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MCL coexpression mm9:922: Difference between revisions

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{{MCL_coexpression_mm9
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regulation of Rho protein signal transduction;0.0271624509120334;!GO:0035021;negative regulation of Rac protein signal transduction;0.0271624509120334;!GO:0008060;ARF GTPase activator activity;0.0271624509120334;!GO:0050828;regulation of liquid surface tension;0.0271624509120334;20388!GO:0035020;regulation of Rac protein signal transduction;0.0271624509120334;!GO:0051058;negative regulation of small GTPase mediated signal transduction;0.0271624509120334;!GO:0030336;negative regulation of cell migration;0.0429612841110319;!GO:0005100;Rho GTPase activator activity;0.0429612841110319;!GO:0016601;Rac protein signal transduction;0.0429612841110319;!GO:0051271;negative regulation of cell motility;0.0429612841110319;!GO:0007585;respiratory gaseous exchange;0.0429612841110319;20388!GO:0040013;negative regulation of 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|gostat_on_MCL_coexpression=GO:0035024;negative regulation of Rho protein signal transduction;0.0271624509120334;!GO:0035021;negative regulation of Rac protein signal transduction;0.0271624509120334;!GO:0008060;ARF GTPase activator activity;0.0271624509120334;!GO:0050828;regulation of liquid surface tension;0.0271624509120334;20388!GO:0035020;regulation of Rac protein signal transduction;0.0271624509120334;!GO:0051058;negative regulation of small GTPase mediated signal transduction;0.0271624509120334;!GO:0030336;negative regulation of cell migration;0.0429612841110319;!GO:0005100;Rho GTPase activator activity;0.0429612841110319;!GO:0016601;Rac protein signal transduction;0.0429612841110319;!GO:0051271;negative regulation of cell motility;0.0429612841110319;!GO:0007585;respiratory gaseous exchange;0.0429612841110319;20388!GO:0040013;negative regulation of locomotion;0.0429612841110319;!
|ontology_enrichment_celltype=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0005177!4.50e-11!79;UBERON:0009569!7.56e-11!66;UBERON:0002100!1.04e-09!90;UBERON:0002048!1.85e-09!14;UBERON:0000117!1.85e-09!14;UBERON:0000171!1.85e-09!14;UBERON:0000170!1.85e-09!14;UBERON:0005597!1.85e-09!14;UBERON:0000118!1.85e-09!14;UBERON:0005153!3.26e-08!17
|tfbs_overrepresentation_for_novel_motifs=0.393008,0.289542,0.367606,0.434198,0.260188,0.448401,0.538088,0.515265,1.02512,0.170907,0.494602,0.526159,0.173454,0.550255,0.275867,0,0.742571,0.252772,0.483643,0.29826,0.332107,0.223663,0.549359,0.258745,0.374936,0.577606,0.153291,0.469052,0.303071,0.118137,0.455168,0.843667,0.250677,0.425071,0.276324,0.363049,0.678971,0.522578,0.221921,0.195877,0.256422,0.460258,0.450632,0.27776,0.209497,0.423266,0.662995,0.484612,0.386968,0.825035,0.725127,0.604356,0.732634,0.985264,1.00271,0.557354,0.314394,0.513517,0.447041,0.555328,0.823643,0.613749,0.560836,0.713876,0.568415,0.754324,1.139,1.48833,0.818971,1.34113,0.349355,0.178433,0.236196,1.03623,0.853709,0.409836,0.42492,0.651651,0.806481,0.892913,0.179489,0.759925,0.612313,0.167672,0.920903,0.789543,0.293679,0.376919,0.667883,1.65055,1.20871,0.925879,0.856465,0.265734,0.62322,1.73859,0.510015,0.859272,0.663249,0.681235,0.679141,0.843387,0.967837,0.725721,0.724668,0.459825,0.784351,0.480639,0.903338,0.333829,0.386136,0.96962,0.337254,0.499714,1.21576,0.254749,0.603195,0.437894,0.743872,1.24715,1.04163,0.692953,0.579418,0.650748,1.26989,0.810177,0.546178,0.849691,1.13749,0.268537,0.950857,0.427043,1.10792,0.570914,1.23736,0.061199,0.401212,0.461647,1.18819,2.01886,1.6187,1.14372,0.591394,0.854131,0.718197,0.460705,0.666107,1.9792,0.403515,0.261837,0.381863,0.780212,0.986833,0.598134,0.569994,1.06851,0.605358,1.42739,0.39061,0.400939,1.1977,0.920047,0.810622,0.383936,0.714896,0.562634,0.676555,2.24207,0.331912
|tfbs_overrepresentation_jaspar=MA0003.1;0.127295,MA0004.1;0.434673,MA0006.1;0.747445,MA0007.1;0.419994,MA0009.1;0.870101,MA0014.1;1.16295,MA0017.1;0.296816,MA0019.1;0.688051,MA0024.1;0.826339,MA0025.1;1.10341,MA0027.1;2.51754,MA0028.1;0.281528,MA0029.1;0.804619,MA0030.1;0.811181,MA0031.1;0.775627,MA0038.1;0.577528,MA0040.1;0.882616,MA0041.1;0.360875,MA0042.1;0.348174,MA0043.1;0.966833,MA0046.1;0.906029,MA0048.1;0.102483,MA0050.1;0.472794,MA0051.1;0.586414,MA0052.1;0.890676,MA0055.1;0.0283571,MA0056.1;0,MA0057.1;0.31126,MA0058.1;0.341628,MA0059.1;0.353484,MA0060.1;0.574356,MA0061.1;0.224905,MA0063.1;0,MA0066.1;0.566617,MA0067.1;1.21448,MA0068.1;0.319589,MA0069.1;0.891016,MA0070.1;0.881319,MA0071.1;0.471969,MA0072.1;0.872842,MA0073.1;0.934832,MA0074.1;0.531046,MA0076.1;0.315013,MA0077.1;0.851175,MA0078.1;0.61926,MA0081.1;0.980744,MA0083.1;0.96604,MA0084.1;1.54225,MA0087.1;0.922929,MA0088.1;0.49616,MA0089.1;0,MA0090.1;0.401197,MA0091.1;0.447561,MA0092.1;0.401504,MA0093.1;0.289361,MA0095.1;0,MA0098.1;0,MA0100.1;1.29122,MA0101.1;0.362124,MA0103.1;0.307078,MA0105.1;0.133231,MA0106.1;0.626997,MA0107.1;0.301222,MA0108.2;0.710846,MA0109.1;0,MA0111.1;0.415012,MA0113.1;0.598933,MA0114.1;0.222763,MA0115.1;0.969632,MA0116.1;0.27152,MA0117.1;0.937363,MA0119.1;0.951747,MA0122.1;0.957212,MA0124.1;1.16127,MA0125.1;1.0872,MA0130.1;0,MA0131.1;0.683521,MA0132.1;0,MA0133.1;0,MA0135.1;1.00325,MA0136.1;1.35732,MA0139.1;0.169849,MA0140.1;1.29098,MA0141.1;0.325895,MA0142.1;0.761136,MA0143.1;0.615203,MA0144.1;0.225588,MA0145.1;0.246409,MA0146.1;0.636109,MA0147.1;0.236889,MA0148.1;0.450593,MA0149.1;0.367458,MA0062.2;0.426733,MA0035.2;1.30087,MA0039.2;0.812684,MA0138.2;0.675599,MA0002.2;0.513194,MA0137.2;0.32312,MA0104.2;0.18504,MA0047.2;0.576767,MA0112.2;0.90045,MA0065.2;0.247168,MA0150.1;1.07698,MA0151.1;0,MA0152.1;0.576873,MA0153.1;1.01988,MA0154.1;0.100744,MA0155.1;0.579465,MA0156.1;1.52462,MA0157.1;0.729116,MA0158.1;0,MA0159.1;1.276,MA0160.1;0.453546,MA0161.1;0,MA0162.1;0.0925951,MA0163.1;1.36861,MA0164.1;0.551114,MA0080.2;2.26,MA0018.2;0.560731,MA0099.2;0.669311,MA0079.2;0.174131,MA0102.2;1.59466,MA0258.1;0.60477,MA0259.1;0.227035,MA0442.1;0
}}

Latest revision as of 16:06, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr11:97011339..97011398,-p1@Tbkbp1
Mm9::chr12:27100064..27100079,-p2@Rnf144a
Mm9::chr16:95680624..95680630,-p@chr16:95680624..95680630
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Mm9::chr16:95680889..95680991,-p1@Erg
Mm9::chr18:38146824..38146828,-p@chr18:38146824..38146828
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Mm9::chr18:38158368..38158425,-p1@Arap3
Mm9::chr18:38159171..38159194,-p@chr18:38159171..38159194
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Mm9::chr6:72254313..72254324,+p8@Sftpb


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

GO IDGO nameFDR corrected p-value
GO:0035024negative regulation of Rho protein signal transduction0.0271624509120334
GO:0035021negative regulation of Rac protein signal transduction0.0271624509120334
GO:0008060ARF GTPase activator activity0.0271624509120334
GO:0050828regulation of liquid surface tension0.0271624509120334
GO:0035020regulation of Rac protein signal transduction0.0271624509120334
GO:0051058negative regulation of small GTPase mediated signal transduction0.0271624509120334
GO:0030336negative regulation of cell migration0.0429612841110319
GO:0005100Rho GTPase activator activity0.0429612841110319
GO:0016601Rac protein signal transduction0.0429612841110319
GO:0051271negative regulation of cell motility0.0429612841110319
GO:0007585respiratory gaseous exchange0.0429612841110319
GO:0040013negative regulation of locomotion0.0429612841110319



Relative expression of the co-expression cluster over median <br>Analyst:




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><br>uberon_data<br><br>

Uber Anatomy
Ontology termp-valuen
trunk region element4.50e-1179
subdivision of trunk7.56e-1166
trunk1.04e-0990
lung1.85e-0914
respiratory tube1.85e-0914
respiration organ1.85e-0914
pair of lungs1.85e-0914
lung primordium1.85e-0914
lung bud1.85e-0914
epithelial bud3.26e-0817


TFBS overrepresentation<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)
MA0003.10.127295
MA0004.10.434673
MA0006.10.747445
MA0007.10.419994
MA0009.10.870101
MA0014.11.16295
MA0017.10.296816
MA0019.10.688051
MA0024.10.826339
MA0025.11.10341
MA0027.12.51754
MA0028.10.281528
MA0029.10.804619
MA0030.10.811181
MA0031.10.775627
MA0038.10.577528
MA0040.10.882616
MA0041.10.360875
MA0042.10.348174
MA0043.10.966833
MA0046.10.906029
MA0048.10.102483
MA0050.10.472794
MA0051.10.586414
MA0052.10.890676
MA0055.10.0283571
MA0056.10
MA0057.10.31126
MA0058.10.341628
MA0059.10.353484
MA0060.10.574356
MA0061.10.224905
MA0063.10
MA0066.10.566617
MA0067.11.21448
MA0068.10.319589
MA0069.10.891016
MA0070.10.881319
MA0071.10.471969
MA0072.10.872842
MA0073.10.934832
MA0074.10.531046
MA0076.10.315013
MA0077.10.851175
MA0078.10.61926
MA0081.10.980744
MA0083.10.96604
MA0084.11.54225
MA0087.10.922929
MA0088.10.49616
MA0089.10
MA0090.10.401197
MA0091.10.447561
MA0092.10.401504
MA0093.10.289361
MA0095.10
MA0098.10
MA0100.11.29122
MA0101.10.362124
MA0103.10.307078
MA0105.10.133231
MA0106.10.626997
MA0107.10.301222
MA0108.20.710846
MA0109.10
MA0111.10.415012
MA0113.10.598933
MA0114.10.222763
MA0115.10.969632
MA0116.10.27152
MA0117.10.937363
MA0119.10.951747
MA0122.10.957212
MA0124.11.16127
MA0125.11.0872
MA0130.10
MA0131.10.683521
MA0132.10
MA0133.10
MA0135.11.00325
MA0136.11.35732
MA0139.10.169849
MA0140.11.29098
MA0141.10.325895
MA0142.10.761136
MA0143.10.615203
MA0144.10.225588
MA0145.10.246409
MA0146.10.636109
MA0147.10.236889
MA0148.10.450593
MA0149.10.367458
MA0062.20.426733
MA0035.21.30087
MA0039.20.812684
MA0138.20.675599
MA0002.20.513194
MA0137.20.32312
MA0104.20.18504
MA0047.20.576767
MA0112.20.90045
MA0065.20.247168
MA0150.11.07698
MA0151.10
MA0152.10.576873
MA0153.11.01988
MA0154.10.100744
MA0155.10.579465
MA0156.11.52462
MA0157.10.729116
MA0158.10
MA0159.11.276
MA0160.10.453546
MA0161.10
MA0162.10.0925951
MA0163.11.36861
MA0164.10.551114
MA0080.22.26
MA0018.20.560731
MA0099.20.669311
MA0079.20.174131
MA0102.21.59466
MA0258.10.60477
MA0259.10.227035
MA0442.10
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