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Coexpression cluster:C776: Difference between revisions

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|tfbs_overrepresentation_for_novel_motifs=0.253158,0.0749074,0.690333,0.975357,0.21227,0.371921,0.44126,0.121034,0.11927,0.363831,0.344881,0.481459,0.0905352,0.430675,0.606477,0.651838,0.650562,0.972743,0.0986515,0.339956,0.246975,0.221361,0.36495,0.599268,0.779948,0.50266,0.267398,0.952441,0.214796,0.885559,0.325512,0.685875,0.14393,0.0919867,0.184525,0.687406,0.182011,0.372963,0.492146,0.347538,0.540033,0.311187,0.101961,0.60355,0.00493315,0.273032,0.442265,0.335245,0.0209574,0.214901,0.515974,0.453148,0.179579,0.760015,0.908824,0.433372,0.623552,0.40339,0.240754,0.402472,0.725346,0.444449,0.119615,0.624068,0.461047,0.591283,0.99547,1.35949,0.675894,1.19869,0.811076,1.28337,0.0464399,0.906867,0.0876634,0.273699,0.251446,0.607953,0.672773,0.280653,0.101808,0.623044,0.46072,0.778826,0.856604,0.00700967,0.0364455,1.30398,0.540459,1.45821,1.08742,0.830286,0.702047,0.892354,0.212875,0.159241,0.663027,0.743159,0.544807,0.0567143,0.494695,0.696605,0.737766,0.654073,0.580349,0.340854,0.638916,0.427507,0.285742,0.199366,0.712243,0.735091,0.242288,0.353283,1.04009,0.533593,0.0485013,0.324453,0.58906,0.461431,0.898765,0.538171,0.966635,0.471181,1.14929,0.608677,1.11065,0.706859,0.940494,0.482616,0.830959,0.328039,0.954592,1.18111,1.10012,0.0617084,0.32024,0.363513,1.05827,1.9115,1.51034,1.02151,0.437004,0.739749,0.582016,0.395692,1.39001,1.75262,0.308276,0.146851,0.160217,0.0216333,0.831331,0.365167,1.12922,1.22899,0.525224,0.582239,0.780063,0.261307,1.02032,0.813307,0.672017,0.264042,0.597299,0.459987,0.427322,0.440034,0.000550667
|tfbs_overrepresentation_for_novel_motifs=0.253158,0.0749074,0.690333,0.975357,0.21227,0.371921,0.44126,0.121034,0.11927,0.363831,0.344881,0.481459,0.0905352,0.430675,0.606477,0.651838,0.650562,0.972743,0.0986515,0.339956,0.246975,0.221361,0.36495,0.599268,0.779948,0.50266,0.267398,0.952441,0.214796,0.885559,0.325512,0.685875,0.14393,0.0919867,0.184525,0.687406,0.182011,0.372963,0.492146,0.347538,0.540033,0.311187,0.101961,0.60355,0.00493315,0.273032,0.442265,0.335245,0.0209574,0.214901,0.515974,0.453148,0.179579,0.760015,0.908824,0.433372,0.623552,0.40339,0.240754,0.402472,0.725346,0.444449,0.119615,0.624068,0.461047,0.591283,0.99547,1.35949,0.675894,1.19869,0.811076,1.28337,0.0464399,0.906867,0.0876634,0.273699,0.251446,0.607953,0.672773,0.280653,0.101808,0.623044,0.46072,0.778826,0.856604,0.00700967,0.0364455,1.30398,0.540459,1.45821,1.08742,0.830286,0.702047,0.892354,0.212875,0.159241,0.663027,0.743159,0.544807,0.0567143,0.494695,0.696605,0.737766,0.654073,0.580349,0.340854,0.638916,0.427507,0.285742,0.199366,0.712243,0.735091,0.242288,0.353283,1.04009,0.533593,0.0485013,0.324453,0.58906,0.461431,0.898765,0.538171,0.966635,0.471181,1.14929,0.608677,1.11065,0.706859,0.940494,0.482616,0.830959,0.328039,0.954592,1.18111,1.10012,0.0617084,0.32024,0.363513,1.05827,1.9115,1.51034,1.02151,0.437004,0.739749,0.582016,0.395692,1.39001,1.75262,0.308276,0.146851,0.160217,0.0216333,0.831331,0.365167,1.12922,1.22899,0.525224,0.582239,0.780063,0.261307,1.02032,0.813307,0.672017,0.264042,0.597299,0.459987,0.427322,0.440034,0.000550667
|tfbs_overrepresentation_jaspar=MA0003.1;0.000103786,MA0004.1;1.64978,MA0006.1;0.210781,MA0007.1;0.332734,MA0009.1;0.79061,MA0014.1;0.00227771,MA0017.1;0.24363,MA0019.1;0.486183,MA0024.1;0.688373,MA0025.1;0.921763,MA0027.1;2.39404,MA0028.1;0.224112,MA0029.1;0.707146,MA0030.1;0.696006,MA0031.1;0.633489,MA0038.1;0.443833,MA0040.1;0.712837,MA0041.1;0.366339,MA0042.1;0.895841,MA0043.1;0.790919,MA0046.1;0.779945,MA0048.1;0.0494179,MA0050.1;0.338274,MA0051.1;0.439895,MA0052.1;0.716602,MA0055.1;0.0496191,MA0056.1;0,MA0057.1;0.703296,MA0058.1;0.265212,MA0059.1;0.729981,MA0060.1;0.119532,MA0061.1;0.330174,MA0063.1;0,MA0066.1;0.444231,MA0067.1;1.1037,MA0068.1;1.95025,MA0069.1;0.776171,MA0070.1;0.765217,MA0071.1;0.40788,MA0072.1;0.760818,MA0073.1;0.0112492,MA0074.1;0.439193,MA0076.1;0.278993,MA0077.1;0.753278,MA0078.1;0.533387,MA0081.1;0.26424,MA0083.1;0.79797,MA0084.1;1.28962,MA0087.1;0.758426,MA0088.1;0.0234479,MA0089.1;0,MA0090.1;0.291627,MA0091.1;2.50413,MA0092.1;0.318032,MA0093.1;1.79894,MA0095.1;0,MA0098.1;0,MA0100.1;0.456802,MA0101.1;1.16085,MA0103.1;0.587485,MA0105.1;0.645738,MA0106.1;0.482519,MA0107.1;0.924453,MA0108.2;0.630531,MA0109.1;0,MA0111.1;0.819774,MA0113.1;0.498009,MA0114.1;0.153042,MA0115.1;1.02805,MA0116.1;0.481808,MA0117.1;0.827487,MA0119.1;0.250314,MA0122.1;0.852927,MA0124.1;0.98702,MA0125.1;0.904129,MA0130.1;0,MA0131.1;0.550695,MA0132.1;0,MA0133.1;0,MA0135.1;0.820382,MA0136.1;0.450422,MA0139.1;0.307853,MA0140.1;0.405425,MA0141.1;0.2626,MA0142.1;0.602852,MA0143.1;0.498176,MA0144.1;0.142196,MA0145.1;0.02761,MA0146.1;0.0109959,MA0147.1;1.51125,MA0148.1;1.72853,MA0149.1;0.396509,MA0062.2;0.0969238,MA0035.2;1.04409,MA0039.2;0.00136845,MA0138.2;0.534556,MA0002.2;0.725804,MA0137.2;0.229531,MA0104.2;0.760822,MA0047.2;1.18756,MA0112.2;0.0251803,MA0065.2;0.11899,MA0150.1;0.781086,MA0151.1;0,MA0152.1;1.05873,MA0153.1;0.887528,MA0154.1;0.0391503,MA0155.1;0.0230394,MA0156.1;0.231442,MA0157.1;0.576556,MA0158.1;0,MA0159.1;0.162854,MA0160.1;0.386031,MA0161.1;0,MA0162.1;0.00470038,MA0163.1;0.585549,MA0164.1;0.509774,MA0080.2;0.21336,MA0018.2;0.483823,MA0099.2;0.411824,MA0079.2;0.12952,MA0102.2;1.32663,MA0258.1;0.135061,MA0259.1;1.54967,MA0442.1;0
}}
}}

Revision as of 19:26, 22 January 2013


Full id: C776_chorionic_placenta_Smooth_Aortic_Fibroblast_leiomyoma_mesothelioma



Phase1 CAGE Peaks

Hg19::chr9:118916228..118916241,+p18@PAPPA
Hg19::chr9:118916249..118916260,+p11@PAPPA
Hg19::chr9:118950325..118950341,+p22@PAPPA
Hg19::chr9:118973954..118973965,+p@chr9:118973954..118973965
+
Hg19::chr9:119094607..119094618,+p50@PAPPA
Hg19::chr9:119160527..119160548,+p@chr9:119160527..119160548
+
Hg19::chr9:119160571..119160596,+p@chr9:119160571..119160596
+
Hg19::chr9:119160673..119160717,+p@chr9:119160673..119160717
+
Hg19::chr9:119161224..119161240,+p17@PAPPA
Hg19::chr9:119162143..119162169,+p14@PAPPA
Hg19::chr9:119163686..119163705,+p10@PAPPA


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
skeletal muscle tissue1.57e-1962
striated muscle tissue1.57e-1962
myotome1.57e-1962
muscle tissue1.41e-1864
musculature1.41e-1864
musculature of body1.41e-1864
artery1.20e-1742
arterial blood vessel1.20e-1742
arterial system1.20e-1742
systemic artery7.85e-1733
systemic arterial system7.85e-1733
somite1.10e-1571
presomitic mesoderm1.10e-1571
presumptive segmental plate1.10e-1571
dermomyotome1.10e-1571
trunk paraxial mesoderm1.10e-1571
paraxial mesoderm2.54e-1572
presumptive paraxial mesoderm2.54e-1572
dense mesenchyme tissue5.73e-1573
splanchnic layer of lateral plate mesoderm2.86e-1483
vasculature3.10e-1478
vascular system3.10e-1478
cardiovascular system1.36e-13109
epithelial vesicle2.40e-1378
circulatory system6.74e-13112
multilaminar epithelium7.57e-1383
epithelial tube open at both ends3.80e-1259
blood vessel3.80e-1259
blood vasculature3.80e-1259
vascular cord3.80e-1259
vessel1.72e-0968
smooth muscle tissue3.44e-0915
trunk mesenchyme4.00e-09122
epithelial tube6.96e-09117
blood vessel smooth muscle6.96e-0810
arterial system smooth muscle6.96e-0810
artery smooth muscle tissue6.96e-0810
aorta smooth muscle tissue6.96e-0810
unilaminar epithelium8.19e-08148
aorta1.79e-0721
aortic system1.79e-0721
mesenchyme2.55e-07160
entire embryonic mesenchyme2.55e-07160
trunk3.61e-07199
vasculature of organ5.82e-0711
artery wall7.90e-074
tunica adventitia of artery7.90e-074
adventitia7.90e-074
tunica adventitia of blood vessel7.90e-074
aorta tunica adventitia7.90e-074
aorta wall7.90e-074
Disease
Ontology termp-valuen
ovarian cancer1.64e-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)
MA0003.10.000103786
MA0004.11.64978
MA0006.10.210781
MA0007.10.332734
MA0009.10.79061
MA0014.10.00227771
MA0017.10.24363
MA0019.10.486183
MA0024.10.688373
MA0025.10.921763
MA0027.12.39404
MA0028.10.224112
MA0029.10.707146
MA0030.10.696006
MA0031.10.633489
MA0038.10.443833
MA0040.10.712837
MA0041.10.366339
MA0042.10.895841
MA0043.10.790919
MA0046.10.779945
MA0048.10.0494179
MA0050.10.338274
MA0051.10.439895
MA0052.10.716602
MA0055.10.0496191
MA0056.10
MA0057.10.703296
MA0058.10.265212
MA0059.10.729981
MA0060.10.119532
MA0061.10.330174
MA0063.10
MA0066.10.444231
MA0067.11.1037
MA0068.11.95025
MA0069.10.776171
MA0070.10.765217
MA0071.10.40788
MA0072.10.760818
MA0073.10.0112492
MA0074.10.439193
MA0076.10.278993
MA0077.10.753278
MA0078.10.533387
MA0081.10.26424
MA0083.10.79797
MA0084.11.28962
MA0087.10.758426
MA0088.10.0234479
MA0089.10
MA0090.10.291627
MA0091.12.50413
MA0092.10.318032
MA0093.11.79894
MA0095.10
MA0098.10
MA0100.10.456802
MA0101.11.16085
MA0103.10.587485
MA0105.10.645738
MA0106.10.482519
MA0107.10.924453
MA0108.20.630531
MA0109.10
MA0111.10.819774
MA0113.10.498009
MA0114.10.153042
MA0115.11.02805
MA0116.10.481808
MA0117.10.827487
MA0119.10.250314
MA0122.10.852927
MA0124.10.98702
MA0125.10.904129
MA0130.10
MA0131.10.550695
MA0132.10
MA0133.10
MA0135.10.820382
MA0136.10.450422
MA0139.10.307853
MA0140.10.405425
MA0141.10.2626
MA0142.10.602852
MA0143.10.498176
MA0144.10.142196
MA0145.10.02761
MA0146.10.0109959
MA0147.11.51125
MA0148.11.72853
MA0149.10.396509
MA0062.20.0969238
MA0035.21.04409
MA0039.20.00136845
MA0138.20.534556
MA0002.20.725804
MA0137.20.229531
MA0104.20.760822
MA0047.21.18756
MA0112.20.0251803
MA0065.20.11899
MA0150.10.781086
MA0151.10
MA0152.11.05873
MA0153.10.887528
MA0154.10.0391503
MA0155.10.0230394
MA0156.10.231442
MA0157.10.576556
MA0158.10
MA0159.10.162854
MA0160.10.386031
MA0161.10
MA0162.10.00470038
MA0163.10.585549
MA0164.10.509774
MA0080.20.21336
MA0018.20.483823
MA0099.20.411824
MA0079.20.12952
MA0102.21.32663
MA0258.10.135061
MA0259.11.54967
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

No analysis results for this cluster

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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