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Coexpression cluster:C2766: Difference between revisions

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{{Coexpression_clusters
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7587,0.285122,0.22741,0.203996,0.276721,0.321965,0.264707,0.450113|tfbs_overrepresentation_for_novel_motifs=0.590005,1.03954,0.581696,0.741427,0.534346,0.739643,0.821651,0.395818,0.392841,0.462021,1.68405,0.867962,0.341754,1.89595,0.532789,0.559384,1.05593,0.471262,0.356737,0.223552,0.581762,0.505745,0.731221,0.528529,0.632849,0.892087,0.849366,0.728867,0.537869,0.297585,1.63433,2.47734,0.433165,0.344471,0.49475,0.285913,0.491074,0.740899,1.17228,2.59922,0.493145,0.66492,0.183156,0.53106,1.59529,0.61613,0.822818,0.694903,0.173425,0.538016,0.90714,0.83543,0.25073,1.17354,1.33024,0.812467,0.54284,0.777235,0.806003,0.776148,1.13655,0.825354,0.393426,2.3411,0.844545,0.991076,1.42026,1.79268,1.08337,1.62905,0.650393,0.402607,0.248021,1.32819,0.336329,0.859396,0.305238,1.00941,1.08,0.62601,0.362435,1.02594,0.844168,0.399165,1.27559,0.353274,0.6318,0.291738,0.934646,1.89266,1.51507,1.24792,1.11156,0.441618,0.535192,0.456994,0.354969,2.60183,0.939507,0.272395,0.465545,1.1057,1.14983,1.05974,0.979006,1.67377,1.04326,0.805616,0.632569,1.28386,0.594299,1.14697,0.575476,0.717043,1.46636,0.489254,1.27972,0.681522,0.988625,0.444962,1.31973,0.932085,0.736652,0.856196,1.57854,1.0102,0.814847,1.11673,1.36323,0.458105,1.24863,0.68598,1.37788,0.852645,1.52813,0.283547,0.676268,0.729481,1.48509,2.34913,1.94535,1.44718,0.8167,1.15194,0.980848,0.768101,0.963351,2.1895,0.661255,0.437774,0.234974,0.175846,1.24902,0.383416,0.824835,1.65997,0.917558,0.518428,0.632914,0.600782,1.44595,1.23002,1.07918,0.604379,0.997702,0.843324,0.423521,0.820225,6.53028|tfbs_overrepresentation_jaspar=MA0003.1;5.41581,MA0004.1;0.71247,MA0006.1;0.532262,MA0007.1;0.6918,MA0009.1;1.20602,MA0014.1;9.60141,MA0017.1;0.577281,MA0019.1;0.873355,MA0024.1;1.09684,MA0025.1;1.34373,MA0027.1;2.83281,MA0028.1;0.550763,MA0029.1;1.11704,MA0030.1;1.10506,MA0031.1;1.03735,MA0038.1;0.824639,MA0040.1;1.12314,MA0041.1;0.732902,MA0042.1;0.697662,MA0043.1;1.20635,MA0046.1;1.19471,MA0048.1;0.25531,MA0050.1;0.69864,MA0051.1;1.91805,MA0052.1;1.12718,MA0055.1;0.125954,MA0056.1;0,MA0057.1;1.98521,MA0058.1;0.605914,MA0059.1;0.604454,MA0060.1;0.393285,MA0061.1;0.360128,MA0063.1;0,MA0066.1;1.92841,MA0067.1;1.53181,MA0068.1;0.313194,MA0069.1;1.19071,MA0070.1;1.17908,MA0071.1;0.782546,MA0072.1;1.1744,MA0073.1;1.18043,MA0074.1;0.819248,MA0076.1;0.623864,MA0077.1;1.16637,MA0078.1;0.926725,MA0081.1;0.604638,MA0083.1;1.21381,MA0084.1;1.72172,MA0087.1;1.17185,MA0088.1;1.02755,MA0089.1;0,MA0090.1;0.640115,MA0091.1;0.715356,MA0092.1;0.673508,MA0093.1;0.535768,MA0095.1;0,MA0098.1;0,MA0100.1;0.83965,MA0101.1;0.539569,MA0103.1;0.521546,MA0105.1;12.0668,MA0106.1;2.01886,MA0107.1;0.453492,MA0108.2;1.03412,MA0109.1;0,MA0111.1;0.655276,MA0113.1;0.886811,MA0114.1;0.447443,MA0115.1;1.45393,MA0116.1;7.71329,MA0117.1;1.24497,MA0119.1;0.586221,MA0122.1;1.27173,MA0124.1;1.41151,MA0125.1;1.32534,MA0130.1;0,MA0131.1;0.94608,MA0132.1;0,MA0133.1;0,MA0135.1;1.23748,MA0136.1;0.832277,MA0139.1;3.39971,MA0140.1;0.779643,MA0141.1;0.602484,MA0142.1;1.00381,MA0143.1;0.887001,MA0144.1;0.430413,MA0145.1;1.08195,MA0146.1;0.481,MA0147.1;0.46175,MA0148.1;0.739888,MA0149.1;0.769072,MA0062.2;1.66396,MA0035.2;0.778873,MA0039.2;2.01147,MA0138.2;0.928035,MA0002.2;0.379056,MA0137.2;0.558189,MA0104.2;0.392359,MA0047.2;0.856092,MA0112.2;0.187982,MA0065.2;1.09513,MA0150.1;0.633493,MA0151.1;0,MA0152.1;0.78681,MA0153.1;1.30799,MA0154.1;0.649108,MA0155.1;0.180766,MA0156.1;2.36058,MA0157.1;0.97481,MA0158.1;0,MA0159.1;0.462502,MA0160.1;0.756582,MA0161.1;0,MA0162.1;2.80246,MA0163.1;1.90765,MA0164.1;0.90014,MA0080.2;2.27911,MA0018.2;0.870662,MA0099.2;0.7872,MA0079.2;5.41326,MA0102.2;1.75932,MA0258.1;0.418966,MA0259.1;0.471671,MA0442.1;0}}
|full_id=C2766_Smooth_Hair_spindle_leiomyoma_Endothelial_bone_Multipotent
|id=C2766
}}

Latest revision as of 12:12, 17 September 2013


Full id: C2766_Smooth_Hair_spindle_leiomyoma_Endothelial_bone_Multipotent



Phase1 CAGE Peaks

Hg19::chr4:10117949..10117979,-p8@WDR1
Hg19::chr4:10118001..10118022,-p7@WDR1
Hg19::chr4:10118034..10118074,-p6@WDR1
Hg19::chr4:10118075..10118107,-p5@WDR1


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
mesodermal cell7.86e-37121
somatic cell1.14e-20588
fibroblast1.42e-2076
muscle precursor cell1.26e-1958
myoblast1.26e-1958
multi-potent skeletal muscle stem cell1.26e-1958
smooth muscle cell1.84e-1943
smooth muscle myoblast1.84e-1943
contractile cell2.80e-1959
muscle cell8.23e-1955
embryonic cell4.64e-18250
vascular associated smooth muscle cell5.13e-1832
electrically responsive cell4.05e-1761
electrically active cell4.05e-1761
non-terminally differentiated cell2.28e-16106
lining cell1.10e-1558
barrier cell1.10e-1558
animal cell6.26e-14679
eukaryotic cell6.26e-14679
multi fate stem cell4.42e-13427
meso-epithelial cell1.42e-1245
endothelial cell3.72e-1236
somatic stem cell4.35e-12433
endothelial cell of vascular tree1.98e-1124
stem cell7.63e-11441
blood vessel endothelial cell8.37e-1018
embryonic blood vessel endothelial progenitor cell8.37e-1018
native cell4.94e-07722
Uber Anatomy
Ontology termp-valuen
vasculature4.67e-3178
vascular system4.67e-3178
vessel3.32e-2768
epithelial tube open at both ends2.70e-2559
blood vessel2.70e-2559
blood vasculature2.70e-2559
vascular cord2.70e-2559
splanchnic layer of lateral plate mesoderm1.33e-2483
mesoderm2.20e-24315
mesoderm-derived structure2.20e-24315
presumptive mesoderm2.20e-24315
cardiovascular system3.47e-24109
circulatory system2.17e-23112
artery2.18e-2242
arterial blood vessel2.18e-2242
arterial system2.18e-2242
epithelial vesicle3.49e-2178
epithelial tube1.38e-20117
somite5.45e-1971
presomitic mesoderm5.45e-1971
presumptive segmental plate5.45e-1971
dermomyotome5.45e-1971
trunk paraxial mesoderm5.45e-1971
dense mesenchyme tissue9.49e-1973
paraxial mesoderm2.17e-1872
presumptive paraxial mesoderm2.17e-1872
unilaminar epithelium8.20e-18148
systemic artery3.74e-1733
systemic arterial system3.74e-1733
skeletal muscle tissue5.02e-1762
striated muscle tissue5.02e-1762
myotome5.02e-1762
multilaminar epithelium1.13e-1683
muscle tissue1.20e-1664
musculature1.20e-1664
musculature of body1.20e-1664
lateral plate mesoderm4.43e-16203
trunk mesenchyme6.00e-16122
musculoskeletal system2.51e-14167
mesenchyme3.73e-14160
entire embryonic mesenchyme3.73e-14160
anatomical system3.53e-12624
multi-cellular organism3.69e-12656
anatomical group5.57e-12625
aorta1.06e-1021
aortic system1.06e-1021
trunk7.66e-10199
blood vessel endothelium8.37e-1018
endothelium8.37e-1018
cardiovascular system endothelium8.37e-1018
cell layer4.83e-09309
organism subdivision8.17e-09264
epithelium1.70e-08306
simple squamous epithelium1.77e-0822
squamous epithelium3.66e-0825
developing anatomical structure1.13e-07581
embryonic structure1.41e-07564
germ layer4.08e-07560
germ layer / neural crest4.08e-07560
embryonic tissue4.08e-07560
presumptive structure4.08e-07560
germ layer / neural crest derived structure4.08e-07560
epiblast (generic)4.08e-07560


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)
MA0003.15.41581
MA0004.10.71247
MA0006.10.532262
MA0007.10.6918
MA0009.11.20602
MA0014.19.60141
MA0017.10.577281
MA0019.10.873355
MA0024.11.09684
MA0025.11.34373
MA0027.12.83281
MA0028.10.550763
MA0029.11.11704
MA0030.11.10506
MA0031.11.03735
MA0038.10.824639
MA0040.11.12314
MA0041.10.732902
MA0042.10.697662
MA0043.11.20635
MA0046.11.19471
MA0048.10.25531
MA0050.10.69864
MA0051.11.91805
MA0052.11.12718
MA0055.10.125954
MA0056.10
MA0057.11.98521
MA0058.10.605914
MA0059.10.604454
MA0060.10.393285
MA0061.10.360128
MA0063.10
MA0066.11.92841
MA0067.11.53181
MA0068.10.313194
MA0069.11.19071
MA0070.11.17908
MA0071.10.782546
MA0072.11.1744
MA0073.11.18043
MA0074.10.819248
MA0076.10.623864
MA0077.11.16637
MA0078.10.926725
MA0081.10.604638
MA0083.11.21381
MA0084.11.72172
MA0087.11.17185
MA0088.11.02755
MA0089.10
MA0090.10.640115
MA0091.10.715356
MA0092.10.673508
MA0093.10.535768
MA0095.10
MA0098.10
MA0100.10.83965
MA0101.10.539569
MA0103.10.521546
MA0105.112.0668
MA0106.12.01886
MA0107.10.453492
MA0108.21.03412
MA0109.10
MA0111.10.655276
MA0113.10.886811
MA0114.10.447443
MA0115.11.45393
MA0116.17.71329
MA0117.11.24497
MA0119.10.586221
MA0122.11.27173
MA0124.11.41151
MA0125.11.32534
MA0130.10
MA0131.10.94608
MA0132.10
MA0133.10
MA0135.11.23748
MA0136.10.832277
MA0139.13.39971
MA0140.10.779643
MA0141.10.602484
MA0142.11.00381
MA0143.10.887001
MA0144.10.430413
MA0145.11.08195
MA0146.10.481
MA0147.10.46175
MA0148.10.739888
MA0149.10.769072
MA0062.21.66396
MA0035.20.778873
MA0039.22.01147
MA0138.20.928035
MA0002.20.379056
MA0137.20.558189
MA0104.20.392359
MA0047.20.856092
MA0112.20.187982
MA0065.21.09513
MA0150.10.633493
MA0151.10
MA0152.10.78681
MA0153.11.30799
MA0154.10.649108
MA0155.10.180766
MA0156.12.36058
MA0157.10.97481
MA0158.10
MA0159.10.462502
MA0160.10.756582
MA0161.10
MA0162.12.80246
MA0163.11.90765
MA0164.10.90014
MA0080.22.27911
MA0018.20.870662
MA0099.20.7872
MA0079.25.41326
MA0102.21.75932
MA0258.10.418966
MA0259.10.471671
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
E2F1#186944.907389214879320.001724022357361790.010669303803064
ELF1#199744.258097958807540.003041525565781240.0161180174834903
ETS1#211337.296570691651750.00400857377511390.0192103627999413
GABPB1#255335.300762877136630.01012678824234270.0378780759702755
HEY1#2346244.040111043105710.00375304636917980.0186454385762901
HMGN3#932436.133910792512940.006640696683324720.0283092257198151
POU2F2#545249.106124057742520.000145395665174930.00188609835737231
SIN3A#2594245.408884726815140.001168172384885160.00797612158113368
TAF1#687243.343046285745290.008005664898701650.032296957523003
TBP#690843.706770687096390.005296377814784350.0244799257655453
ZBTB7A#5134147.35190930787590.000342223540015990.00347139513361791
ZEB1#6935312.66632401315790.000793336075912850.00613378934203895



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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