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Coexpression cluster:C757: Difference between revisions

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|tfbs_overrepresentation_for_novel_motifs=0.253158,3.9889,0.246925,0.373402,0.21227,0.371921,0.44126,1.25736,0.379568,0.363831,0.344881,0.481459,0.628958,0.430675,0.211157,0.230406,0.650562,0.168654,5.16118,2.36819,0.246975,0.423587,0.36495,0.599268,0.28596,0.50266,4.69143,0.363006,0.615097,3.05999,0.325512,0.685875,0.442593,1.57013,0.542692,4.39335,0.182011,0.372963,0.163827,3.73006,0.540033,0.836994,0.471149,1.13723,0.777723,0.273032,0.442265,0.335245,0.437532,0.214901,0.515974,0.453148,0.403355,0.760015,0.908824,0.433372,0.218374,0.40339,0.240754,0.402472,0.725346,0.444449,0.380466,0.624068,0.461047,0.591283,0.99547,1.35949,0.675894,1.19869,0.811076,0.394628,0.396939,0.906867,0.0876634,0.576459,0.914146,0.607953,0.672773,0.280653,0.682395,0.623044,0.46072,0.123028,0.856604,0.400752,0.607979,0.0654897,0.540459,1.45821,1.08742,0.830286,0.702047,0.456075,0.212875,1.49285,0.322542,0.743159,0.544807,0.792069,0.164861,0.696605,0.737766,0.654073,0.580349,0.340854,0.638916,0.427507,0.285742,0.578396,0.712243,0.735091,1.26108,0.353283,1.04009,0.533593,0.275187,0.324453,0.58906,0.151445,0.898765,1.33067,0.369441,0.471181,1.14929,0.608677,0.435413,0.706859,0.940494,0.482616,0.830959,0.328039,0.954592,0.468088,1.10012,1.26269,0.32024,0.363513,1.05827,1.9115,1.51034,1.02151,0.437004,0.739749,0.582016,1.02425,0.566218,1.75262,0.830443,0.449933,0.655201,0.234905,0.831331,0.113748,0.444001,1.22899,0.525224,0.582239,0.286011,0.261307,1.02032,0.813307,0.672017,0.729849,0.597299,0.459987,1.36371,0.440034,0.860859
|tfbs_overrepresentation_for_novel_motifs=0.253158,3.9889,0.246925,0.373402,0.21227,0.371921,0.44126,1.25736,0.379568,0.363831,0.344881,0.481459,0.628958,0.430675,0.211157,0.230406,0.650562,0.168654,5.16118,2.36819,0.246975,0.423587,0.36495,0.599268,0.28596,0.50266,4.69143,0.363006,0.615097,3.05999,0.325512,0.685875,0.442593,1.57013,0.542692,4.39335,0.182011,0.372963,0.163827,3.73006,0.540033,0.836994,0.471149,1.13723,0.777723,0.273032,0.442265,0.335245,0.437532,0.214901,0.515974,0.453148,0.403355,0.760015,0.908824,0.433372,0.218374,0.40339,0.240754,0.402472,0.725346,0.444449,0.380466,0.624068,0.461047,0.591283,0.99547,1.35949,0.675894,1.19869,0.811076,0.394628,0.396939,0.906867,0.0876634,0.576459,0.914146,0.607953,0.672773,0.280653,0.682395,0.623044,0.46072,0.123028,0.856604,0.400752,0.607979,0.0654897,0.540459,1.45821,1.08742,0.830286,0.702047,0.456075,0.212875,1.49285,0.322542,0.743159,0.544807,0.792069,0.164861,0.696605,0.737766,0.654073,0.580349,0.340854,0.638916,0.427507,0.285742,0.578396,0.712243,0.735091,1.26108,0.353283,1.04009,0.533593,0.275187,0.324453,0.58906,0.151445,0.898765,1.33067,0.369441,0.471181,1.14929,0.608677,0.435413,0.706859,0.940494,0.482616,0.830959,0.328039,0.954592,0.468088,1.10012,1.26269,0.32024,0.363513,1.05827,1.9115,1.51034,1.02151,0.437004,0.739749,0.582016,1.02425,0.566218,1.75262,0.830443,0.449933,0.655201,0.234905,0.831331,0.113748,0.444001,1.22899,0.525224,0.582239,0.286011,0.261307,1.02032,0.813307,0.672017,0.729849,0.597299,0.459987,1.36371,0.440034,0.860859
|tfbs_overrepresentation_jaspar=MA0003.1;0.342276,MA0004.1;0.349539,MA0006.1;1.14056,MA0007.1;0.332734,MA0009.1;0.79061,MA0014.1;0.114225,MA0017.1;0.682686,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;0.337481,MA0043.1;0.790919,MA0046.1;0.779945,MA0048.1;1.12059,MA0050.1;0.338274,MA0051.1;0.439895,MA0052.1;0.716602,MA0055.1;9.11537,MA0056.1;0,MA0057.1;0.397382,MA0058.1;0.732537,MA0059.1;0.2641,MA0060.1;0.119532,MA0061.1;0.100525,MA0063.1;0,MA0066.1;1.12972,MA0067.1;1.1037,MA0068.1;0.0758327,MA0069.1;0.776171,MA0070.1;0.765217,MA0071.1;1.85155,MA0072.1;0.760818,MA0073.1;4.87136e-05,MA0074.1;1.11883,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;0.755189,MA0089.1;0,MA0090.1;0.291627,MA0091.1;0.927876,MA0092.1;0.318032,MA0093.1;0.61153,MA0095.1;0,MA0098.1;0,MA0100.1;0.456802,MA0101.1;0.216017,MA0103.1;1.74349,MA0105.1;0.15707,MA0106.1;0.482519,MA0107.1;0.156959,MA0108.2;0.630531,MA0109.1;0,MA0111.1;0.819774,MA0113.1;0.498009,MA0114.1;1.45594,MA0115.1;1.02805,MA0116.1;0.935607,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;1.06363,MA0140.1;0.405425,MA0141.1;2.05996,MA0142.1;0.602852,MA0143.1;0.498176,MA0144.1;0.438224,MA0145.1;0.822953,MA0146.1;0.315774,MA0147.1;0.946858,MA0148.1;0.372124,MA0149.1;0.396509,MA0062.2;0.0969238,MA0035.2;0.404774,MA0039.2;0.267159,MA0138.2;1.323,MA0002.2;0.111226,MA0137.2;0.649788,MA0104.2;0.760822,MA0047.2;0.47109,MA0112.2;2.02459,MA0065.2;0.527167,MA0150.1;0.286461,MA0151.1;0,MA0152.1;0.411494,MA0153.1;0.887528,MA0154.1;0.153348,MA0155.1;0.245306,MA0156.1;0.231442,MA0157.1;0.576556,MA0158.1;0,MA0159.1;0.948902,MA0160.1;1.7766,MA0161.1;0,MA0162.1;0.00470038,MA0163.1;0.0158063,MA0164.1;0.509774,MA0080.2;0.21336,MA0018.2;0.483823,MA0099.2;1.05945,MA0079.2;0.0388923,MA0102.2;1.32663,MA0258.1;1.94665,MA0259.1;0.504687,MA0442.1;0
}}
}}

Revision as of 19:25, 22 January 2013


Full id: C757_Olfactory_Neutrophils_aorta_Fibroblast_Lens_mesothelioma_Aortic



Phase1 CAGE Peaks

Hg19::chr14:69349614..69349637,+p@chr14:69349614..69349637
+
Hg19::chr22:36682774..36682817,+p@chr22:36682774..36682817
+
Hg19::chr22:36684761..36684805,+p@chr22:36684761..36684805
+
Hg19::chr22:36688197..36688263,+p@chr22:36688197..36688263
+
Hg19::chr22:36690168..36690197,+p@chr22:36690168..36690197
+
Hg19::chr22:36690205..36690252,+p@chr22:36690205..36690252
+
Hg19::chr22:36693008..36693035,+p@chr22:36693008..36693035
+
Hg19::chr22:36695012..36695036,+p@chr22:36695012..36695036
+
Hg19::chr22:36696887..36696930,+p@chr22:36696887..36696930
+
Hg19::chr22:36696968..36697005,+p@chr22:36696968..36697005
+
Hg19::chr22:36697574..36697599,+p@chr22:36697574..36697599
+


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 cell5.97e-10121
fibroblast1.14e-0976
animal cell5.75e-09679
eukaryotic cell5.75e-09679
somatic cell1.11e-08588
embryonic cell1.54e-08250
native cell2.09e-07722
Uber Anatomy
Ontology termp-valuen
cardiovascular system9.97e-08109
circulatory system1.20e-07112


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)
MA0003.10.342276
MA0004.10.349539
MA0006.11.14056
MA0007.10.332734
MA0009.10.79061
MA0014.10.114225
MA0017.10.682686
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
MA0042.10.337481
MA0043.10.790919
MA0046.10.779945
MA0048.11.12059
MA0050.10.338274
MA0051.10.439895
MA0052.10.716602
MA0055.19.11537
MA0056.10
MA0057.10.397382
MA0058.10.732537
MA0059.10.2641
MA0060.10.119532
MA0061.10.100525
MA0063.10
MA0066.11.12972
MA0067.11.1037
MA0068.10.0758327
MA0069.10.776171
MA0070.10.765217
MA0071.11.85155
MA0072.10.760818
MA0073.14.87136e-05
MA0074.11.11883
MA0076.10.278993
MA0077.10.753278
MA0078.10.533387
MA0081.10.26424
MA0083.10.79797
MA0084.11.28962
MA0087.10.758426
MA0088.10.755189
MA0089.10
MA0090.10.291627
MA0091.10.927876
MA0092.10.318032
MA0093.10.61153
MA0095.10
MA0098.10
MA0100.10.456802
MA0101.10.216017
MA0103.11.74349
MA0105.10.15707
MA0106.10.482519
MA0107.10.156959
MA0108.20.630531
MA0109.10
MA0111.10.819774
MA0113.10.498009
MA0114.11.45594
MA0115.11.02805
MA0116.10.935607
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
MA0139.11.06363
MA0140.10.405425
MA0141.12.05996
MA0142.10.602852
MA0143.10.498176
MA0144.10.438224
MA0145.10.822953
MA0146.10.315774
MA0147.10.946858
MA0148.10.372124
MA0149.10.396509
MA0062.20.0969238
MA0035.20.404774
MA0039.20.267159
MA0138.21.323
MA0002.20.111226
MA0137.20.649788
MA0104.20.760822
MA0047.20.47109
MA0112.22.02459
MA0065.20.527167
MA0150.10.286461
MA0151.10
MA0152.10.411494
MA0153.10.887528
MA0154.10.153348
MA0155.10.245306
MA0156.10.231442
MA0157.10.576556
MA0158.10
MA0159.10.948902
MA0160.11.7766
MA0161.10
MA0162.10.00470038
MA0163.10.0158063
MA0164.10.509774
MA0080.20.21336
MA0018.20.483823
MA0099.21.05945
MA0079.20.0388923
MA0102.21.32663
MA0258.11.94665
MA0259.10.504687
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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