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Coexpression cluster:C2156: Difference between revisions

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|tfbs_overrepresentation_for_novel_motifs=0.590005,0.298605,0.581696,0.741427,0.534346,0.739643,1.92131,1.02453,0.392841,0.902371,0.706765,0.867962,0.905351,0.809319,0.532789,0.559384,1.05593,0.471262,0.938585,0.223552,1.42279,0.975621,0.731221,0.528529,1.53003,0.892087,0.316693,1.72987,0.537869,0.297585,0.682839,1.09415,0.433165,0.344471,0.49475,0.0842336,0.491074,1.75478,0.463978,0.371755,0.493145,0.66492,0.539378,0.53106,0.0946706,0.61613,0.822818,0.694903,0.173425,0.538016,0.90714,0.83543,0.25073,1.17354,1.33024,0.812467,0.54284,0.777235,0.297448,1.8276,1.13655,0.825354,0.393426,1.02706,1.96835,0.991076,1.42026,1.79268,1.08337,1.62905,0.650393,0.402607,0.248021,1.32819,0.893276,0.321165,0.305238,1.00941,1.08,0.62601,0.362435,1.02594,0.844168,0.399165,1.27559,0.109222,0.221873,1.44378,0.934646,1.89266,1.51507,2.78853,1.11156,0.441618,0.535192,0.456994,0.354969,1.15558,0.939507,0.272395,2.04634,1.1057,1.14983,1.05974,0.979006,0.701817,1.04326,0.805616,1.52945,0.516141,0.594299,1.14697,0.575476,0.717043,1.46636,0.489254,1.85914,0.681522,0.988625,0.444962,1.31973,0.932085,0.736652,0.856196,1.57854,1.0102,0.814847,1.11673,3.02112,0.458105,1.24863,0.68598,1.37788,0.852645,1.52813,0.283547,0.676268,0.729481,1.48509,2.34913,1.94535,1.44718,0.8167,1.15194,0.980848,3.02315,0.963351,2.1895,0.661255,0.437774,0.234974,1.58968,1.24902,0.383416,0.824835,1.65997,0.917558,0.518428,0.632914,0.600782,1.44595,1.23002,1.07918,0.604379,0.997702,0.843324,1.90479,0.820225,1.00378
|tfbs_overrepresentation_for_novel_motifs=0.590005,0.298605,0.581696,0.741427,0.534346,0.739643,1.92131,1.02453,0.392841,0.902371,0.706765,0.867962,0.905351,0.809319,0.532789,0.559384,1.05593,0.471262,0.938585,0.223552,1.42279,0.975621,0.731221,0.528529,1.53003,0.892087,0.316693,1.72987,0.537869,0.297585,0.682839,1.09415,0.433165,0.344471,0.49475,0.0842336,0.491074,1.75478,0.463978,0.371755,0.493145,0.66492,0.539378,0.53106,0.0946706,0.61613,0.822818,0.694903,0.173425,0.538016,0.90714,0.83543,0.25073,1.17354,1.33024,0.812467,0.54284,0.777235,0.297448,1.8276,1.13655,0.825354,0.393426,1.02706,1.96835,0.991076,1.42026,1.79268,1.08337,1.62905,0.650393,0.402607,0.248021,1.32819,0.893276,0.321165,0.305238,1.00941,1.08,0.62601,0.362435,1.02594,0.844168,0.399165,1.27559,0.109222,0.221873,1.44378,0.934646,1.89266,1.51507,2.78853,1.11156,0.441618,0.535192,0.456994,0.354969,1.15558,0.939507,0.272395,2.04634,1.1057,1.14983,1.05974,0.979006,0.701817,1.04326,0.805616,1.52945,0.516141,0.594299,1.14697,0.575476,0.717043,1.46636,0.489254,1.85914,0.681522,0.988625,0.444962,1.31973,0.932085,0.736652,0.856196,1.57854,1.0102,0.814847,1.11673,3.02112,0.458105,1.24863,0.68598,1.37788,0.852645,1.52813,0.283547,0.676268,0.729481,1.48509,2.34913,1.94535,1.44718,0.8167,1.15194,0.980848,3.02315,0.963351,2.1895,0.661255,0.437774,0.234974,1.58968,1.24902,0.383416,0.824835,1.65997,0.917558,0.518428,0.632914,0.600782,1.44595,1.23002,1.07918,0.604379,0.997702,0.843324,1.90479,0.820225,1.00378
|tfbs_overrepresentation_jaspar=MA0003.1;0.720743,MA0004.1;1.69588,MA0006.1;0.532262,MA0007.1;1.65296,MA0009.1;1.20602,MA0014.1;0.896009,MA0017.1;3.53539,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;0.709734,MA0050.1;0.69864,MA0051.1;0.820063,MA0052.1;1.12718,MA0055.1;0.125954,MA0056.1;0,MA0057.1;0.248209,MA0058.1;3.66086,MA0059.1;4.90158,MA0060.1;0.393285,MA0061.1;5.61029,MA0063.1;0,MA0066.1;0.825101,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;0.214613,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;0.536981,MA0089.1;0,MA0090.1;0.640115,MA0091.1;0.715356,MA0092.1;0.673508,MA0093.1;2.27878,MA0095.1;0,MA0098.1;0,MA0100.1;0.83965,MA0101.1;0.539569,MA0103.1;0.521546,MA0105.1;2.66951,MA0106.1;3.33935,MA0107.1;0.453492,MA0108.2;1.03412,MA0109.1;0,MA0111.1;0.655276,MA0113.1;0.886811,MA0114.1;1.98562,MA0115.1;1.45393,MA0116.1;2.01976,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;1.63368,MA0140.1;0.779643,MA0141.1;0.602484,MA0142.1;1.00381,MA0143.1;0.887001,MA0144.1;0.430413,MA0145.1;1.70272,MA0146.1;0.481,MA0147.1;2.03364,MA0148.1;0.739888,MA0149.1;0.769072,MA0062.2;0.353589,MA0035.2;0.778873,MA0039.2;3.07509,MA0138.2;0.928035,MA0002.2;0.379056,MA0137.2;0.558189,MA0104.2;1.79838,MA0047.2;0.856092,MA0112.2;2.35508,MA0065.2;4.07926,MA0150.1;0.633493,MA0151.1;0,MA0152.1;0.78681,MA0153.1;1.30799,MA0154.1;1.88496,MA0155.1;0.180766,MA0156.1;0.560797,MA0157.1;0.97481,MA0158.1;0,MA0159.1;2.03616,MA0160.1;0.756582,MA0161.1;0,MA0162.1;1.06783,MA0163.1;0.539587,MA0164.1;0.90014,MA0080.2;0.535868,MA0018.2;0.870662,MA0099.2;0.7872,MA0079.2;7.00686,MA0102.2;1.75932,MA0258.1;0.418966,MA0259.1;2.06681,MA0442.1;0
}}
}}

Revision as of 20:27, 22 January 2013


Full id: C2156_Mesenchymal_Smooth_leiomyoma_Fibroblast_Myoblast_Preadipocyte_Hair



Phase1 CAGE Peaks

Hg19::chr11:65687158..65687216,+p4@DRAP1
Hg19::chr11:65687222..65687240,+p7@DRAP1
Hg19::chr11:65687243..65687276,+p8@DRAP1
Hg19::chr11:65687362..65687436,+p3@DRAP1


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
epithelial vesicle2.76e-2078
somite7.69e-2071
presomitic mesoderm7.69e-2071
presumptive segmental plate7.69e-2071
dermomyotome7.69e-2071
trunk paraxial mesoderm7.69e-2071
dense mesenchyme tissue9.82e-2073
multilaminar epithelium1.05e-1983
paraxial mesoderm1.85e-1972
presumptive paraxial mesoderm1.85e-1972
artery2.39e-1742
arterial blood vessel2.39e-1742
arterial system2.39e-1742
skeletal muscle tissue4.70e-1662
striated muscle tissue4.70e-1662
myotome4.70e-1662
systemic artery9.57e-1533
systemic arterial system9.57e-1533
muscle tissue1.51e-1464
musculature1.51e-1464
musculature of body1.51e-1464
surface structure6.16e-1499
vessel1.04e-1368
vasculature2.12e-1378
vascular system2.12e-1378
epithelial tube open at both ends3.16e-1359
blood vessel3.16e-1359
blood vasculature3.16e-1359
vascular cord3.16e-1359
unilaminar epithelium5.18e-12148
splanchnic layer of lateral plate mesoderm7.20e-1183
cardiovascular system2.15e-10109
trunk mesenchyme2.93e-10122
integument3.24e-1046
integumental system3.24e-1046
mesenchyme1.46e-09160
entire embryonic mesenchyme1.46e-09160
skin of body4.97e-0941
circulatory system5.20e-09112
organism subdivision5.35e-08264
aorta7.14e-0821
aortic system7.14e-0821
mesoderm2.70e-07315
mesoderm-derived structure2.70e-07315
presumptive mesoderm2.70e-07315
epithelial tube3.25e-07117
musculoskeletal system4.90e-07167
trunk6.75e-07199


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)
MA0003.10.720743
MA0004.11.69588
MA0006.10.532262
MA0007.11.65296
MA0009.11.20602
MA0014.10.896009
MA0017.13.53539
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
MA0048.10.709734
MA0050.10.69864
MA0051.10.820063
MA0052.11.12718
MA0055.10.125954
MA0056.10
MA0057.10.248209
MA0058.13.66086
MA0059.14.90158
MA0060.10.393285
MA0061.15.61029
MA0063.10
MA0066.10.825101
MA0067.11.53181
MA0068.10.313194
MA0069.11.19071
MA0070.11.17908
MA0071.10.782546
MA0072.11.1744
MA0073.10.214613
MA0074.10.819248
MA0076.10.623864
MA0077.11.16637
MA0078.10.926725
MA0081.10.604638
MA0083.11.21381
MA0084.11.72172
MA0087.11.17185
MA0088.10.536981
MA0089.10
MA0090.10.640115
MA0091.10.715356
MA0092.10.673508
MA0093.12.27878
MA0095.10
MA0098.10
MA0100.10.83965
MA0101.10.539569
MA0103.10.521546
MA0105.12.66951
MA0106.13.33935
MA0107.10.453492
MA0108.21.03412
MA0109.10
MA0111.10.655276
MA0113.10.886811
MA0114.11.98562
MA0115.11.45393
MA0116.12.01976
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
MA0139.11.63368
MA0140.10.779643
MA0141.10.602484
MA0142.11.00381
MA0143.10.887001
MA0144.10.430413
MA0145.11.70272
MA0146.10.481
MA0147.12.03364
MA0148.10.739888
MA0149.10.769072
MA0062.20.353589
MA0035.20.778873
MA0039.23.07509
MA0138.20.928035
MA0002.20.379056
MA0137.20.558189
MA0104.21.79838
MA0047.20.856092
MA0112.22.35508
MA0065.24.07926
MA0150.10.633493
MA0151.10
MA0152.10.78681
MA0153.11.30799
MA0154.11.88496
MA0155.10.180766
MA0156.10.560797
MA0157.10.97481
MA0158.10
MA0159.12.03616
MA0160.10.756582
MA0161.10
MA0162.11.06783
MA0163.10.539587
MA0164.10.90014
MA0080.20.535868
MA0018.20.870662
MA0099.20.7872
MA0079.27.00686
MA0102.21.75932
MA0258.10.418966
MA0259.12.06681
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
BCL11A#53335214.18472755180350.007108328585298740.0296149165916713
BCL3#602217.27355140186920.004834494208076070.0226711750975375
BCLAF1#9774316.23948570759140.000380256706766480.00376539586593196
CCNT2#90534.752151182721970.01386206996689490.0487028434795308
E2F6#187645.017155731697390.00157802193473060.00995151457287175
EBF1#187936.679850134926750.005184294118278910.0240352684964235
EGR1#195844.988179094810140.001615011500076050.0101285165469551
EP300#203335.08045629466740.01144298405398240.0418714109597739
ETS1#211337.296570691651750.00400857377511390.0191980298298308
FOSL1#8061329.78518478727986.26173959487248e-050.00102487043025997
GABPB1#255335.300762877136630.01012678824234270.0378401301338831
GATA3#2625213.6182581786030.00769665208093340.03168804536132
HDAC2#3066310.06171517746970.00156372754474740.00992127702119396
HNF4A#3172211.56614518147680.01057585681762490.0390597605974938
HNF4G#3174321.56506689483510.0001638032421292610.00203538926885638
JUND#372735.245997956403270.01043432751748420.0386696970156678
MAX#414946.452555509007120.0005767613195645490.00484526829584958
MEF2C#4208220.6556772463120.003402570579445040.0173550043341796
MXI1#460137.471178721569470.003741314738550960.0186234769543646
MYC#460945.22228187160940.001344309395272740.00885793873393624
NR2C2#7182324.46095817893070.0001125906063438030.00155499211001593
PAX5#507946.669565531177830.0005052774169483260.0044322751678705
PBX3#5090210.95725634337210.01174530180688030.0428216007613201
SMC3#9126311.28369963369960.001115802366868050.00765457720660357
SP2#6668213.07676524692230.008330036536614940.0328022278051251
STAT1#6772315.52994062289940.000434088655175550.00404819939797118
STAT2#6773232.63188559322030.001379588775125520.0089810429523988
TCF7L2#693438.077632422353010.002978381685834620.0158574227613622



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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