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Coexpression cluster:C1687: Difference between revisions

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|tfbs_overrepresentation_for_novel_motifs=0.508327,0.0561813,0.500341,0.654974,1.15291,0.653236,0.733342,0.324142,1.55025,0.106358,0.621241,0.778743,0.274093,0.721271,0.453496,0.478935,0.963929,0.395009,0.784337,0.167776,0.500405,0.384437,0.645033,0.44943,0.549618,0.802434,0.25115,0.642741,0.458349,0.233785,0.598009,1.00172,0.359091,0.27659,0.417272,0.0526856,0.413782,0.654459,0.388123,0.301779,2.80632,0.580638,0.414516,0.451846,0.218848,0.533483,0.734485,0.609718,1.28013,0.458489,0.817229,0.746838,0.191745,1.08035,1.2359,0.724351,0.4631,0.689906,0.233662,0.688844,1.04369,0.736968,0.321912,0.935408,0.755773,0.899893,1.32544,1.69665,0.991065,1.53343,0.566575,0.330474,0.189341,2.76015,0.269111,0.255232,0.240727,0.917983,2.26106,0.543014,0.796279,0.934302,0.755403,1.57121,1.18161,0.0719601,0.166306,0.228496,0.844289,1.79645,1.41984,1.15413,1.01895,3.53517,0.455791,0.99322,3.02869,1.06255,0.849074,0.211081,1.01093,1.01316,1.05685,0.967698,0.88799,0.616433,0.951411,0.717647,0.549347,0.437618,0.512457,1.05402,0.494368,0.631235,1.37132,0.412056,0.084145,0.596731,0.897476,0.370186,1.22546,0.841768,0.650322,0.767198,1.48307,0.918767,1.72534,1.02407,1.2687,0.382577,1.15483,0.601055,1.28328,0.763715,1.43285,0.221105,0.591636,0.643339,1.38998,2.25246,1.84906,1.35224,0.728494,1.05895,0.889806,0.680988,0.87256,2.09294,0.577088,0.363423,0.177807,0.126633,1.15522,0.312599,5.61831,1.56426,1.93328,0.439798,0.54968,0.518696,1.35101,1.13636,0.98692,0.522159,0.906429,0.754576,0.35004,0.731946,0.0214572
|tfbs_overrepresentation_for_novel_motifs=0.508327,0.0561813,0.500341,0.654974,1.15291,0.653236,0.733342,0.324142,1.55025,0.106358,0.621241,0.778743,0.274093,0.721271,0.453496,0.478935,0.963929,0.395009,0.784337,0.167776,0.500405,0.384437,0.645033,0.44943,0.549618,0.802434,0.25115,0.642741,0.458349,0.233785,0.598009,1.00172,0.359091,0.27659,0.417272,0.0526856,0.413782,0.654459,0.388123,0.301779,2.80632,0.580638,0.414516,0.451846,0.218848,0.533483,0.734485,0.609718,1.28013,0.458489,0.817229,0.746838,0.191745,1.08035,1.2359,0.724351,0.4631,0.689906,0.233662,0.688844,1.04369,0.736968,0.321912,0.935408,0.755773,0.899893,1.32544,1.69665,0.991065,1.53343,0.566575,0.330474,0.189341,2.76015,0.269111,0.255232,0.240727,0.917983,2.26106,0.543014,0.796279,0.934302,0.755403,1.57121,1.18161,0.0719601,0.166306,0.228496,0.844289,1.79645,1.41984,1.15413,1.01895,3.53517,0.455791,0.99322,3.02869,1.06255,0.849074,0.211081,1.01093,1.01316,1.05685,0.967698,0.88799,0.616433,0.951411,0.717647,0.549347,0.437618,0.512457,1.05402,0.494368,0.631235,1.37132,0.412056,0.084145,0.596731,0.897476,0.370186,1.22546,0.841768,0.650322,0.767198,1.48307,0.918767,1.72534,1.02407,1.2687,0.382577,1.15483,0.601055,1.28328,0.763715,1.43285,0.221105,0.591636,0.643339,1.38998,2.25246,1.84906,1.35224,0.728494,1.05895,0.889806,0.680988,0.87256,2.09294,0.577088,0.363423,0.177807,0.126633,1.15522,0.312599,5.61831,1.56426,1.93328,0.439798,0.54968,0.518696,1.35101,1.13636,0.98692,0.522159,0.906429,0.754576,0.35004,0.731946,0.0214572
|tfbs_overrepresentation_jaspar=MA0003.1;0.00991994,MA0004.1;0.626788,MA0006.1;0.452993,MA0007.1;0.606704,MA0009.1;1.11255,MA0014.1;0.0418333,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;1.55893,MA0042.1;0.612397,MA0043.1;1.11288,MA0046.1;1.10134,MA0048.1;0.195817,MA0050.1;1.48918,MA0051.1;0.731787,MA0052.1;1.03442,MA0055.1;0.0853006,MA0056.1;0,MA0057.1;0.189508,MA0058.1;0.523638,MA0059.1;0.522232,MA0060.1;0.321781,MA0061.1;1.44118,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;0.00220137,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;2.44595,MA0088.1;0.132006,MA0089.1;0,MA0090.1;3.44434,MA0091.1;0.629594,MA0092.1;0.588959,MA0093.1;0.456342,MA0095.1;0,MA0098.1;0,MA0100.1;0.750974,MA0101.1;2.02769,MA0103.1;0.442769,MA0105.1;0.175503,MA0106.1;0.779931,MA0107.1;1.74965,MA0108.2;0.94238,MA0109.1;0,MA0111.1;1.40074,MA0113.1;0.797251,MA0114.1;0.372523,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;1.76068,MA0139.1;0.277033,MA0140.1;2.78334,MA0141.1;0.520334,MA0142.1;0.912455,MA0143.1;0.797437,MA0144.1;0.356507,MA0145.1;0.143698,MA0146.1;0.0359558,MA0147.1;0.386018,MA0148.1;0.653474,MA0149.1;0.681935,MA0062.2;0.284987,MA0035.2;0.691506,MA0039.2;0.0118463,MA0138.2;0.837782,MA0002.2;0.83106,MA0137.2;0.47779,MA0104.2;0.320919,MA0047.2;0.767096,MA0112.2;0.136971,MA0065.2;0.146576,MA0150.1;3.41602,MA0151.1;0,MA0152.1;0.69926,MA0153.1;1.21379,MA0154.1;0.172764,MA0155.1;0.130813,MA0156.1;0.480289,MA0157.1;2.04894,MA0158.1;0,MA0159.1;0.386729,MA0160.1;0.669748,MA0161.1;0,MA0162.1;0.0592265,MA0163.1;0.0439995,MA0164.1;0.810347,MA0080.2;0.456437,MA0018.2;0.781393,MA0099.2;0.699641,MA0079.2;3.83292e-05,MA0102.2;1.66336,MA0258.1;0.345771,MA0259.1;0.395396,MA0442.1;0
}}
}}

Revision as of 20:06, 22 January 2013


Full id: C1687_liposarcoma_basal_Preadipocyte_Fibroblast_mesenchymal_Smooth_leiomyoma



Phase1 CAGE Peaks

Hg19::chr12:78333942..78333956,+p4@NAV3
Hg19::chr12:78334017..78334054,+p2@NAV3
Hg19::chr12:78334061..78334110,+p1@NAV3
Hg19::chr12:78334115..78334165,+p3@NAV3
Hg19::chr12:78334166..78334180,+p6@NAV3


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>

Cell Type
Ontology termp-valuen
mesodermal cell1.09e-30121
fibroblast3.58e-2376
animal cell1.42e-20679
eukaryotic cell1.42e-20679
embryonic cell7.68e-20250
muscle precursor cell2.14e-1958
myoblast2.14e-1958
multi-potent skeletal muscle stem cell2.14e-1958
muscle cell7.12e-1855
contractile cell9.35e-1759
smooth muscle cell7.09e-1643
smooth muscle myoblast7.09e-1643
electrically responsive cell8.01e-1561
electrically active cell8.01e-1561
non-terminally differentiated cell1.66e-14106
vascular associated smooth muscle cell3.01e-1432
skin fibroblast1.15e-1223
somatic cell1.26e-12588
native cell1.40e-12722
squamous epithelial cell5.56e-1163
lining cell5.71e-1158
barrier cell5.71e-1158
mesothelial cell9.40e-1019
preadipocyte2.98e-0712
endothelial cell of vascular tree6.42e-0724
somatic stem cell6.52e-07433
multi fate stem cell7.36e-07427
aortic smooth muscle cell9.30e-0710
Uber Anatomy
Ontology termp-valuen
somite4.36e-2071
presomitic mesoderm4.36e-2071
presumptive segmental plate4.36e-2071
dermomyotome4.36e-2071
trunk paraxial mesoderm4.36e-2071
unilaminar epithelium8.76e-20148
dense mesenchyme tissue1.67e-1973
paraxial mesoderm1.86e-1972
presumptive paraxial mesoderm1.86e-1972
epithelial vesicle6.45e-1978
vasculature2.04e-1878
vascular system2.04e-1878
multilaminar epithelium4.13e-1883
skeletal muscle tissue1.52e-1762
striated muscle tissue1.52e-1762
myotome1.52e-1762
muscle tissue6.31e-1764
musculature6.31e-1764
musculature of body6.31e-1764
vessel7.07e-1768
trunk mesenchyme1.48e-16122
epithelial tube open at both ends7.52e-1659
blood vessel7.52e-1659
blood vasculature7.52e-1659
vascular cord7.52e-1659
artery2.25e-1542
arterial blood vessel2.25e-1542
arterial system2.25e-1542
trunk2.43e-14199
splanchnic layer of lateral plate mesoderm5.05e-1483
organism subdivision1.87e-13264
epithelial tube3.57e-13117
cardiovascular system4.72e-13109
systemic artery2.20e-1233
systemic arterial system2.20e-1233
circulatory system5.03e-12112
mesenchyme2.29e-11160
entire embryonic mesenchyme2.29e-11160
surface structure3.37e-1199
skin of body1.25e-1041
integument1.42e-1046
integumental system1.42e-1046
aorta1.89e-0821
aortic system1.89e-0821
smooth muscle tissue1.45e-0715
cell layer9.15e-07309
blood vessel smooth muscle9.30e-0710
arterial system smooth muscle9.30e-0710
artery smooth muscle tissue9.30e-0710
aorta smooth muscle tissue9.30e-0710
Disease
Ontology termp-valuen
ovarian cancer1.09e-0814


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)
MA0003.10.00991994
MA0004.10.626788
MA0006.10.452993
MA0007.10.606704
MA0009.11.11255
MA0014.10.0418333
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
MA0041.11.55893
MA0042.10.612397
MA0043.11.11288
MA0046.11.10134
MA0048.10.195817
MA0050.11.48918
MA0051.10.731787
MA0052.11.03442
MA0055.10.0853006
MA0056.10
MA0057.10.189508
MA0058.10.523638
MA0059.10.522232
MA0060.10.321781
MA0061.11.44118
MA0063.10
MA0066.10.736721
MA0067.11.43651
MA0068.10.247962
MA0069.11.09737
MA0070.11.08584
MA0071.10.695094
MA0072.11.0812
MA0073.10.00220137
MA0074.10.730989
MA0076.10.540943
MA0077.11.07324
MA0078.10.836493
MA0081.10.522409
MA0083.11.12028
MA0084.11.62584
MA0087.12.44595
MA0088.10.132006
MA0089.10
MA0090.13.44434
MA0091.10.629594
MA0092.10.588959
MA0093.10.456342
MA0095.10
MA0098.10
MA0100.10.750974
MA0101.12.02769
MA0103.10.442769
MA0105.10.175503
MA0106.10.779931
MA0107.11.74965
MA0108.20.94238
MA0109.10
MA0111.11.40074
MA0113.10.797251
MA0114.10.372523
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
MA0136.11.76068
MA0139.10.277033
MA0140.12.78334
MA0141.10.520334
MA0142.10.912455
MA0143.10.797437
MA0144.10.356507
MA0145.10.143698
MA0146.10.0359558
MA0147.10.386018
MA0148.10.653474
MA0149.10.681935
MA0062.20.284987
MA0035.20.691506
MA0039.20.0118463
MA0138.20.837782
MA0002.20.83106
MA0137.20.47779
MA0104.20.320919
MA0047.20.767096
MA0112.20.136971
MA0065.20.146576
MA0150.13.41602
MA0151.10
MA0152.10.69926
MA0153.11.21379
MA0154.10.172764
MA0155.10.130813
MA0156.10.480289
MA0157.12.04894
MA0158.10
MA0159.10.386729
MA0160.10.669748
MA0161.10
MA0162.10.0592265
MA0163.10.0439995
MA0164.10.810347
MA0080.20.456437
MA0018.20.781393
MA0099.20.699641
MA0079.23.83292e-05
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
EP300#203356.77394172622327.00901578206049e-050.00110726758321376
FOS#235358.99795530889441.69470025615156e-050.000388824253190274
GATA2#2624512.7449317335542.9719152914525e-060.00010113517794852
JUN#3725512.51282919233633.25800591331781e-060.00010905861525032
JUND#372756.994663941871035.97069468343598e-050.000983399120081012
STAT3#6774510.51946499715427.759040745861e-060.000220262695421847
TCF7L2#6934510.77017656313736.89693748574565e-060.000199586936567966



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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