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MCL coexpression mm9:867: Difference between revisions

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|ontology_enrichment_uberon=UBERON:0002369!4.71e-52!7;UBERON:0006858!4.71e-52!7;UBERON:0003064!6.42e-26!14;UBERON:0005172!3.68e-09!49;UBERON:0005173!3.68e-09!49;UBERON:0002417!3.68e-09!49;UBERON:0000916!3.68e-09!49;UBERON:0005256!9.07e-08!45;UBERON:0003104!3.20e-07!61;UBERON:0009142!3.20e-07!61
|ontology_enrichment_uberon=UBERON:0002369!4.71e-52!7;UBERON:0006858!4.71e-52!7;UBERON:0003064!6.42e-26!14;UBERON:0005172!3.68e-09!49;UBERON:0005173!3.68e-09!49;UBERON:0002417!3.68e-09!49;UBERON:0000916!3.68e-09!49;UBERON:0005256!9.07e-08!45;UBERON:0003104!3.20e-07!61;UBERON:0009142!3.20e-07!61
|tfbs_overrepresentation_for_novel_motifs=0.393008,0.289542,0.367606,0.434198,0.260188,0.448401,0.538088,0.173246,0.535519,0.687027,0.494602,0.526159,0.515774,0.550255,0.756943,0,0.742571,0.252772,0.938682,0.620214,0.332107,0.223663,0.549359,0.717658,0.374936,0.577606,0.153291,0.469052,0.303071,0.376624,0.455168,0.843667,0.699026,0.136998,0.276324,0.363049,0.242032,0.522578,1.8457,0.195877,0.712303,0.460258,0.204736,0.761266,0.209497,0.423266,0.662995,0.484612,0.687215,0.305876,0.725127,0.604356,0.112729,0.985264,1.00271,0.557354,0.314394,0.513517,0.447041,0.555328,0.823643,0.613749,0.560836,0.713876,0.568415,0.754324,1.139,1.48833,0.818971,1.34113,0.349355,0.178433,0.0665967,1.03623,0.853709,0.813951,1.35784,0.651651,0.806481,1.60272,0.179489,0.759925,0.612313,0.167672,0.920903,0.025519,0.0299392,0.376919,0.667883,1.65055,1.20871,0.925879,0.856465,0.733735,0.218233,0.202284,0.510015,0.859272,0.663249,0.332938,0.242106,0.843387,0.967837,0.725721,0.724668,0.459825,0.784351,0.480639,0.340849,0.333829,0.386136,0.96962,0.337254,0.499714,1.21576,0.708441,0.333069,0.437894,0.743872,0.238599,1.04163,1.65536,0.579418,0.650748,1.26989,0.810177,0.546178,0.849691,1.13749,0.740166,2.18589,0.427043,1.10792,0.570914,1.23736,0.220515,0.401212,0.461647,1.18819,2.01886,1.6187,1.14372,0.591394,0.854131,0.718197,0.460705,0.666107,1.9792,0.403515,0.261837,0.120154,0.0553085,0.986833,0.598134,0.569994,1.06851,0.605358,0.287226,0.39061,0.400939,1.1977,0.920047,0.810622,0.998505,0.714896,0.562634,0.240994,1.30183,0.166768
|tfbs_overrepresentation_for_novel_motifs=0.393008,0.289542,0.367606,0.434198,0.260188,0.448401,0.538088,0.173246,0.535519,0.687027,0.494602,0.526159,0.515774,0.550255,0.756943,0,0.742571,0.252772,0.938682,0.620214,0.332107,0.223663,0.549359,0.717658,0.374936,0.577606,0.153291,0.469052,0.303071,0.376624,0.455168,0.843667,0.699026,0.136998,0.276324,0.363049,0.242032,0.522578,1.8457,0.195877,0.712303,0.460258,0.204736,0.761266,0.209497,0.423266,0.662995,0.484612,0.687215,0.305876,0.725127,0.604356,0.112729,0.985264,1.00271,0.557354,0.314394,0.513517,0.447041,0.555328,0.823643,0.613749,0.560836,0.713876,0.568415,0.754324,1.139,1.48833,0.818971,1.34113,0.349355,0.178433,0.0665967,1.03623,0.853709,0.813951,1.35784,0.651651,0.806481,1.60272,0.179489,0.759925,0.612313,0.167672,0.920903,0.025519,0.0299392,0.376919,0.667883,1.65055,1.20871,0.925879,0.856465,0.733735,0.218233,0.202284,0.510015,0.859272,0.663249,0.332938,0.242106,0.843387,0.967837,0.725721,0.724668,0.459825,0.784351,0.480639,0.340849,0.333829,0.386136,0.96962,0.337254,0.499714,1.21576,0.708441,0.333069,0.437894,0.743872,0.238599,1.04163,1.65536,0.579418,0.650748,1.26989,0.810177,0.546178,0.849691,1.13749,0.740166,2.18589,0.427043,1.10792,0.570914,1.23736,0.220515,0.401212,0.461647,1.18819,2.01886,1.6187,1.14372,0.591394,0.854131,0.718197,0.460705,0.666107,1.9792,0.403515,0.261837,0.120154,0.0553085,0.986833,0.598134,0.569994,1.06851,0.605358,0.287226,0.39061,0.400939,1.1977,0.920047,0.810622,0.998505,0.714896,0.562634,0.240994,1.30183,0.166768
|tfbs_overrepresentation_jaspar=MA0003.1;0.0545917,MA0004.1;0.434673,MA0006.1;0.271714,MA0007.1;0.419994,MA0009.1;0.870101,MA0014.1;0.162935,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;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;1.2091,MA0056.1;0,MA0057.1;0.0935008,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;2.06781,MA0072.1;0.872842,MA0073.1;0.0216016,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;0.787675,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;0.506952,MA0140.1;0.519484,MA0141.1;0.869985,MA0142.1;0.761136,MA0143.1;0.615203,MA0144.1;0.640537,MA0145.1;0.0701568,MA0146.1;0.198184,MA0147.1;0.236889,MA0148.1;0.450593,MA0149.1;0.367458,MA0062.2;0.137653,MA0035.2;1.30087,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;0.902537,MA0150.1;0.419883,MA0151.1;0,MA0152.1;0.576873,MA0153.1;1.01988,MA0154.1;0.677425,MA0155.1;0.579465,MA0156.1;0.314185,MA0157.1;0.729116,MA0158.1;0,MA0159.1;0.246253,MA0160.1;1.14982,MA0161.1;0,MA0162.1;0.71453,MA0163.1;0.408151,MA0164.1;1.35808,MA0080.2;0.302064,MA0018.2;0.560731,MA0099.2;0.669311,MA0079.2;0.0137335,MA0102.2;1.59466,MA0258.1;0.60477,MA0259.1;0.227035,MA0442.1;0
}}
}}

Revision as of 12:26, 23 January 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr10:61183340..61183369,+p2@Aifm2
Mm9::chr13:4149879..4149899,-p1@Akr1c18
Mm9::chr16:35652352..35652356,-p@chr16:35652352..35652356
-
Mm9::chr17:74573101..74573114,-p@chr17:74573101..74573114
-
Mm9::chr18:36446929..36446940,+p@chr18:36446929..36446940
+
Mm9::chr1:89724864..89724867,+p@chr1:89724864..89724867
+
Mm9::chr6:139790173..139790179,+p3@Pik3c2g
Mm9::chr7:107064299..107064302,+p@chr7:107064299..107064302
+


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:004700620-alpha-hydroxysteroid dehydrogenase activity0.0124180500009131
GO:0008208C21-steroid hormone catabolic process0.0124180500009131
GO:0006709progesterone catabolic process0.0124180500009131
GO:0007567parturition0.0149004353413323
GO:0035005phosphatidylinositol-4-phosphate 3-kinase activity0.0149004353413323
GO:0042447hormone catabolic process0.0159634401118253
GO:0042448progesterone metabolic process0.0159634401118253
GO:0031575G1/S transition checkpoint0.0177269539092413
GO:0005662DNA replication factor A complex0.0177269539092413
GO:0006706steroid catabolic process0.0177269539092413
GO:0046332SMAD binding0.0177269539092413
GO:00163031-phosphatidylinositol-3-kinase activity0.0177269539092413
GO:0043601nuclear replisome0.0177269539092413
GO:0046854phosphoinositide phosphorylation0.0177269539092413
GO:0030894replisome0.0177269539092413
GO:0035004phosphoinositide 3-kinase activity0.0177269539092413
GO:0005829cytosol0.0177269539092413
GO:0005942phosphoinositide 3-kinase complex0.0177269539092413
GO:0043596nuclear replication fork0.0177269539092413
GO:0016307phosphatidylinositol phosphate kinase activity0.0177269539092413
GO:0046834lipid phosphorylation0.0177269539092413
GO:0007093mitotic cell cycle checkpoint0.0219921147550164
GO:0008207C21-steroid hormone metabolic process0.0274994885915881
GO:0003697single-stranded DNA binding0.0278947196260274
GO:0044255cellular lipid metabolic process0.0278947196260274
GO:0016229steroid dehydrogenase activity0.0278947196260274
GO:0003690double-stranded DNA binding0.0278947196260274
GO:0001727lipid kinase activity0.0278947196260274
GO:0030258lipid modification0.0294376102880969
GO:0005657replication fork0.0294376102880969
GO:0000075cell cycle checkpoint0.0294376102880969
GO:0006629lipid metabolic process0.0294376102880969
GO:0007088regulation of mitosis0.0294376102880969
GO:0044242cellular lipid catabolic process0.0294376102880969
GO:0004428inositol or phosphatidylinositol kinase activity0.0294376102880969
GO:0006915apoptosis0.0294376102880969
GO:0012501programmed cell death0.0295802256395712
GO:0008219cell death0.0304413879208736
GO:0016265death0.0304413879208736
GO:0005737cytoplasm0.0305063617587466
GO:0048522positive regulation of cellular process0.0365604791767483
GO:0048015phosphoinositide-mediated signaling0.0376593496314086
GO:0030384phosphoinositide metabolic process0.0376593496314086
GO:0016491oxidoreductase activity0.0376593496314086
GO:0019867outer membrane0.0379414103506081
GO:0043566structure-specific DNA binding0.0387239938629354
GO:0048518positive regulation of biological process0.0421566997893442
GO:0005625soluble fraction0.0424979738084686
GO:0006650glycerophospholipid metabolic process0.0437507936601084
GO:0050660FAD binding0.0437507936601084
GO:0044454nuclear chromosome part0.0486768931967854



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
adrenal gland4.71e-527
adrenal/interrenal gland4.71e-527
intermediate mesoderm6.42e-2614
abdomen element3.68e-0949
abdominal segment element3.68e-0949
abdominal segment of trunk3.68e-0949
abdomen3.68e-0949
trunk mesenchyme9.07e-0845
mesenchyme3.20e-0761
entire embryonic mesenchyme3.20e-0761


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
MA0007.10.419994
MA0009.10.870101
MA0014.10.162935
MA0017.10.804572
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
MA0055.11.2091
MA0056.10
MA0057.10.0935008
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
MA0071.12.06781
MA0072.10.872842
MA0073.10.0216016
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
MA0093.10.787675
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
MA0139.10.506952
MA0140.10.519484
MA0141.10.869985
MA0142.10.761136
MA0143.10.615203
MA0144.10.640537
MA0145.10.0701568
MA0146.10.198184
MA0147.10.236889
MA0148.10.450593
MA0149.10.367458
MA0062.20.137653
MA0035.21.30087
MA0039.20.00752803
MA0138.20.675599
MA0002.20.513194
MA0137.20.32312
MA0104.20.18504
MA0047.20.576767
MA0112.20.0701537
MA0065.20.902537
MA0150.10.419883
MA0151.10
MA0152.10.576873
MA0153.11.01988
MA0154.10.677425
MA0155.10.579465
MA0156.10.314185
MA0157.10.729116
MA0158.10
MA0159.10.246253
MA0160.11.14982
MA0161.10
MA0162.10.71453
MA0163.10.408151
MA0164.11.35808
MA0080.20.302064
MA0018.20.560731
MA0099.20.669311
MA0079.20.0137335
MA0102.21.59466
MA0258.10.60477
MA0259.10.227035
MA0442.10
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