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Coexpression cluster:C1901: Difference between revisions

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|tfbs_overrepresentation_for_novel_motifs=1.26722,0.787587,0.500341,0.654974,0.454983,0.653236,1.73914,0.324142,1.55025,0.345702,0.621241,0.778743,0.274093,0.721271,0.453496,1.20439,0.963929,1.80748,3.03925,0.167776,0.500405,0.121147,0.645033,0.44943,1.35492,0.802434,0.25115,0.642741,0.458349,0.659743,0.598009,1.00172,1.68319,0.27659,0.417272,6.29178,0.413782,0.654459,0.388123,0.301779,0.415749,1.42042,6.75451,0.451846,0.218848,1.32072,0.734485,0.609718,4.8153,1.16046,0.817229,0.746838,0.191745,1.08035,1.2359,0.724351,0.4631,0.689906,0.659455,0.688844,1.04369,0.736968,0.86107,0.935408,0.755773,0.899893,1.32544,1.69665,0.991065,1.53343,0.566575,0.330474,0.554326,1.23387,0.269111,0.255232,2.72671,0.917983,0.987729,0.543014,0.293154,0.934302,0.755403,0.327263,1.18161,0.0719601,0.166306,2.64291,0.844289,1.79645,1.41984,1.15413,1.01895,0.96134,0.455791,0.381528,1.42387,1.06255,0.849074,2.52127,0.389604,1.01316,1.05685,0.967698,0.88799,0.616433,0.951411,0.717647,0.549347,0.437618,0.512457,1.05402,0.494368,1.52665,1.37132,0.412056,0.084145,0.596731,0.897476,0.370186,1.22546,0.841768,0.650322,0.767198,1.48307,0.918767,2.89249,1.02407,1.2687,0.382577,1.15483,0.601055,1.28328,1.80194,1.43285,1.18046,0.591636,0.643339,1.38998,2.25246,1.84906,1.35224,0.728494,1.05895,0.889806,1.63047,0.87256,2.09294,0.577088,0.363423,0.526389,0.126633,1.15522,0.312599,0.736459,1.56426,0.827475,0.439798,0.54968,0.518696,1.35101,1.13636,0.98692,0.522159,0.906429,0.754576,0.923751,0.731946,2.39025
|tfbs_overrepresentation_jaspar=MA0003.1;0.737422,MA0004.1;0.626788,MA0006.1;0.452993,MA0007.1;0.606704,MA0009.1;1.11255,MA0014.1;0.660087,MA0017.1;0.496101,MA0019.1;0.784036,MA0024.1;1.00439,MA0025.1;1.24931,MA0027.1;2.73598,MA0028.1;0.470679,MA0029.1;1.02437,MA0030.1;1.01252,MA0031.1;0.945567,MA0038.1;0.736268,MA0040.1;1.03042,MA0041.1;0.64667,MA0042.1;0.612397,MA0043.1;1.11288,MA0046.1;1.10134,MA0048.1;0.569896,MA0050.1;0.613347,MA0051.1;0.731787,MA0052.1;1.03442,MA0055.1;0.603517,MA0056.1;0,MA0057.1;1.66737,MA0058.1;0.523638,MA0059.1;0.522232,MA0060.1;0.321781,MA0061.1;0.291022,MA0063.1;0,MA0066.1;0.736721,MA0067.1;1.43651,MA0068.1;0.247962,MA0069.1;1.09737,MA0070.1;1.08584,MA0071.1;0.695094,MA0072.1;1.0812,MA0073.1;2.08296,MA0074.1;0.730989,MA0076.1;0.540943,MA0077.1;1.07324,MA0078.1;0.836493,MA0081.1;0.522409,MA0083.1;1.12028,MA0084.1;1.62584,MA0087.1;1.07867,MA0088.1;0.132006,MA0089.1;0,MA0090.1;0.556637,MA0091.1;0.629594,MA0092.1;1.43794,MA0093.1;0.456342,MA0095.1;0,MA0098.1;0,MA0100.1;0.750974,MA0101.1;0.459973,MA0103.1;0.442769,MA0105.1;0.175503,MA0106.1;0.779931,MA0107.1;0.378225,MA0108.2;0.94238,MA0109.1;0,MA0111.1;0.5713,MA0113.1;0.797251,MA0114.1;2.60288,MA0115.1;1.35895,MA0116.1;0.382106,MA0117.1;1.1512,MA0119.1;0.504689,MA0122.1;1.17777,MA0124.1;1.31673,MA0125.1;1.23103,MA0130.1;0,MA0131.1;0.855546,MA0132.1;0,MA0133.1;0,MA0135.1;1.14377,MA0136.1;0.743749,MA0139.1;0.277033,MA0140.1;0.692258,MA0141.1;0.520334,MA0142.1;0.912455,MA0143.1;0.797437,MA0144.1;0.938075,MA0145.1;0.143698,MA0146.1;7.08905,MA0147.1;0.386018,MA0148.1;0.653474,MA0149.1;0.681935,MA0062.2;0.284987,MA0035.2;0.691506,MA0039.2;0.527987,MA0138.2;0.837782,MA0002.2;1.50443,MA0137.2;0.47779,MA0104.2;0.320919,MA0047.2;0.767096,MA0112.2;1.96224,MA0065.2;6.08113,MA0150.1;0.550239,MA0151.1;0,MA0152.1;0.69926,MA0153.1;1.21379,MA0154.1;0.514087,MA0155.1;0.409315,MA0156.1;0.480289,MA0157.1;0.883854,MA0158.1;0,MA0159.1;0.386729,MA0160.1;0.669748,MA0161.1;0,MA0162.1;0.469165,MA0163.1;4.46402,MA0164.1;0.810347,MA0080.2;0.456437,MA0018.2;0.781393,MA0099.2;0.699641,MA0079.2;5.7251,MA0102.2;1.66336,MA0258.1;0.345771,MA0259.1;0.395396,MA0442.1;0
}}
}}

Revision as of 20:16, 22 January 2013


Full id: C1901_Cardiac_tridermal_Mesenchymal_sacrococcigeal_Hepatic_Smooth_Myoblast



Phase1 CAGE Peaks

Hg19::chr2:27301468..27301496,+p1@EMILIN1
Hg19::chr2:27301500..27301546,+p2@EMILIN1
Hg19::chr2:27301559..27301574,+p3@EMILIN1
Hg19::chr2:27301661..27301672,+p4@EMILIN1
Hg19::chr2:27301682..27301693,+p5@EMILIN1


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>

Uber Anatomy
Ontology termp-valuen
dense mesenchyme tissue3.87e-2773
somite9.99e-2771
presomitic mesoderm9.99e-2771
presumptive segmental plate9.99e-2771
dermomyotome9.99e-2771
trunk paraxial mesoderm9.99e-2771
paraxial mesoderm1.80e-2672
presumptive paraxial mesoderm1.80e-2672
muscle tissue2.70e-2564
musculature2.70e-2564
musculature of body2.70e-2564
epithelial vesicle8.68e-2578
skeletal muscle tissue1.49e-2462
striated muscle tissue1.49e-2462
myotome1.49e-2462
trunk mesenchyme7.10e-20122
multilaminar epithelium2.22e-1983
mesenchyme1.27e-18160
entire embryonic mesenchyme1.27e-18160
splanchnic layer of lateral plate mesoderm2.48e-1483
multi-cellular organism1.88e-13656
mesoderm9.09e-13315
mesoderm-derived structure9.09e-13315
presumptive mesoderm9.09e-13315
tissue9.45e-13773
unilaminar epithelium1.72e-12148
multi-tissue structure2.70e-12342
vasculature6.51e-1278
vascular system6.51e-1278
circulatory system1.13e-11112
cardiovascular system1.99e-11109
anatomical system9.47e-10624
epithelial tube9.95e-10117
anatomical group1.45e-09625
cell layer2.11e-09309
epithelial tube open at both ends2.34e-0959
blood vessel2.34e-0959
blood vasculature2.34e-0959
vascular cord2.34e-0959
heart3.62e-0924
primitive heart tube3.62e-0924
primary heart field3.62e-0924
anterior lateral plate mesoderm3.62e-0924
heart tube3.62e-0924
heart primordium3.62e-0924
cardiac mesoderm3.62e-0924
cardiogenic plate3.62e-0924
heart rudiment3.62e-0924
primary circulatory organ3.88e-0927
epithelium4.19e-09306
systemic artery5.76e-0933
systemic arterial system5.76e-0933
vessel5.97e-0968
artery8.96e-0942
arterial blood vessel8.96e-0942
arterial system8.96e-0942
smooth muscle tissue1.39e-0815
germ layer2.15e-08560
germ layer / neural crest2.15e-08560
embryonic tissue2.15e-08560
presumptive structure2.15e-08560
germ layer / neural crest derived structure2.15e-08560
epiblast (generic)2.15e-08560
organism subdivision2.19e-08264
embryonic structure3.69e-08564
trunk8.66e-08199
musculoskeletal system1.27e-07167
anatomical cluster1.32e-07373


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)
MA0003.10.737422
MA0004.10.626788
MA0006.10.452993
MA0007.10.606704
MA0009.11.11255
MA0014.10.660087
MA0017.10.496101
MA0019.10.784036
MA0024.11.00439
MA0025.11.24931
MA0027.12.73598
MA0028.10.470679
MA0029.11.02437
MA0030.11.01252
MA0031.10.945567
MA0038.10.736268
MA0040.11.03042
MA0041.10.64667
MA0042.10.612397
MA0043.11.11288
MA0046.11.10134
MA0048.10.569896
MA0050.10.613347
MA0051.10.731787
MA0052.11.03442
MA0055.10.603517
MA0056.10
MA0057.11.66737
MA0058.10.523638
MA0059.10.522232
MA0060.10.321781
MA0061.10.291022
MA0063.10
MA0066.10.736721
MA0067.11.43651
MA0068.10.247962
MA0069.11.09737
MA0070.11.08584
MA0071.10.695094
MA0072.11.0812
MA0073.12.08296
MA0074.10.730989
MA0076.10.540943
MA0077.11.07324
MA0078.10.836493
MA0081.10.522409
MA0083.11.12028
MA0084.11.62584
MA0087.11.07867
MA0088.10.132006
MA0089.10
MA0090.10.556637
MA0091.10.629594
MA0092.11.43794
MA0093.10.456342
MA0095.10
MA0098.10
MA0100.10.750974
MA0101.10.459973
MA0103.10.442769
MA0105.10.175503
MA0106.10.779931
MA0107.10.378225
MA0108.20.94238
MA0109.10
MA0111.10.5713
MA0113.10.797251
MA0114.12.60288
MA0115.11.35895
MA0116.10.382106
MA0117.11.1512
MA0119.10.504689
MA0122.11.17777
MA0124.11.31673
MA0125.11.23103
MA0130.10
MA0131.10.855546
MA0132.10
MA0133.10
MA0135.11.14377
MA0136.10.743749
MA0139.10.277033
MA0140.10.692258
MA0141.10.520334
MA0142.10.912455
MA0143.10.797437
MA0144.10.938075
MA0145.10.143698
MA0146.17.08905
MA0147.10.386018
MA0148.10.653474
MA0149.10.681935
MA0062.20.284987
MA0035.20.691506
MA0039.20.527987
MA0138.20.837782
MA0002.21.50443
MA0137.20.47779
MA0104.20.320919
MA0047.20.767096
MA0112.21.96224
MA0065.26.08113
MA0150.10.550239
MA0151.10
MA0152.10.69926
MA0153.11.21379
MA0154.10.514087
MA0155.10.409315
MA0156.10.480289
MA0157.10.883854
MA0158.10
MA0159.10.386729
MA0160.10.669748
MA0161.10
MA0162.10.469165
MA0163.14.46402
MA0164.10.810347
MA0080.20.456437
MA0018.20.781393
MA0099.20.699641
MA0079.25.7251
MA0102.21.66336
MA0258.10.345771
MA0259.10.395396
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
EGR1#195854.988179094810140.0003237398000590710.00330961834165714
EP300#203356.77394172622327.00901578206049e-050.00110911302918578
RAD21#5885510.35503389545638.39503550283973e-060.00022958080986674
USF1#739156.361499277207969.59569864925045e-050.00136963943040736
YY1#752854.911170749853860.00034993140821360.0035283342674667



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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