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Coexpression cluster:C2390: Difference between revisions

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|tfbs_overrepresentation_for_novel_motifs=0.590005,1.03954,0.581696,0.741427,0.534346,0.739643,0.821651,0.395818,0.392841,1.44778,0.706765,0.867962,0.341754,0.809319,0.532789,0.559384,1.05593,0.471262,0.938585,0.635753,0.581762,0.975621,0.731221,0.528529,1.53003,0.892087,0.316693,0.728867,0.537869,0.297585,0.682839,1.09415,0.433165,0.344471,2.14358,0.0842336,1.23038,0.740899,0.463978,1.72725,0.493145,0.66492,1.03152,0.53106,1.59529,0.61613,0.822818,0.694903,0.173425,0.538016,0.90714,0.83543,0.699149,1.17354,1.33024,0.812467,0.54284,0.777235,0.297448,0.776148,1.13655,0.825354,0.393426,1.02706,0.844545,0.991076,1.42026,1.79268,1.08337,1.62905,1.5667,0.402607,1.98423,1.32819,0.893276,1.54953,0.305238,1.00941,1.08,0.62601,0.362435,1.02594,0.844168,0.399165,1.27559,2.34631,1.18341,0.291738,0.934646,1.89266,1.51507,1.24792,1.11156,0.441618,0.535192,2.0177,0.354969,1.15558,0.939507,0.272395,0.465545,1.1057,1.14983,1.05974,0.979006,0.701817,1.04326,0.805616,0.632569,0.516141,0.594299,2.58439,0.575476,1.70537,1.46636,0.489254,1.27972,0.681522,0.988625,0.444962,1.31973,0.932085,0.736652,0.856196,1.57854,1.0102,0.814847,1.11673,1.36323,0.458105,1.24863,0.68598,1.37788,0.852645,1.52813,0.283547,0.676268,0.729481,1.48509,2.34913,1.94535,1.44718,0.8167,1.15194,0.980848,0.768101,0.963351,2.1895,0.661255,0.437774,1.91548,6.57915,1.24902,4.69098,0.824835,1.65997,0.917558,0.518428,0.632914,0.600782,1.44595,1.23002,1.07918,0.604379,0.997702,0.843324,1.08488,0.820225,4.32515
|tfbs_overrepresentation_jaspar=MA0003.1;4.10305,MA0004.1;0.71247,MA0006.1;0.532262,MA0007.1;0.6918,MA0009.1;1.20602,MA0014.1;4.49713,MA0017.1;0.577281,MA0019.1;0.873355,MA0024.1;1.09684,MA0025.1;1.34373,MA0027.1;2.83281,MA0028.1;1.35734,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;1.30988,MA0050.1;0.69864,MA0051.1;0.820063,MA0052.1;1.12718,MA0055.1;0.791759,MA0056.1;0,MA0057.1;0.248209,MA0058.1;0.605914,MA0059.1;0.604454,MA0060.1;1.80156,MA0061.1;0.360128,MA0063.1;0,MA0066.1;0.825101,MA0067.1;1.53181,MA0068.1;2.31526,MA0069.1;1.19071,MA0070.1;1.17908,MA0071.1;0.782546,MA0072.1;1.1744,MA0073.1;14.5548,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;4.77747,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;1.22348,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;0.457606,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;4.40535,MA0140.1;0.779643,MA0141.1;0.602484,MA0142.1;1.00381,MA0143.1;0.887001,MA0144.1;1.09982,MA0145.1;0.569905,MA0146.1;2.31379,MA0147.1;2.03364,MA0148.1;0.739888,MA0149.1;0.769072,MA0062.2;0.353589,MA0035.2;0.778873,MA0039.2;2.01147,MA0138.2;0.928035,MA0002.2;0.379056,MA0137.2;1.37305,MA0104.2;1.79838,MA0047.2;0.856092,MA0112.2;1.05083,MA0065.2;0.577908,MA0150.1;0.633493,MA0151.1;0,MA0152.1;0.78681,MA0153.1;1.30799,MA0154.1;0.229241,MA0155.1;1.61785,MA0156.1;0.560797,MA0157.1;0.97481,MA0158.1;0,MA0159.1;0.462502,MA0160.1;0.756582,MA0161.1;0,MA0162.1;2.15942,MA0163.1;0.539587,MA0164.1;0.90014,MA0080.2;0.535868,MA0018.2;0.870662,MA0099.2;0.7872,MA0079.2;5.92758,MA0102.2;1.75932,MA0258.1;0.418966,MA0259.1;2.06681,MA0442.1;0
}}
}}

Revision as of 20:37, 22 January 2013


Full id: C2390_Renal_Endothelial_Alveolar_Hepatic_Mesenchymal_Sebocyte_mesothelioma



Phase1 CAGE Peaks

Hg19::chr16:75285508..75285580,-p1@BCAR1
Hg19::chr16:75285587..75285599,-p6@BCAR1
Hg19::chr16:75285612..75285626,-p4@BCAR1
Hg19::chr16:75299845..75299883,-p2@BCAR1


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
cell layer7.20e-28309
epithelium1.24e-26306
anatomical cluster1.60e-24373
anatomical conduit2.34e-23240
vasculature1.79e-2278
vascular system1.79e-2278
multi-cellular organism2.61e-20656
tube6.03e-20192
epithelial tube9.82e-19117
anatomical system3.30e-18624
multi-tissue structure5.30e-18342
anatomical group6.20e-18625
vessel6.44e-1868
organism subdivision3.99e-16264
epithelial tube open at both ends2.18e-1459
blood vessel2.18e-1459
blood vasculature2.18e-1459
vascular cord2.18e-1459
splanchnic layer of lateral plate mesoderm4.55e-1483
unilaminar epithelium1.98e-13148
blood vessel endothelium4.30e-1318
endothelium4.30e-1318
cardiovascular system endothelium4.30e-1318
trunk1.44e-12199
cardiovascular system3.38e-12109
circulatory system5.04e-12112
mesenchyme7.10e-12160
entire embryonic mesenchyme7.10e-12160
simple squamous epithelium2.59e-1122
embryo1.70e-10592
organ part2.72e-10218
trunk mesenchyme8.29e-10122
developing anatomical structure1.01e-09581
structure with developmental contribution from neural crest1.34e-09132
epithelial vesicle2.08e-0978
ectoderm-derived structure2.55e-09171
ectoderm2.55e-09171
presumptive ectoderm2.55e-09171
squamous epithelium3.59e-0925
ecto-epithelium1.72e-08104
embryonic structure4.71e-08564
germ layer4.99e-08560
germ layer / neural crest4.99e-08560
embryonic tissue4.99e-08560
presumptive structure4.99e-08560
germ layer / neural crest derived structure4.99e-08560
epiblast (generic)4.99e-08560
artery8.09e-0842
arterial blood vessel8.09e-0842
arterial system8.09e-0842
nephron epithelium8.94e-0815
renal tubule8.94e-0815
nephron tubule8.94e-0815
nephron8.94e-0815
uriniferous tubule8.94e-0815
nephrogenic mesenchyme8.94e-0815
neural plate1.51e-0782
presumptive neural plate1.51e-0782
parenchyma2.00e-0715
excretory tube2.44e-0716
kidney epithelium2.44e-0716
endothelial tube2.78e-079
arterial system endothelium2.78e-079
endothelium of artery2.78e-079
multilaminar epithelium4.55e-0783
dense mesenchyme tissue9.14e-0773


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)
MA0003.14.10305
MA0004.10.71247
MA0006.10.532262
MA0007.10.6918
MA0009.11.20602
MA0014.14.49713
MA0017.10.577281
MA0019.10.873355
MA0024.11.09684
MA0025.11.34373
MA0027.12.83281
MA0028.11.35734
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
MA0048.11.30988
MA0050.10.69864
MA0051.10.820063
MA0052.11.12718
MA0055.10.791759
MA0056.10
MA0057.10.248209
MA0058.10.605914
MA0059.10.604454
MA0060.11.80156
MA0061.10.360128
MA0063.10
MA0066.10.825101
MA0067.11.53181
MA0068.12.31526
MA0069.11.19071
MA0070.11.17908
MA0071.10.782546
MA0072.11.1744
MA0073.114.5548
MA0074.10.819248
MA0076.10.623864
MA0077.11.16637
MA0078.10.926725
MA0081.10.604638
MA0083.11.21381
MA0084.11.72172
MA0087.11.17185
MA0088.14.77747
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
MA0105.11.22348
MA0106.12.01886
MA0107.10.453492
MA0108.21.03412
MA0109.10
MA0111.10.655276
MA0113.10.886811
MA0114.10.447443
MA0115.11.45393
MA0116.10.457606
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
MA0139.14.40535
MA0140.10.779643
MA0141.10.602484
MA0142.11.00381
MA0143.10.887001
MA0144.11.09982
MA0145.10.569905
MA0146.12.31379
MA0147.12.03364
MA0148.10.739888
MA0149.10.769072
MA0062.20.353589
MA0035.20.778873
MA0039.22.01147
MA0138.20.928035
MA0002.20.379056
MA0137.21.37305
MA0104.21.79838
MA0047.20.856092
MA0112.21.05083
MA0065.20.577908
MA0150.10.633493
MA0151.10
MA0152.10.78681
MA0153.11.30799
MA0154.10.229241
MA0155.11.61785
MA0156.10.560797
MA0157.10.97481
MA0158.10
MA0159.10.462502
MA0160.10.756582
MA0161.10
MA0162.12.15942
MA0163.10.539587
MA0164.10.90014
MA0080.20.535868
MA0018.20.870662
MA0099.20.7872
MA0079.25.92758
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
CCNT2#90534.752151182721970.01386206996689490.048717593474191
E2F4#187439.501045236463330.001850751034728270.0109265453542106
ETS1#211349.728760922202340.0001115955317418140.00154492652963723
FOXA1#316938.311064812039090.002740138182109850.0150350578754529
HEY1#2346244.040111043105710.00375304636917980.0185879646109342
MYC#460945.22228187160940.001344309395272740.00887081120445374
NFYB#4801312.56984494015230.000811456397697350.00618731800533793
POU2F2#545236.829593043306890.004860473775203740.0227562209444794
TAF1#687243.343046285745290.008005664898701650.0321912615545182
TBP#690843.706770687096390.005296377814784350.0243957132662196
YY1#752844.911170749853860.00171871838055440.0106750656524961
ZNF143#7702310.12565741417090.001534861610688180.00976542258657711



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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