
future cardiac ventricle1.61e-131
left cardiac atrium2.06e-131
hindlimb bud2.62e-131
soleus muscle2.62e-131
appendage2.62e-131
lower limb segment2.62e-131
multi-limb segment region2.62e-131
hindlimb muscle2.62e-131
hindlimb zeugopod muscle2.62e-131
paired limb/fin2.62e-131
limb2.62e-131
pelvic appendage2.62e-131
limb segment2.62e-131
paired limb/fin segment2.62e-131
limb muscle2.62e-131
pelvic complex muscle2.62e-131
zeugopod2.62e-131
muscle of leg2.62e-131
paired limb/fin bud2.62e-131
limb bud2.62e-131
pelvic appendage bud2.62e-131
limb/fin field2.62e-131
subdivision of organism along appendicular axis2.62e-131
appendage girdle complex2.62e-131
leg2.62e-131
hindlimb2.62e-131
triceps surae2.62e-131
hindlimb zeugopod2.62e-131
posterior region of body2.62e-131
pelvic complex2.62e-131
limb field2.62e-131
hindlimb/pelvic fin field2.62e-131
penis2.95e-131
intromittent organ2.95e-131
lateral plate mesenchyme2.95e-131
undifferentiated genital tubercle2.95e-131
somatopleure2.95e-131
chest muscle4.77e-131
respiratory system muscle4.77e-131
skeletal muscle of trunk4.77e-131
respiratory system skeletal muscle4.77e-131
thoracic segment muscle4.77e-131
chest organ4.77e-131
muscle of trunk4.77e-131
diaphragm4.77e-131
future diaphragm4.77e-131
pulmonary valve5.38e-131
semi-lunar valve5.38e-131
mitral valve7.68e-131
epididymis1.09e-121
heart3.47e-1224
primitive heart tube3.47e-1224
primary heart field3.47e-1224
anterior lateral plate mesoderm3.47e-1224
heart tube3.47e-1224
heart primordium3.47e-1224
cardiac mesoderm3.47e-1224
cardiogenic plate3.47e-1224
heart rudiment3.47e-1224
blood vessel layer1.52e-077
cardiac atrium2.43e-072
future cardiac atrium2.43e-072
throat3.09e-072
atrioventricular valve4.69e-072
Disease
Ontology termp-valuen
heart disease3.34e-242
vascular disease6.82e-131
ischemia6.82e-131
extrinsic cardiomyopathy6.82e-131
myocardial ischemia6.82e-131
myocardial infarction6.82e-131
cardiovascular system disease1.31e-124


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)
MA0003.10.000233361
MA0004.10.130779
MA0006.10.0525289
MA0007.10.120068
MA0009.10.480543
MA0014.10.00104451
MA0017.10.889393
MA0019.10.227177
MA0024.10.391254
MA0025.10.599238
MA0027.12.03861
MA0028.10.0589063
MA0029.10.407394
MA0030.10.397801
MA0031.10.344829
MA0038.10.569682
MA0040.10.412311
MA0041.10.437147
MA0042.10.123063
MA0043.10.480818
MA0046.11.18753
MA0048.10.055058
MA0050.10.390696
MA0051.10.562815
MA0052.11.87776
MA0055.10.121215
MA0056.10
MA0057.10.015143
MA0058.10.0802423
MA0059.10.575469
MA0060.10.017391
MA0061.10.317574
MA0063.10
MA0066.10.196017
MA0067.10.769322
MA0068.10.00681877
MA0069.10.467738
MA0070.11.15955
MA0071.10.50749
MA0072.11.1512
MA0073.11.88547e-07
MA0074.10.19236
MA0076.10.0879186
MA0077.10.44756
MA0078.10.72884
MA0081.10.27336
MA0083.10.487092
MA0084.10.947429
MA0087.10.452083
MA0088.10.0453304
MA0089.10
MA0090.10.0951695
MA0091.11.32898
MA0092.10.724515
MA0093.10.053707
MA0095.10
MA0098.10
MA0100.10.592379
MA0101.10.44587
MA0103.10.184112
MA0105.10.0974258
MA0106.10.224407
MA0107.10.293146
MA0108.20.342362
MA0109.10
MA0111.10.684165
MA0113.10.236174
MA0114.11.21037
MA0115.10.697973
MA0116.10.030864
MA0117.10.513502
MA0119.10.25231
MA0122.10.53644
MA0124.11.58599
MA0125.10.583056
MA0130.10
MA0131.10.277285
MA0132.10
MA0133.10
MA0135.10.507125
MA0136.10.581198
MA0139.10.0102505
MA0140.10.168354
MA0141.10.270862
MA0142.10.319458
MA0143.10.665621
MA0144.10.25656
MA0145.10.120776
MA0146.10.0138947
MA0147.10.031895
MA0148.10.446835
MA0149.10.94608
MA0062.20.0113502
MA0035.20.167901
MA0039.20.00119817
MA0138.20.264522
MA0002.20.0700986
MA0137.20.0615777
MA0104.20.0784157
MA0047.20.215827
MA0112.20.0502653
MA0065.20.362574
MA0150.10.307678
MA0151.10
MA0152.10.513688
MA0153.10.567879
MA0154.10.0110055
MA0155.10.00401501
MA0156.10.224407
MA0157.10.807311
MA0158.10
MA0159.10.563553
MA0160.10.470272
MA0161.10
MA0162.10.000165262
MA0163.10.000292658
MA0164.11.27209
MA0080.20.438824
MA0018.20.225392
MA0099.20.172833
MA0079.22.60851e-13
MA0102.20.983247
MA0258.10.452847
MA0259.10.138164
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

This analysis result is provided for C0 - C305 clusters.

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