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MCL coexpression mm9:926: Difference between revisions

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{{MCL_coexpression_mm9
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protein kinase activity;0.00971838531944563;19092!GO:0004690;cyclic nucleotide-dependent protein kinase activity;0.00971838531944563;19092!GO:0004908;interleukin-1 receptor activity;0.00971838531944563;17082!GO:0019966;interleukin-1 binding;0.00971838531944563;17082!GO:0019002;GMP binding;0.00971838531944563;19092!GO:0030553;cGMP binding;0.00971838531944563;19092!GO:0005952;cAMP-dependent protein kinase complex;0.00971838531944563;19092!GO:0008603;cAMP-dependent protein kinase regulator activity;0.0113371842039205;19092!GO:0030551;cyclic nucleotide binding;0.0159529763788705;19092!GO:0004907;interleukin receptor activity;0.0247194069537288;17082!GO:0019965;interleukin binding;0.0247194069537288;17082!GO:0019838;growth factor binding;0.0308310436698183;17082!GO:0004896;hematopoietin/interferon-class (D200-domain) cytokine receptor activity;0.0313591463294665;17082!GO:0019887;protein kinase regulator activity;0.0337087347741023;19092!GO:0019955;cytokine 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|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0000014!1.15e-13!5;UBERON:0001003!1.15e-13!5;UBERON:0002097!1.15e-13!5;UBERON:0002199!1.15e-13!5;UBERON:0007029!1.15e-13!5;UBERON:0007376!1.15e-13!5;UBERON:0002416!1.15e-13!5;UBERON:0007383!1.15e-13!5;UBERON:0001135!4.75e-10!3;UBERON:0004237!4.75e-10!3;UBERON:0004695!4.75e-10!3;UBERON:0002111!4.75e-10!3;UBERON:0004178!4.75e-10!3;UBERON:0000947!1.27e-07!4;UBERON:0001637!1.27e-07!4;UBERON:0004573!1.27e-07!4;UBERON:0003509!1.27e-07!4;UBERON:0004571!1.27e-07!4;UBERON:0010191!1.27e-07!4;UBERON:0004572!1.27e-07!4;UBERON:0003102!5.37e-07!22
|tfbs_overrepresentation_for_novel_motifs=0.393008,0.84953,0.367606,0.434198,0.260188,0.448401,0.538088,0.991481,0.535519,0.170907,0.494602,0.526159,0.173454,0.550255,0.756943,0,0.742571,0.252772,0.483643,0.620214,0.332107,0.0622758,0.549359,1.32267,0.374936,0.577606,0.909128,0.469052,0.303071,0.376624,0.455168,0.843667,0.699026,0.136998,0.276324,0.60397,0.242032,0.522578,0.631914,0.570041,0.712303,0.460258,0.450632,0.761266,0.0824666,0.423266,0.662995,0.484612,1.06276,0.305876,0.725127,0.604356,0.732634,0.985264,1.00271,0.557354,0.844204,0.513517,0.447041,0.555328,0.823643,0.613749,0.192045,0.713876,0.568415,0.754324,1.139,1.48833,0.818971,1.34113,0.349355,0.178433,0.0665967,1.03623,0.140213,0.409836,0.42492,0.651651,0.806481,0.336166,0.179489,0.759925,0.612313,0.167672,0.920903,0.025519,0.540827,0.757533,0.667883,1.65055,1.20871,0.925879,0.856465,0.265734,0.218233,1.10739,0.1711,0.859272,0.663249,0.332938,0.242106,0.843387,0.967837,0.725721,0.724668,0.459825,0.784351,0.480639,0.340849,0.333829,1.00333,0.96962,0.337254,0.499714,1.21576,0.708441,0.0359654,0.437894,0.743872,0.670977,1.04163,0.692953,0.579418,0.650748,1.26989,0.810177,0.546178,0.849691,1.13749,0.740166,0.950857,1.09252,1.10792,0.570914,1.23736,0.479867,0.401212,0.461647,1.18819,2.01886,1.6187,1.14372,1.44306,0.854131,0.718197,0.460705,1.59948,1.9792,0.403515,0.261837,0.120154,0.0553085,0.986833,0.598134,0.569994,1.06851,1.47241,0.782826,0.39061,0.400939,1.1977,0.920047,0.810622,0.383936,0.714896,0.562634,0.240994,0.524587,0.0131724
|tfbs_overrepresentation_jaspar=MA0003.1;0.016751,MA0004.1;0.434673,MA0006.1;0.271714,MA0007.1;0.419994,MA0009.1;0.870101,MA0014.1;0.012738,MA0017.1;0.804572,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;1.89978,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;0.0935008,MA0058.1;0.90507,MA0059.1;0.353484,MA0060.1;0.197678,MA0061.1;0.224905,MA0063.1;0,MA0066.1;0.566617,MA0067.1;1.21448,MA0068.1;11.6835,MA0069.1;0.891016,MA0070.1;0.881319,MA0071.1;0.471969,MA0072.1;0.872842,MA0073.1;3.20934,MA0074.1;0.531046,MA0076.1;0.315013,MA0077.1;0.851175,MA0078.1;0.61926,MA0081.1;0.375851,MA0083.1;0.96604,MA0084.1;1.54225,MA0087.1;2.12887,MA0088.1;0.064239,MA0089.1;0,MA0090.1;1.03628,MA0091.1;0.447561,MA0092.1;1.03695,MA0093.1;0.787675,MA0095.1;0,MA0098.1;0,MA0100.1;0.519598,MA0101.1;0.362124,MA0103.1;0.307078,MA0105.1;0.41549,MA0106.1;0.626997,MA0107.1;1.47808,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;0.362692,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;0.550755,MA0139.1;0.169849,MA0140.1;1.29098,MA0141.1;0.325895,MA0142.1;0.761136,MA0143.1;0.615203,MA0144.1;0.640537,MA0145.1;0.246409,MA0146.1;0.0169049,MA0147.1;0.236889,MA0148.1;0.450593,MA0149.1;0.367458,MA0062.2;0.137653,MA0035.2;0.524137,MA0039.2;0.254826,MA0138.2;0.675599,MA0002.2;0.172399,MA0137.2;0.863775,MA0104.2;0.18504,MA0047.2;0.576767,MA0112.2;0.0701537,MA0065.2;0.0704227,MA0150.1;2.82555,MA0151.1;0,MA0152.1;0.576873,MA0153.1;1.01988,MA0154.1;1.12269,MA0155.1;0.275377,MA0156.1;0.314185,MA0157.1;1.73039,MA0158.1;0,MA0159.1;0.246253,MA0160.1;0.453546,MA0161.1;0,MA0162.1;0.230918,MA0163.1;0.0186439,MA0164.1;0.551114,MA0080.2;0.302064,MA0018.2;0.560731,MA0099.2;0.669311,MA0079.2;0.24412,MA0102.2;1.59466,MA0258.1;0.210437,MA0259.1;0.227035,MA0442.1;0
}}

Latest revision as of 16:07, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr11:98909393..98909430,+p@chr11:98909393..98909430
+
Mm9::chr17:64212390..64212429,+p@chr17:64212390..64212429
+
Mm9::chr19:7613621..7613623,+p@chr19:7613621..7613623
+
Mm9::chr1:40496487..40496494,+p3@Il1rl1
Mm9::chr1:40496612..40496633,+p1@Il1rl1
Mm9::chr3:151668462..151668472,-p@chr3:151668462..151668472
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Mm9::chr5:99372782..99372792,-p6@Prkg2
Mm9::chr8:87160297..87160316,+p@chr8:87160297..87160316
+


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:0004692cGMP-dependent protein kinase activity0.00971838531944563
GO:0004690cyclic nucleotide-dependent protein kinase activity0.00971838531944563
GO:0004908interleukin-1 receptor activity0.00971838531944563
GO:0019966interleukin-1 binding0.00971838531944563
GO:0019002GMP binding0.00971838531944563
GO:0030553cGMP binding0.00971838531944563
GO:0005952cAMP-dependent protein kinase complex0.00971838531944563
GO:0008603cAMP-dependent protein kinase regulator activity0.0113371842039205
GO:0030551cyclic nucleotide binding0.0159529763788705
GO:0004907interleukin receptor activity0.0247194069537288
GO:0019965interleukin binding0.0247194069537288
GO:0019838growth factor binding0.0308310436698183
GO:0004896hematopoietin/interferon-class (D200-domain) cytokine receptor activity0.0313591463294665
GO:0019887protein kinase regulator activity0.0337087347741023
GO:0019955cytokine binding0.0337087347741023
GO:0019207kinase regulator activity0.0348969287172017
GO:0045087innate immune response0.0394855055171229



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>cell_data<br>uberon_data<br><br>


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)
MA0003.10.016751
MA0004.10.434673
MA0006.10.271714
MA0007.10.419994
MA0009.10.870101
MA0014.10.012738
MA0017.10.804572
MA0019.10.688051
MA0024.10.826339
MA0025.11.10341
MA0027.12.51754
MA0028.10.281528
MA0029.10.804619
MA0030.11.89978
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
MA0057.10.0935008
MA0058.10.90507
MA0059.10.353484
MA0060.10.197678
MA0061.10.224905
MA0063.10
MA0066.10.566617
MA0067.11.21448
MA0068.111.6835
MA0069.10.891016
MA0070.10.881319
MA0071.10.471969
MA0072.10.872842
MA0073.13.20934
MA0074.10.531046
MA0076.10.315013
MA0077.10.851175
MA0078.10.61926
MA0081.10.375851
MA0083.10.96604
MA0084.11.54225
MA0087.12.12887
MA0088.10.064239
MA0089.10
MA0090.11.03628
MA0091.10.447561
MA0092.11.03695
MA0093.10.787675
MA0095.10
MA0098.10
MA0100.10.519598
MA0101.10.362124
MA0103.10.307078
MA0105.10.41549
MA0106.10.626997
MA0107.11.47808
MA0108.20.710846
MA0109.10
MA0111.10.415012
MA0113.10.598933
MA0114.10.222763
MA0115.10.969632
MA0116.10.27152
MA0117.10.937363
MA0119.10.362692
MA0122.10.957212
MA0124.11.16127
MA0125.11.0872
MA0130.10
MA0131.10.683521
MA0132.10
MA0133.10
MA0135.11.00325
MA0136.10.550755
MA0139.10.169849
MA0140.11.29098
MA0141.10.325895
MA0142.10.761136
MA0143.10.615203
MA0144.10.640537
MA0145.10.246409
MA0146.10.0169049
MA0147.10.236889
MA0148.10.450593
MA0149.10.367458
MA0062.20.137653
MA0035.20.524137
MA0039.20.254826
MA0138.20.675599
MA0002.20.172399
MA0137.20.863775
MA0104.20.18504
MA0047.20.576767
MA0112.20.0701537
MA0065.20.0704227
MA0150.12.82555
MA0151.10
MA0152.10.576873
MA0153.11.01988
MA0154.11.12269
MA0155.10.275377
MA0156.10.314185
MA0157.11.73039
MA0158.10
MA0159.10.246253
MA0160.10.453546
MA0161.10
MA0162.10.230918
MA0163.10.0186439
MA0164.10.551114
MA0080.20.302064
MA0018.20.560731
MA0099.20.669311
MA0079.20.24412
MA0102.21.59466
MA0258.10.210437
MA0259.10.227035
MA0442.10
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