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MCL coexpression mm9:907: Difference between revisions

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|ontology_enrichment_uberon=UBERON:0000467!1.23e-13!308;UBERON:0000480!1.23e-13!308;UBERON:0005423!2.61e-12!304;UBERON:0007023!2.08e-10!51;UBERON:0000923!2.50e-10!291;UBERON:0010316!2.50e-10!291;UBERON:0005291!2.50e-10!291;UBERON:0006598!2.50e-10!291;UBERON:0010317!2.50e-10!291;UBERON:0002532!2.50e-10!291;UBERON:0002050!2.55e-10!294;UBERON:0000477!1.12e-08!244
|ontology_enrichment_uberon=UBERON:0000467!1.23e-13!308;UBERON:0000480!1.23e-13!308;UBERON:0005423!2.61e-12!304;UBERON:0007023!2.08e-10!51;UBERON:0000923!2.50e-10!291;UBERON:0010316!2.50e-10!291;UBERON:0005291!2.50e-10!291;UBERON:0006598!2.50e-10!291;UBERON:0010317!2.50e-10!291;UBERON:0002532!2.50e-10!291;UBERON:0002050!2.55e-10!294;UBERON:0000477!1.12e-08!244
|tfbs_overrepresentation_for_novel_motifs=0.393008,0.121181,0.367606,0.434198,0.720982,0.448401,0.538088,0.515265,0.535519,0.0447303,0.494602,0.526159,0.173454,0.550255,0.756943,0,0.742571,0.703873,0.483643,0.0887261,0.332107,0.0622758,0.549359,0.258745,0.374936,0.577606,0.466037,0.469052,0.303071,0.376624,0.455168,0.843667,0.699026,0.425071,0.276324,0.185086,0.242032,0.522578,0.631914,0.195877,0.712303,0.460258,0.204736,0.27776,0.209497,0.423266,0.662995,0.484612,0.386968,0.305876,0.725127,0.604356,0.362495,0.985264,1.00271,0.557354,0.314394,0.513517,0.447041,0.555328,0.823643,0.613749,0.192045,0.713876,0.568415,0.754324,1.139,1.48833,0.818971,1.34113,0.349355,0.527912,0.0665967,1.03623,0.140213,0.409836,0.42492,0.651651,0.806481,0.336166,0.530481,0.759925,1.48701,0.167672,0.920903,0.025519,0.0299392,0.757533,0.667883,1.65055,1.20871,0.925879,0.856465,0.265734,0.218233,1.10739,0.982739,0.859272,0.663249,0.101559,1.26039,0.843387,0.967837,0.725721,0.724668,0.459825,0.784351,0.480639,0.340849,0.333829,1.00333,0.96962,0.337254,1.24884,1.21576,0.708441,0.143112,0.437894,0.743872,0.238599,1.04163,0.692953,0.579418,0.650748,1.26989,0.810177,0.546178,0.849691,1.13749,0.268537,0.950857,1.09252,1.10792,0.570914,1.23736,0.061199,0.401212,0.461647,1.18819,2.01886,1.6187,1.14372,0.591394,0.854131,0.718197,0.460705,0.666107,1.9792,0.403515,0.261837,0.120154,0.0553085,0.986833,0.207643,0.569994,1.06851,0.605358,0.287226,0.39061,0.400939,1.1977,0.920047,0.810622,0.383936,0.714896,0.562634,0.240994,0.524587,0.166768
|tfbs_overrepresentation_for_novel_motifs=0.393008,0.121181,0.367606,0.434198,0.720982,0.448401,0.538088,0.515265,0.535519,0.0447303,0.494602,0.526159,0.173454,0.550255,0.756943,0,0.742571,0.703873,0.483643,0.0887261,0.332107,0.0622758,0.549359,0.258745,0.374936,0.577606,0.466037,0.469052,0.303071,0.376624,0.455168,0.843667,0.699026,0.425071,0.276324,0.185086,0.242032,0.522578,0.631914,0.195877,0.712303,0.460258,0.204736,0.27776,0.209497,0.423266,0.662995,0.484612,0.386968,0.305876,0.725127,0.604356,0.362495,0.985264,1.00271,0.557354,0.314394,0.513517,0.447041,0.555328,0.823643,0.613749,0.192045,0.713876,0.568415,0.754324,1.139,1.48833,0.818971,1.34113,0.349355,0.527912,0.0665967,1.03623,0.140213,0.409836,0.42492,0.651651,0.806481,0.336166,0.530481,0.759925,1.48701,0.167672,0.920903,0.025519,0.0299392,0.757533,0.667883,1.65055,1.20871,0.925879,0.856465,0.265734,0.218233,1.10739,0.982739,0.859272,0.663249,0.101559,1.26039,0.843387,0.967837,0.725721,0.724668,0.459825,0.784351,0.480639,0.340849,0.333829,1.00333,0.96962,0.337254,1.24884,1.21576,0.708441,0.143112,0.437894,0.743872,0.238599,1.04163,0.692953,0.579418,0.650748,1.26989,0.810177,0.546178,0.849691,1.13749,0.268537,0.950857,1.09252,1.10792,0.570914,1.23736,0.061199,0.401212,0.461647,1.18819,2.01886,1.6187,1.14372,0.591394,0.854131,0.718197,0.460705,0.666107,1.9792,0.403515,0.261837,0.120154,0.0553085,0.986833,0.207643,0.569994,1.06851,0.605358,0.287226,0.39061,0.400939,1.1977,0.920047,0.810622,0.383936,0.714896,0.562634,0.240994,0.524587,0.166768
|tfbs_overrepresentation_jaspar=MA0003.1;0.0545917,MA0004.1;0.434673,MA0006.1;0.271714,MA0007.1;1.07722,MA0009.1;0.870101,MA0014.1;0.012738,MA0017.1;1.46217,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;0.947733,MA0042.1;0.348174,MA0043.1;0.966833,MA0046.1;0.906029,MA0048.1;0.335404,MA0050.1;0.472794,MA0051.1;0.586414,MA0052.1;0.890676,MA0055.1;0.117901,MA0056.1;0,MA0057.1;0.31126,MA0058.1;0.341628,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;0.0965831,MA0069.1;0.891016,MA0070.1;0.881319,MA0071.1;0.471969,MA0072.1;0.872842,MA0073.1;0.312272,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;0.922929,MA0088.1;0.229377,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;0.519598,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;0.633896,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;0.519484,MA0141.1;0.869985,MA0142.1;0.761136,MA0143.1;0.615203,MA0144.1;0.225588,MA0145.1;0.527241,MA0146.1;0.0771944,MA0147.1;0.236889,MA0148.1;0.450593,MA0149.1;0.367458,MA0062.2;0.137653,MA0035.2;0.524137,MA0039.2;0.00752803,MA0138.2;0.675599,MA0002.2;0.513194,MA0137.2;0.32312,MA0104.2;0.18504,MA0047.2;0.576767,MA0112.2;0.0701537,MA0065.2;1.35639,MA0150.1;0.419883,MA0151.1;0,MA0152.1;0.576873,MA0153.1;1.01988,MA0154.1;0.677425,MA0155.1;0.275377,MA0156.1;0.314185,MA0157.1;0.729116,MA0158.1;0,MA0159.1;0.246253,MA0160.1;0.453546,MA0161.1;0,MA0162.1;0.0211019,MA0163.1;0.669601,MA0164.1;0.551114,MA0080.2;0.302064,MA0018.2;0.560731,MA0099.2;0.669311,MA0079.2;0.685525,MA0102.2;1.59466,MA0258.1;0.210437,MA0259.1;0.227035,MA0442.1;0
}}
}}

Revision as of 12:30, 23 January 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr11:60043268..60043282,-p@chr11:60043268..60043282
-
Mm9::chr11:98216623..98216634,+p@chr11:98216623..98216634
+
Mm9::chr11:98218352..98218393,+p@chr11:98218352..98218393
+
Mm9::chr12:101444635..101444669,+p@chr12:101444635..101444669
+
Mm9::chr14:22652104..22652140,+p3@Vdac2
Mm9::chr3:101396429..101396470,-p@chr3:101396429..101396470
-
Mm9::chr4:154932366..154932388,+p@chr4:154932366..154932388
+
Mm9::chr6:17616260..17616279,+p@chr6:17616260..17616279
+


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:00038694-nitrophenylphosphatase activity0.0121607183681279
GO:0031944negative regulation of glucocorticoid metabolic process0.0121607183681279
GO:0031947negative regulation of glucocorticoid biosynthetic process0.0121607183681279
GO:0048521negative regulation of behavior0.0121607183681279
GO:0045989positive regulation of striated muscle contraction0.0121607183681279
GO:0007621negative regulation of female receptivity0.0121607183681279
GO:0005890sodium:potassium-exchanging ATPase complex0.0121607183681279
GO:0007603phototransduction, visible light0.0121607183681279
GO:0050795regulation of behavior0.0121607183681279
GO:0060181female receptivity0.0121607183681279
GO:0045924regulation of female receptivity0.0121607183681279
GO:0031946regulation of glucocorticoid biosynthetic process0.0121607183681279
GO:0006942regulation of striated muscle contraction0.0121607183681279
GO:0060180female mating behavior0.0121607183681279
GO:0030641cellular hydrogen ion homeostasis0.0159587566872052
GO:0031943regulation of glucocorticoid metabolic process0.0159587566872052
GO:0004865type 1 serine/threonine specific protein phosphatase inhibitor activity0.0170180109904335
GO:0007213acetylcholine receptor signaling, muscarinic pathway0.0170180109904335
GO:0006891intra-Golgi vesicle-mediated transport0.0170180109904335
GO:0043388positive regulation of DNA binding0.0170180109904335
GO:0045933positive regulation of muscle contraction0.0170180109904335
GO:0006704glucocorticoid biosynthetic process0.0170180109904335
GO:0045823positive regulation of heart contraction0.0170180109904335
GO:0008599protein phosphatase type 1 regulator activity0.0170180109904335
GO:0008308voltage-gated ion-selective channel activity0.0170180109904335
GO:0045822negative regulation of heart contraction0.0180444616373082
GO:0022892substrate-specific transporter activity0.0180444616373082
GO:0051099positive regulation of binding0.0180444616373082
GO:0019218regulation of steroid metabolic process0.0180444616373082
GO:0030004cellular monovalent inorganic cation homeostasis0.0180444616373082
GO:0015991ATP hydrolysis coupled proton transport0.0180444616373082
GO:0033057reproductive behavior in a multicellular organism0.0180444616373082
GO:0055067monovalent inorganic cation homeostasis0.0180444616373082
GO:0015988energy coupled proton transport, against electrochemical gradient0.0200129639191323
GO:0007617mating behavior0.021260861824116
GO:0008211glucocorticoid metabolic process0.021260861824116
GO:0005391sodium:potassium-exchanging ATPase activity0.0223767893786798
GO:0051101regulation of DNA binding0.0223767893786798
GO:0005795Golgi stack0.0239800433466738
GO:0002026regulation of the force of heart contraction0.0269502260834755
GO:0007618mating0.0269502260834755
GO:0019098reproductive behavior0.0283284086761825
GO:0004864protein phosphatase inhibitor activity0.0316137486258903
GO:0019212phosphatase inhibitor activity0.0350785630125739
GO:0019216regulation of lipid metabolic process0.0350785630125739
GO:0005741mitochondrial outer membrane0.0350785630125739
GO:0051098regulation of binding0.0361342198503228
GO:0030317sperm motility0.0366201476483536
GO:0031968organelle outer membrane0.0366201476483536
GO:0051705behavioral interaction between organisms0.0366201476483536
GO:0007602phototransduction0.0366201476483536
GO:0009584detection of visible light0.0377195160290655
GO:0050962detection of light stimulus during sensory perception0.0377195160290655
GO:0050908detection of light stimulus during visual perception0.0377195160290655
GO:0017111nucleoside-triphosphatase activity0.0393926317897043
GO:0009583detection of light stimulus0.0393926317897043
GO:0042383sarcolemma0.0396695758421618
GO:0016462pyrophosphatase activity0.0396695758421618
GO:0016818hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides0.0396695758421618
GO:0016817hydrolase activity, acting on acid anhydrides0.0396695758421618
GO:0051241negative regulation of multicellular organismal process0.0396695758421618
GO:0006941striated muscle contraction0.0396695758421618
GO:0042493response to drug0.0397496267172885
GO:0007200G-protein signaling, coupled to IP3 second messenger (phospholipase C activating)0.0397496267172885
GO:0019888protein phosphatase regulator activity0.0417358677902161
GO:0006937regulation of muscle contraction0.0417496164970557
GO:0005834heterotrimeric G-protein complex0.0417496164970557
GO:0019208phosphatase regulator activity0.0435752009425995
GO:0042446hormone biosynthetic process0.0435752009425995
GO:0008016regulation of heart contraction0.0435752009425995
GO:0048193Golgi vesicle transport0.0453357959224003
GO:0008217regulation of blood pressure0.0470462002640027
GO:0048015phosphoinositide-mediated signaling0.048363880397671
GO:0003015heart process0.048363880397671
GO:0050909sensory perception of taste0.048363880397671
GO:0009582detection of abiotic stimulus0.048363880397671
GO:0060047heart contraction0.048363880397671
GO:0019867outer membrane0.0499003376276443



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
anatomical system1.23e-13308
anatomical group1.23e-13308
developing anatomical structure2.61e-12304
adult organism2.08e-1051
germ layer2.50e-10291
germ layer / neural crest2.50e-10291
embryonic tissue2.50e-10291
presumptive structure2.50e-10291
germ layer / neural crest derived structure2.50e-10291
epiblast (generic)2.50e-10291
embryonic structure2.55e-10294
anatomical cluster1.12e-08244


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)
MA0003.10.0545917
MA0004.10.434673
MA0006.10.271714
MA0007.11.07722
MA0009.10.870101
MA0014.10.012738
MA0017.11.46217
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
MA0041.10.947733
MA0042.10.348174
MA0043.10.966833
MA0046.10.906029
MA0048.10.335404
MA0050.10.472794
MA0051.10.586414
MA0052.10.890676
MA0055.10.117901
MA0056.10
MA0057.10.31126
MA0058.10.341628
MA0059.10.353484
MA0060.10.197678
MA0061.10.224905
MA0063.10
MA0066.10.566617
MA0067.11.21448
MA0068.10.0965831
MA0069.10.891016
MA0070.10.881319
MA0071.10.471969
MA0072.10.872842
MA0073.10.312272
MA0074.10.531046
MA0076.10.315013
MA0077.10.851175
MA0078.10.61926
MA0081.10.375851
MA0083.10.96604
MA0084.11.54225
MA0087.10.922929
MA0088.10.229377
MA0089.10
MA0090.10.401197
MA0091.10.447561
MA0092.10.401504
MA0093.10.289361
MA0095.10
MA0098.10
MA0100.10.519598
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
MA0114.10.633896
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
MA0140.10.519484
MA0141.10.869985
MA0142.10.761136
MA0143.10.615203
MA0144.10.225588
MA0145.10.527241
MA0146.10.0771944
MA0147.10.236889
MA0148.10.450593
MA0149.10.367458
MA0062.20.137653
MA0035.20.524137
MA0039.20.00752803
MA0138.20.675599
MA0002.20.513194
MA0137.20.32312
MA0104.20.18504
MA0047.20.576767
MA0112.20.0701537
MA0065.21.35639
MA0150.10.419883
MA0151.10
MA0152.10.576873
MA0153.11.01988
MA0154.10.677425
MA0155.10.275377
MA0156.10.314185
MA0157.10.729116
MA0158.10
MA0159.10.246253
MA0160.10.453546
MA0161.10
MA0162.10.0211019
MA0163.10.669601
MA0164.10.551114
MA0080.20.302064
MA0018.20.560731
MA0099.20.669311
MA0079.20.685525
MA0102.21.59466
MA0258.10.210437
MA0259.10.227035
MA0442.10
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