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Coexpression cluster:C634: Difference between revisions

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|tfbs_overrepresentation_for_novel_motifs=0.554539,7.7317,0.183956,0.297884,0.153879,0.296522,0.360887,0.270053,0.26618,0.586318,0.271739,0.398649,0.779126,0.925865,0.152923,0.169541,0.560096,0.37375,1.75445,3.90528,0.184,0.974005,0.290113,0.150321,0.623871,0.418678,2.02464,0.288329,0.156049,4.97831,0.254115,1.44899,0.658757,1.68246,0.810791,5.75509,0.12818,0.806075,1.76076,3.72707,0.129369,0.241157,0.0105046,0.903144,0.46015,0.206995,0.361827,0.262957,0.456684,0.15614,0.431291,0.372023,0.485552,0.666176,1.90083,0.353512,0.15913,0.325599,2.41813,0.324748,0.632472,0.95435,0.26694,0.534578,0.379438,0.503101,0.896916,1.25738,0.584559,1.09778,1.21759,0.987824,0.0242598,0.80977,0.0530506,1.54608,2.48458,0.519091,0.581542,0.61268,2.35217,0.533593,0.37913,0.274429,0.760489,0.218798,0.20656,0.0370991,0.454557,1.35556,0.98765,0.734737,0.609873,0.331798,0.154399,1.18021,0.476274,0.649779,0.458696,6.03911,0.113893,0.6046,0.644537,0.563483,0.492631,0.268065,0.548871,0.348037,0.623411,0.142849,0.561401,0.641937,0.531469,0.279418,0.940917,0.796977,0.145638,0.253155,1.25153,1.13724,0.801818,0.452379,0.294241,1.00953,1.04884,0.519787,0.355419,0.614537,0.842806,0.719563,0.735394,0.256408,0.856671,1.00316,1.00021,0.323556,1.28757,1.43309,0.95886,1.80749,1.40745,0.922589,0.938959,0.646464,1.23712,2.34127,0.47912,1.64894,1.2469,1.6366,0.712398,0.466341,0.735758,0.254041,0.363452,1.12781,0.440071,0.870811,0.218554,0.196611,0.921409,0.718143,0.580811,0.199028,0.508869,0.378443,1.56937,0.945224,3.27784
|tfbs_overrepresentation_for_novel_motifs=0.554539,7.7317,0.183956,0.297884,0.153879,0.296522,0.360887,0.270053,0.26618,0.586318,0.271739,0.398649,0.779126,0.925865,0.152923,0.169541,0.560096,0.37375,1.75445,3.90528,0.184,0.974005,0.290113,0.150321,0.623871,0.418678,2.02464,0.288329,0.156049,4.97831,0.254115,1.44899,0.658757,1.68246,0.810791,5.75509,0.12818,0.806075,1.76076,3.72707,0.129369,0.241157,0.0105046,0.903144,0.46015,0.206995,0.361827,0.262957,0.456684,0.15614,0.431291,0.372023,0.485552,0.666176,1.90083,0.353512,0.15913,0.325599,2.41813,0.324748,0.632472,0.95435,0.26694,0.534578,0.379438,0.503101,0.896916,1.25738,0.584559,1.09778,1.21759,0.987824,0.0242598,0.80977,0.0530506,1.54608,2.48458,0.519091,0.581542,0.61268,2.35217,0.533593,0.37913,0.274429,0.760489,0.218798,0.20656,0.0370991,0.454557,1.35556,0.98765,0.734737,0.609873,0.331798,0.154399,1.18021,0.476274,0.649779,0.458696,6.03911,0.113893,0.6046,0.644537,0.563483,0.492631,0.268065,0.548871,0.348037,0.623411,0.142849,0.561401,0.641937,0.531469,0.279418,0.940917,0.796977,0.145638,0.253155,1.25153,1.13724,0.801818,0.452379,0.294241,1.00953,1.04884,0.519787,0.355419,0.614537,0.842806,0.719563,0.735394,0.256408,0.856671,1.00316,1.00021,0.323556,1.28757,1.43309,0.95886,1.80749,1.40745,0.922589,0.938959,0.646464,1.23712,2.34127,0.47912,1.64894,1.2469,1.6366,0.712398,0.466341,0.735758,0.254041,0.363452,1.12781,0.440071,0.870811,0.218554,0.196611,0.921409,0.718143,0.580811,0.199028,0.508869,0.378443,1.56937,0.945224,3.27784
|tfbs_overrepresentation_jaspar=MA0003.1;0.426302,MA0004.1;0.275994,MA0006.1;0.152601,MA0007.1;0.260673,MA0009.1;0.695988,MA0014.1;0.0165986,MA0017.1;0.534321,MA0019.1;0.403106,MA0024.1;0.59663,MA0025.1;0.824398,MA0027.1;2.28954,MA0028.1;0.164086,MA0029.1;0.614815,MA0030.1;0.604021,MA0031.1;0.543644,MA0038.1;0.363295,MA0040.1;0.620334,MA0041.1;0.291389,MA0042.1;0.264992,MA0043.1;0.69629,MA0046.1;0.685589,MA0048.1;1.58526,MA0050.1;0.265714,MA0051.1;0.359609,MA0052.1;0.623986,MA0055.1;7.34042,MA0056.1;0,MA0057.1;0.10396,MA0058.1;0.200063,MA0059.1;0.199079,MA0060.1;0.0773489,MA0061.1;0.224865,MA0063.1;0,MA0066.1;0.363668,MA0067.1;1.00375,MA0068.1;0.169955,MA0069.1;0.681911,MA0070.1;0.671241,MA0071.1;1.58009,MA0072.1;0.666958,MA0073.1;2.02629e-05,MA0074.1;0.358953,MA0076.1;0.212295,MA0077.1;0.65962,MA0078.1;0.447828,MA0081.1;0.578007,MA0083.1;0.703169,MA0084.1;1.18798,MA0087.1;0.664629,MA0088.1;0.491738,MA0089.1;0,MA0090.1;0.223576,MA0091.1;0.278153,MA0092.1;0.691297,MA0093.1;0.154754,MA0095.1;0,MA0098.1;0,MA0100.1;0.375452,MA0101.1;0.1571,MA0103.1;0.448026,MA0105.1;0.225264,MA0106.1;0.399649,MA0107.1;0.107387,MA0108.2;0.540797,MA0109.1;0,MA0111.1;0.234271,MA0113.1;0.414278,MA0114.1;1.68233,MA0115.1;0.929032,MA0116.1;1.1824,MA0117.1;0.732,MA0119.1;0.548507,MA0122.1;0.756889,MA0124.1;0.888592,MA0125.1;0.807083,MA0130.1;0,MA0131.1;0.464307,MA0132.1;0,MA0133.1;0,MA0135.1;0.725055,MA0136.1;0.369468,MA0139.1;0.206516,MA0140.1;0.327488,MA0141.1;1.71348,MA0142.1;0.514195,MA0143.1;0.414436,MA0144.1;1.08559,MA0145.1;0.547424,MA0146.1;5.77643,MA0147.1;0.36013,MA0148.1;0.296708,MA0149.1;0.319221,MA0062.2;0.0599644,MA0035.2;0.326883,MA0039.2;0.166952,MA0138.2;2.95971,MA0002.2;0.531015,MA0137.2;0.504333,MA0104.2;0.265556,MA0047.2;0.388882,MA0112.2;2.83904,MA0065.2;1.18489,MA0150.1;0.218956,MA0151.1;0,MA0152.1;0.886132,MA0153.1;0.790794,MA0154.1;1.39905,MA0155.1;0.0101184,MA0156.1;0.170442,MA0157.1;0.489002,MA0158.1;0,MA0159.1;0.112236,MA0160.1;1.50795,MA0161.1;0,MA0162.1;0.00136062,MA0163.1;0.0183776,MA0164.1;0.425415,MA0080.2;0.154815,MA0018.2;0.400879,MA0099.2;0.333432,MA0079.2;0.0619564,MA0102.2;1.22472,MA0258.1;1.54793,MA0259.1;0.374338,MA0442.1;0
}}
}}

Revision as of 19:19, 22 January 2013


Full id: C634_Neutrophils_mesothelioma_Olfactory_Hair_Prostate_Alveolar_Lens



Phase1 CAGE Peaks

Hg19::chr22:36678570..36678625,-p11@MYH9
Hg19::chr22:36681202..36681214,-p@chr22:36681202..36681214
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Hg19::chr22:36685158..36685175,-p@chr22:36685158..36685175
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Hg19::chr22:36685210..36685219,-p@chr22:36685210..36685219
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Hg19::chr22:36685324..36685335,-p@chr22:36685324..36685335
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Hg19::chr22:36689488..36689518,-p@chr22:36689488..36689518
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Hg19::chr22:36690236..36690263,-p@chr22:36690236..36690263
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Hg19::chr22:36690269..36690301,-p@chr22:36690269..36690301
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Hg19::chr22:36691027..36691044,-p@chr22:36691027..36691044
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Hg19::chr22:36691062..36691080,-p@chr22:36691062..36691080
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Hg19::chr22:36691699..36691718,-p@chr22:36691699..36691718
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Hg19::chr22:36696939..36696962,-p5@MYH9
Hg19::chr22:36697014..36697048,-p12@MYH9
Hg19::chr22:36708215..36708237,-p@chr22:36708215..36708237
-


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
somatic cell7.23e-19588
native cell1.95e-16722
animal cell3.52e-16679
eukaryotic cell3.52e-16679
mesodermal cell2.24e-10121
embryonic cell1.83e-08250
lining cell2.19e-0758
barrier cell2.19e-0758
epithelial cell of nephron3.88e-0715
kidney cell5.41e-0717
kidney epithelial cell5.41e-0717
fibroblast5.88e-0776
Uber Anatomy
Ontology termp-valuen
circulatory system2.67e-08112
mesoderm2.68e-08315
mesoderm-derived structure2.68e-08315
presumptive mesoderm2.68e-08315
cardiovascular system3.96e-08109
epithelial tube6.53e-08117
vasculature1.21e-0778
vascular system1.21e-0778
nephron epithelium3.88e-0715
renal tubule3.88e-0715
nephron tubule3.88e-0715
nephron3.88e-0715
uriniferous tubule3.88e-0715
nephrogenic mesenchyme3.88e-0715
vessel8.69e-0768


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)
MA0003.10.426302
MA0004.10.275994
MA0006.10.152601
MA0007.10.260673
MA0009.10.695988
MA0014.10.0165986
MA0017.10.534321
MA0019.10.403106
MA0024.10.59663
MA0025.10.824398
MA0027.12.28954
MA0028.10.164086
MA0029.10.614815
MA0030.10.604021
MA0031.10.543644
MA0038.10.363295
MA0040.10.620334
MA0041.10.291389
MA0042.10.264992
MA0043.10.69629
MA0046.10.685589
MA0048.11.58526
MA0050.10.265714
MA0051.10.359609
MA0052.10.623986
MA0055.17.34042
MA0056.10
MA0057.10.10396
MA0058.10.200063
MA0059.10.199079
MA0060.10.0773489
MA0061.10.224865
MA0063.10
MA0066.10.363668
MA0067.11.00375
MA0068.10.169955
MA0069.10.681911
MA0070.10.671241
MA0071.11.58009
MA0072.10.666958
MA0073.12.02629e-05
MA0074.10.358953
MA0076.10.212295
MA0077.10.65962
MA0078.10.447828
MA0081.10.578007
MA0083.10.703169
MA0084.11.18798
MA0087.10.664629
MA0088.10.491738
MA0089.10
MA0090.10.223576
MA0091.10.278153
MA0092.10.691297
MA0093.10.154754
MA0095.10
MA0098.10
MA0100.10.375452
MA0101.10.1571
MA0103.10.448026
MA0105.10.225264
MA0106.10.399649
MA0107.10.107387
MA0108.20.540797
MA0109.10
MA0111.10.234271
MA0113.10.414278
MA0114.11.68233
MA0115.10.929032
MA0116.11.1824
MA0117.10.732
MA0119.10.548507
MA0122.10.756889
MA0124.10.888592
MA0125.10.807083
MA0130.10
MA0131.10.464307
MA0132.10
MA0133.10
MA0135.10.725055
MA0136.10.369468
MA0139.10.206516
MA0140.10.327488
MA0141.11.71348
MA0142.10.514195
MA0143.10.414436
MA0144.11.08559
MA0145.10.547424
MA0146.15.77643
MA0147.10.36013
MA0148.10.296708
MA0149.10.319221
MA0062.20.0599644
MA0035.20.326883
MA0039.20.166952
MA0138.22.95971
MA0002.20.531015
MA0137.20.504333
MA0104.20.265556
MA0047.20.388882
MA0112.22.83904
MA0065.21.18489
MA0150.10.218956
MA0151.10
MA0152.10.886132
MA0153.10.790794
MA0154.11.39905
MA0155.10.0101184
MA0156.10.170442
MA0157.10.489002
MA0158.10
MA0159.10.112236
MA0160.11.50795
MA0161.10
MA0162.10.00136062
MA0163.10.0183776
MA0164.10.425415
MA0080.20.154815
MA0018.20.400879
MA0099.20.333432
MA0079.20.0619564
MA0102.21.22472
MA0258.11.54793
MA0259.10.374338
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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