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Coexpression cluster:C1253: Difference between revisions

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{{Coexpression_clusters
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,0.282922,1.12779,0.307642,0.459366,0.921877,0.340293,0.265117,3.82518,1.47235,1.22101,0.511111,0.346342,0.684981,0.617179,0.373994,0.941629,1.09491,0.595623,0.350547,0.562713,0.897759,0.561701,0.905643,0.60771,0.224801,1.87621,0.625758,0.76514,1.18348,1.55228,0.854088,1.38987,0.4462,0.232216,2.41224,1.0929,0.531388,0.971313,0.473656,0.782748,0.850825,0.424224,0.200147,1.87399,0.625403,0.229431,1.04131,14.8042,2.21468,0.146388,0.711163,1.65172,1.27705,1.01423,0.881388,0.26423,0.343884,0.277058,1.07593,0.924148,1.70279,1.92468,0.28424,0.875714,0.918549,0.831244,1.78098,4.27664,0.815341,0.589207,0.43012,1.57162,0.395884,0.915771,0.988112,2.18413,1.22894,0.304323,0.155979,0.474472,0.762789,0.736663,1.0846,0.708722,0.525076,0.636741,1.33983,0.783512,0.597853,0.886402,1.12733,0.76179,1.01492,0.47854,1.14174,0.633392,1.28996,0.140417,0.469685,0.518459,1.24743,2.10682,1.70417,1.21002,0.59959,0.920609,0.755332,0.554217,0.738579,1.94751,0.456039,2.86323,0.106334,8.63219,1.0153,0.216774,0.607223,1.42052,0.694887,0.329354,0.430431,0.401655,1.2088,0.996724,0.850033,0.404861,0.7715,0.624608,2.78458,0.602897,0.0992692|tfbs_overrepresentation_jaspar=MA0003.1;6.06978,MA0004.1;0.502801,MA0006.1;0.904424,MA0007.1;0.483857,MA0009.1;0.973289,MA0014.1;3.71689,MA0017.1;0.380797,MA0019.1;0.652951,MA0024.1;0.867125,MA0025.1;1.10816,MA0027.1;2.59001,MA0028.1;0.35747,MA0029.1;0.886702,MA0030.1;0.875089,MA0031.1;0.809638,MA0038.1;0.60704,MA0040.1;0.892629,MA0041.1;0.521615,MA0042.1;0.48922,MA0043.1;0.973609,MA0046.1;0.962263,MA0048.1;0.766755,MA0050.1;0.490116,MA0051.1;0.602745,MA0052.1;0.896548,MA0055.1;0.158296,MA0056.1;0,MA0057.1;5.50125,MA0058.1;0.406232,MA0059.1;0.404929,MA0060.1;0.224688,MA0061.1;0.198335,MA0063.1;0,MA0066.1;0.607474,MA0067.1;1.29359,MA0068.1;0.162298,MA0069.1;0.958358,MA0070.1;0.947018,MA0071.1;0.567661,MA0072.1;0.942461,MA0073.1;47.3634,MA0074.1;1.46532,MA0076.1;0.422297,MA0077.1;0.934645,MA0078.1;0.703614,MA0081.1;0.405093,MA0083.1;0.980893,MA0084.1;1.48179,MA0087.1;0.939982,MA0088.1;2.49421,MA0089.1;0,MA0090.1;0.436918,MA0091.1;0.505453,MA0092.1;0.467172,MA0093.1;0.344385,MA0095.1;0,MA0098.1;0,MA0100.1;0.621149,MA0101.1;0.347695,MA0103.1;0.332048,MA0105.1;2.96525,MA0106.1;0.648997,MA0107.1;1.3795,MA0108.2;0.806528,MA0109.1;0,MA0111.1;0.45062,MA0113.1;0.665691,MA0114.1;0.269076,MA0115.1;1.21667,MA0116.1;0.277571,MA0117.1;1.01134,MA0119.1;0.388712,MA0122.1;1.03753,MA0124.1;1.17486,MA0125.1;1.0901,MA0130.1;0,MA0131.1;0.722072,MA0132.1;0,MA0133.1;0,MA0135.1;1.00402,MA0136.1;0.614215,MA0139.1;7.77512,MA0140.1;0.564957,MA0141.1;0.403171,MA0142.1;0.777365,MA0143.1;0.66587,MA0144.1;0.254954,MA0145.1;0.581146,MA0146.1;0.324987,MA0147.1;0.281049,MA0148.1;0.528066,MA0149.1;0.555119,MA0062.2;0.193221,MA0035.2;0.564239,MA0039.2;12.6411,MA0138.2;0.704862,MA0002.2;0.213296,MA0137.2;0.36398,MA0104.2;0.636673,MA0047.2;0.636643,MA0112.2;0.944394,MA0065.2;0.591589,MA0150.1;0.430951,MA0151.1;0,MA0152.1;0.571637,MA0153.1;1.07307,MA0154.1;6.98609,MA0155.1;0.250175,MA0156.1;0.36627,MA0157.1;0.749547,MA0158.1;0,MA0159.1;1.40717,MA0160.1;0.543522,MA0161.1;0,MA0162.1;9.53143,MA0163.1;2.18017,MA0164.1;0.678332,MA0080.2;0.344472,MA0018.2;0.650405,MA0099.2;0.572,MA0079.2;36.7457,MA0102.2;1.51913,MA0258.1;0.245543,MA0259.1;1.43531,MA0442.1;0}}
|full_id=C1253_Fibroblast_Smooth_Cardiac_Mesenchymal_Adipocyte_mesenchymal_Wilms
|id=C1253
}}

Latest revision as of 11:41, 17 September 2013


Full id: C1253_Fibroblast_Smooth_Cardiac_Mesenchymal_Adipocyte_mesenchymal_Wilms



Phase1 CAGE Peaks

Hg19::chr1:182992405..182992422,+p5@LAMC1
Hg19::chr1:182992442..182992453,+p9@LAMC1
Hg19::chr1:182992521..182992541,+p7@LAMC1
Hg19::chr1:182992545..182992630,+p1@LAMC1
Hg19::chr1:182992639..182992662,+p4@LAMC1
Hg19::chr1:182992682..182992705,+p3@LAMC1
Hg19::chr1:182992728..182992739,+p8@LAMC1


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>disease_data<br>

Uber Anatomy
Ontology termp-valuen
splanchnic layer of lateral plate mesoderm5.95e-2283
vasculature1.92e-2078
vascular system1.92e-2078
somite2.29e-2071
presomitic mesoderm2.29e-2071
presumptive segmental plate2.29e-2071
dermomyotome2.29e-2071
trunk paraxial mesoderm2.29e-2071
epithelial vesicle2.51e-2078
dense mesenchyme tissue3.24e-2073
mesenchyme9.03e-20160
entire embryonic mesenchyme9.03e-20160
paraxial mesoderm1.02e-1972
presumptive paraxial mesoderm1.02e-1972
unilaminar epithelium1.11e-19148
skeletal muscle tissue1.69e-1962
striated muscle tissue1.69e-1962
myotome1.69e-1962
multilaminar epithelium2.85e-1983
muscle tissue3.55e-1964
musculature3.55e-1964
musculature of body3.55e-1964
epithelial tube1.13e-18117
trunk1.78e-18199
trunk mesenchyme3.42e-18122
vessel1.44e-1768
circulatory system2.43e-17112
organism subdivision3.38e-17264
cardiovascular system6.35e-17109
epithelial tube open at both ends1.22e-1659
blood vessel1.22e-1659
blood vasculature1.22e-1659
vascular cord1.22e-1659
artery2.06e-1542
arterial blood vessel2.06e-1542
arterial system2.06e-1542
systemic artery1.55e-1333
systemic arterial system1.55e-1333
multi-cellular organism2.11e-13656
cell layer1.01e-10309
anatomical system2.55e-10624
epithelium2.85e-10306
anatomical group4.83e-10625
primary circulatory organ8.19e-1027
heart1.30e-0924
primitive heart tube1.30e-0924
primary heart field1.30e-0924
anterior lateral plate mesoderm1.30e-0924
heart tube1.30e-0924
heart primordium1.30e-0924
cardiac mesoderm1.30e-0924
cardiogenic plate1.30e-0924
heart rudiment1.30e-0924
multi-tissue structure4.24e-09342
mesoderm4.30e-09315
mesoderm-derived structure4.30e-09315
presumptive mesoderm4.30e-09315
anatomical cluster1.38e-08373
aorta4.79e-0821
aortic system4.79e-0821
surface structure5.07e-0899
organ component layer1.59e-0766
adipose tissue3.22e-0714
compound organ6.11e-0768
integument6.32e-0746
integumental system6.32e-0746
anatomical conduit9.74e-07240
Disease
Ontology termp-valuen
ovarian cancer3.97e-0714


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)
MA0003.16.06978
MA0004.10.502801
MA0006.10.904424
MA0007.10.483857
MA0009.10.973289
MA0014.13.71689
MA0017.10.380797
MA0019.10.652951
MA0024.10.867125
MA0025.11.10816
MA0027.12.59001
MA0028.10.35747
MA0029.10.886702
MA0030.10.875089
MA0031.10.809638
MA0038.10.60704
MA0040.10.892629
MA0041.10.521615
MA0042.10.48922
MA0043.10.973609
MA0046.10.962263
MA0048.10.766755
MA0050.10.490116
MA0051.10.602745
MA0052.10.896548
MA0055.10.158296
MA0056.10
MA0057.15.50125
MA0058.10.406232
MA0059.10.404929
MA0060.10.224688
MA0061.10.198335
MA0063.10
MA0066.10.607474
MA0067.11.29359
MA0068.10.162298
MA0069.10.958358
MA0070.10.947018
MA0071.10.567661
MA0072.10.942461
MA0073.147.3634
MA0074.11.46532
MA0076.10.422297
MA0077.10.934645
MA0078.10.703614
MA0081.10.405093
MA0083.10.980893
MA0084.11.48179
MA0087.10.939982
MA0088.12.49421
MA0089.10
MA0090.10.436918
MA0091.10.505453
MA0092.10.467172
MA0093.10.344385
MA0095.10
MA0098.10
MA0100.10.621149
MA0101.10.347695
MA0103.10.332048
MA0105.12.96525
MA0106.10.648997
MA0107.11.3795
MA0108.20.806528
MA0109.10
MA0111.10.45062
MA0113.10.665691
MA0114.10.269076
MA0115.11.21667
MA0116.10.277571
MA0117.11.01134
MA0119.10.388712
MA0122.11.03753
MA0124.11.17486
MA0125.11.0901
MA0130.10
MA0131.10.722072
MA0132.10
MA0133.10
MA0135.11.00402
MA0136.10.614215
MA0139.17.77512
MA0140.10.564957
MA0141.10.403171
MA0142.10.777365
MA0143.10.66587
MA0144.10.254954
MA0145.10.581146
MA0146.10.324987
MA0147.10.281049
MA0148.10.528066
MA0149.10.555119
MA0062.20.193221
MA0035.20.564239
MA0039.212.6411
MA0138.20.704862
MA0002.20.213296
MA0137.20.36398
MA0104.20.636673
MA0047.20.636643
MA0112.20.944394
MA0065.20.591589
MA0150.10.430951
MA0151.10
MA0152.10.571637
MA0153.11.07307
MA0154.16.98609
MA0155.10.250175
MA0156.10.36627
MA0157.10.749547
MA0158.10
MA0159.11.40717
MA0160.10.543522
MA0161.10
MA0162.19.53143
MA0163.12.18017
MA0164.10.678332
MA0080.20.344472
MA0018.20.650405
MA0099.20.572
MA0079.236.7457
MA0102.21.51913
MA0258.10.245543
MA0259.11.43531
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
CTCF#1066453.828754552196450.003387371192681340.0172943713332248
E2F1#186964.206333612753710.0004135232017007640.00393835032486103
EGR1#195874.988179094810141.30079520165561e-050.00031823319293912
GABPB1#255377.067683836182171.13438576906404e-064.66066543411798e-05
HEY1#2346274.040111043105715.68979821988558e-050.000950931087032534
NR3C1#2908714.9730233311735.91757635984462e-094.70697454261852e-07
POLR2A#543072.147453176558070.004747636447610280.0223511721489348
TAF1#687273.343046285745290.0002142336319622450.00246739592947783
TFAP2A#702037.079414731304980.006452554472180970.0280312107033862



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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