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MCL coexpression mm9:490: Difference between revisions

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{{MCL_coexpression_mm9
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constituent of ribosome;1.1560965530981e-11;27207,68193,20115,270106,269261,20091!GO:0005840;ribosome;1.1560965530981e-11;27207,68193,20115,270106,269261,20091!GO:0006412;translation;2.47125359463791e-09;27207,68193,20115,270106,269261,20091!GO:0030529;ribonucleoprotein complex;2.47125359463791e-09;27207,68193,20115,270106,269261,20091!GO:0005830;cytosolic ribosome (sensu Eukaryota);6.28824516811436e-09;20115,270106,269261,20091!GO:0009059;macromolecule biosynthetic process;1.51370744461185e-08;27207,68193,20115,270106,269261,20091!GO:0044249;cellular biosynthetic process;6.13456154576301e-08;27207,68193,20115,270106,269261,20091!GO:0044445;cytosolic part;6.13456154576301e-08;20115,270106,269261,20091!GO:0042254;ribosome biogenesis and assembly;1.6730756480992e-07;20115,270106,269261,20091!GO:0009058;biosynthetic process;2.90028914512514e-07;27207,68193,20115,270106,269261,20091!GO:0022613;ribonucleoprotein complex biogenesis and assembly;7.4709628513972e-07;20115,270106,269261,20091!GO:0043232;intracellular non-membrane-bound organelle;1.01014948585804e-06;27207,68193,20115,270106,269261,20091!GO:0043228;non-membrane-bound organelle;1.01014948585804e-06;27207,68193,20115,270106,269261,20091!GO:0032991;macromolecular complex;5.48773926092803e-06;27207,68193,20115,270106,269261,20091!GO:0005829;cytosol;5.54327868465435e-06;20115,270106,269261,20091!GO:0044267;cellular protein metabolic process;2.60624487579232e-05;27207,68193,20115,270106,269261,20091!GO:0044260;cellular macromolecule metabolic process;2.60624487579232e-05;27207,68193,20115,270106,269261,20091!GO:0010467;gene expression;2.60624487579232e-05;27207,68193,20115,270106,269261,20091!GO:0019538;protein metabolic process;2.83025096999369e-05;27207,68193,20115,270106,269261,20091!GO:0044444;cytoplasmic part;5.50534752153308e-05;27207,68193,20115,270106,269261,20091!GO:0006996;organelle organization and biogenesis;0.000423234878212024;20115,270106,269261,20091!GO:0003723;RNA binding;0.00105955097781562;27207,20115,269261!GO:0005737;cytoplasm;0.00128464468842842;27207,68193,20115,270106,269261,20091!GO:0043170;macromolecule metabolic process;0.00128464468842842;27207,68193,20115,270106,269261,20091!GO:0044238;primary metabolic process;0.00286419718910655;27207,68193,20115,270106,269261,20091!GO:0044237;cellular metabolic process;0.00286419718910655;27207,68193,20115,270106,269261,20091!GO:0016043;cellular component organization and biogenesis;0.00562950163876434;20115,270106,269261,20091!GO:0043229;intracellular organelle;0.00562950163876434;27207,68193,20115,270106,269261,20091!GO:0043226;organelle;0.00562950163876434;27207,68193,20115,270106,269261,20091!GO:0005843;cytosolic small ribosomal subunit (sensu Eukaryota);0.00765632666923851;20115!GO:0019843;rRNA binding;0.0121575059345522;27207!GO:0044424;intracellular 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|gostat_on_MCL_coexpression=GO:0003735;structural constituent of ribosome;1.1560965530981e-11;27207,68193,20115,270106,269261,20091!GO:0005840;ribosome;1.1560965530981e-11;27207,68193,20115,270106,269261,20091!GO:0006412;translation;2.47125359463791e-09;27207,68193,20115,270106,269261,20091!GO:0030529;ribonucleoprotein complex;2.47125359463791e-09;27207,68193,20115,270106,269261,20091!GO:0005830;cytosolic ribosome (sensu Eukaryota);6.28824516811436e-09;20115,270106,269261,20091!GO:0009059;macromolecule biosynthetic process;1.51370744461185e-08;27207,68193,20115,270106,269261,20091!GO:0044249;cellular biosynthetic process;6.13456154576301e-08;27207,68193,20115,270106,269261,20091!GO:0044445;cytosolic part;6.13456154576301e-08;20115,270106,269261,20091!GO:0042254;ribosome biogenesis and assembly;1.6730756480992e-07;20115,270106,269261,20091!GO:0009058;biosynthetic process;2.90028914512514e-07;27207,68193,20115,270106,269261,20091!GO:0022613;ribonucleoprotein complex biogenesis and assembly;7.4709628513972e-07;20115,270106,269261,20091!GO:0043232;intracellular non-membrane-bound organelle;1.01014948585804e-06;27207,68193,20115,270106,269261,20091!GO:0043228;non-membrane-bound organelle;1.01014948585804e-06;27207,68193,20115,270106,269261,20091!GO:0032991;macromolecular complex;5.48773926092803e-06;27207,68193,20115,270106,269261,20091!GO:0005829;cytosol;5.54327868465435e-06;20115,270106,269261,20091!GO:0044267;cellular protein metabolic process;2.60624487579232e-05;27207,68193,20115,270106,269261,20091!GO:0044260;cellular macromolecule metabolic process;2.60624487579232e-05;27207,68193,20115,270106,269261,20091!GO:0010467;gene expression;2.60624487579232e-05;27207,68193,20115,270106,269261,20091!GO:0019538;protein metabolic process;2.83025096999369e-05;27207,68193,20115,270106,269261,20091!GO:0044444;cytoplasmic part;5.50534752153308e-05;27207,68193,20115,270106,269261,20091!GO:0006996;organelle organization and biogenesis;0.000423234878212024;20115,270106,269261,20091!GO:0003723;RNA binding;0.00105955097781562;27207,20115,269261!GO:0005737;cytoplasm;0.00128464468842842;27207,68193,20115,270106,269261,20091!GO:0043170;macromolecule metabolic process;0.00128464468842842;27207,68193,20115,270106,269261,20091!GO:0044238;primary metabolic process;0.00286419718910655;27207,68193,20115,270106,269261,20091!GO:0044237;cellular metabolic process;0.00286419718910655;27207,68193,20115,270106,269261,20091!GO:0016043;cellular component organization and biogenesis;0.00562950163876434;20115,270106,269261,20091!GO:0043229;intracellular organelle;0.00562950163876434;27207,68193,20115,270106,269261,20091!GO:0043226;organelle;0.00562950163876434;27207,68193,20115,270106,269261,20091!GO:0005843;cytosolic small ribosomal subunit (sensu Eukaryota);0.00765632666923851;20115!GO:0019843;rRNA binding;0.0121575059345522;27207!GO:0044424;intracellular part;0.0148822751252279;27207,68193,20115,270106,269261,20091!GO:0015935;small ribosomal subunit;0.0148822751252279;20115!GO:0005622;intracellular;0.0173222684612825;27207,68193,20115,270106,269261,20091!GO:0033279;ribosomal subunit;0.0288723918971308;20115!GO:0005730;nucleolus;0.0481465775613396;269261!
|ontology_enrichment_celltype=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=
|tfbs_overrepresentation_for_novel_motifs=1.12351,0.0531438,0.548514,0.238864,0.356286,0.250289,0.867472,0.800034,0.485477,0.563871,0.785008,0.314655,0.0577792,0.335151,0.120865,0,0.505674,0.105493,0.422292,0.0839024,0.939233,0.0504052,1.59643,0.353775,0.561942,0.35869,0.178452,0.736859,0.851419,0.547046,2.02463,0.598971,0.104128,0.15332,2.47568,0.0221233,0.667121,1.51547,0.0859217,0.0703677,0.107883,0.720345,0.121081,0.122151,0.2594,0.651235,0.433813,0.279902,0.356013,0.8599,0.48979,0.381972,0.281801,0.732469,0.749094,0.904193,0.147717,0.303999,0.166653,0.339495,1.41979,0.390204,0.516848,0.479581,2.49857,0.516415,0.880067,1.22155,0.576002,1.07689,0.515225,0.218482,0.0555827,0.781142,1.01021,0.144279,0.153229,1.90541,0.564426,0.163487,0.0610891,0.521544,0.388944,1.18289,0.671442,0.206398,0.0027123,0.297913,1.11664,1.38183,0.947651,0.676142,0.610915,0.365956,0.284335,0.0741053,0.790304,0.613539,0.43404,0.101478,0.325002,0.59871,0.715894,0.490329,1.22674,0.259558,0.543989,0.758665,0.16693,0.161774,0.201092,0.717588,0.493275,1.44634,0.954503,0.346836,0.694694,0.241826,0.506861,0.31898,0.786314,0.46068,0.360259,0.422901,1.00724,0.567849,0.331666,0.60459,0.8786,0.115924,0.699779,1.22651,0.850049,0.352905,0.975524,0.0491355,0.212784,0.261043,0.927716,1.74768,1.35029,0.884624,0.370659,0.608735,0.483498,0.260275,1.11321,1.7082,0.614595,0.726856,0.556427,0.119607,0.733963,0.266555,0.352111,0.81211,0.382849,0.803531,0.204546,1.79503,0.93695,0.670634,0.568261,0.199399,0.480505,0.345769,0.0978842,0.313326,0.104898
|tfbs_overrepresentation_jaspar=MA0003.1;0.601088,MA0004.1;0.67248,MA0006.1;0.756673,MA0007.1;0.227553,MA0009.1;0.623671,MA0014.1;0.457814,MA0017.1;0.420732,MA0019.1;0.456268,MA0024.1;0.582844,MA0025.1;0.845702,MA0027.1;2.24512,MA0028.1;3.99822,MA0029.1;0.562703,MA0030.1;0.568779,MA0031.1;0.535959,MA0038.1;0.358622,MA0040.1;0.635404,MA0041.1;0.536212,MA0042.1;0.172351,MA0043.1;1.70101,MA0046.1;0.657417,MA0048.1;0.0239691,MA0050.1;0.743895,MA0051.1;0.366328,MA0052.1;0.642973,MA0055.1;0.00245735,MA0056.1;0,MA0057.1;0.0903541,MA0058.1;0.968034,MA0059.1;0.522737,MA0060.1;0.071412,MA0061.1;0.295622,MA0063.1;0,MA0066.1;0.921885,MA0067.1;0.953264,MA0068.1;0.0945752,MA0069.1;0.643292,MA0070.1;0.634186,MA0071.1;0.742345,MA0072.1;0.626238,MA0073.1;3.61478e-05,MA0074.1;0.318792,MA0076.1;4.33051,MA0077.1;0.605975,MA0078.1;0.395048,MA0081.1;0.56362,MA0083.1;0.714187,MA0084.1;1.27474,MA0087.1;0.673355,MA0088.1;0.499348,MA0089.1;0,MA0090.1;0.610307,MA0091.1;0.24961,MA0092.1;0.610874,MA0093.1;0.40751,MA0095.1;0,MA0098.1;0,MA0100.1;0.309116,MA0101.1;0.182791,MA0103.1;0.14251,MA0105.1;0.0373599,MA0106.1;0.401864,MA0107.1;0.138378,MA0108.2;0.476838,MA0109.1;0,MA0111.1;0.223614,MA0113.1;0.377232,MA0114.1;0.609093,MA0115.1;0.717599,MA0116.1;0.37608,MA0117.1;0.686999,MA0119.1;0.183219,MA0122.1;0.705806,MA0124.1;0.901619,MA0125.1;0.830088,MA0130.1;0,MA0131.1;1.14691,MA0132.1;0,MA0133.1;0,MA0135.1;0.749615,MA0136.1;1.60065,MA0139.1;0.20466,MA0140.1;0.30902,MA0141.1;0.155997,MA0142.1;0.522654,MA0143.1;0.391481,MA0144.1;0.617592,MA0145.1;0.0124347,MA0146.1;0.383608,MA0147.1;0.31605,MA0148.1;0.252062,MA0149.1;0.18682,MA0062.2;6.49285,MA0035.2;0.312946,MA0039.2;0.242567,MA0138.2;0.445088,MA0002.2;0.796194,MA0137.2;0.467774,MA0104.2;0.229221,MA0047.2;0.357963,MA0112.2;0.160225,MA0065.2;0.160972,MA0150.1;0.227466,MA0151.1;0,MA0152.1;0.358055,MA0153.1;0.765498,MA0154.1;0.10034,MA0155.1;0.0157857,MA0156.1;1.42296,MA0157.1;0.493416,MA0158.1;0,MA0159.1;1.12623,MA0160.1;0.254455,MA0161.1;0,MA0162.1;0.170606,MA0163.1;0.0289848,MA0164.1;0.335886,MA0080.2;0.430071,MA0018.2;0.91064,MA0099.2;0.439458,MA0079.2;0.00035791,MA0102.2;1.32652,MA0258.1;0.572032,MA0259.1;0.621948,MA0442.1;0
}}

Latest revision as of 15:23, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr11:97643723..97643734,-p2@LOC100044627
p2@Rpl23
Mm9::chr12:29320779..29320817,-p1@Rps7
Mm9::chr14:25309900..25309911,+p2@LOC677113
p2@Rps24
Mm9::chr15:34372984..34373027,-p1@Gm12191
p1@Gm6109
p1@Gm7429
p1@Rpl30-ps10
p1@Rpl30
Mm9::chr16:55966451..55966484,+p3@Rpl24
p3@Zbtb11
Mm9::chr2:32817185..32817212,+p1@Rpl12
Mm9::chr3:85946564..85946580,-p2@Rps3a
Mm9::chr3:85946606..85946611,-p3@Rps3a
Mm9::chr4:86503269..86503319,-p1@Gm13654
p1@LOC639593
p1@Rps6
Mm9::chr5:65782647..65782690,-p1@Gm5451
p1@Rpl9
Mm9::chr6:115758783..115758797,-p2@Gm6251
p2@LOC100504872
p2@Rpl32
Mm9::chr7:123477646..123477702,-p1@Gm12270
p1@Gm15483
p1@Gm6834
p1@Rps13
Mm9::chr7:52379725..52379769,-p1@Rps11
Mm9::chr8:125626259..125626320,+p1@Gm10071
p1@Gm12918
p1@Gm15710
p1@Rpl13
Mm9::chr9:44215712..44215766,+p1@Gm6988
p1@Rps25


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:0003735structural constituent of ribosome1.1560965530981e-11
GO:0005840ribosome1.1560965530981e-11
GO:0006412translation2.47125359463791e-09
GO:0030529ribonucleoprotein complex2.47125359463791e-09
GO:0005830cytosolic ribosome (sensu Eukaryota)6.28824516811436e-09
GO:0009059macromolecule biosynthetic process1.51370744461185e-08
GO:0044249cellular biosynthetic process6.13456154576301e-08
GO:0044445cytosolic part6.13456154576301e-08
GO:0042254ribosome biogenesis and assembly1.6730756480992e-07
GO:0009058biosynthetic process2.90028914512514e-07
GO:0022613ribonucleoprotein complex biogenesis and assembly7.4709628513972e-07
GO:0043232intracellular non-membrane-bound organelle1.01014948585804e-06
GO:0043228non-membrane-bound organelle1.01014948585804e-06
GO:0032991macromolecular complex5.48773926092803e-06
GO:0005829cytosol5.54327868465435e-06
GO:0044267cellular protein metabolic process2.60624487579232e-05
GO:0044260cellular macromolecule metabolic process2.60624487579232e-05
GO:0010467gene expression2.60624487579232e-05
GO:0019538protein metabolic process2.83025096999369e-05
GO:0044444cytoplasmic part5.50534752153308e-05
GO:0006996organelle organization and biogenesis0.000423234878212024
GO:0003723RNA binding0.00105955097781562
GO:0005737cytoplasm0.00128464468842842
GO:0043170macromolecule metabolic process0.00128464468842842
GO:0044238primary metabolic process0.00286419718910655
GO:0044237cellular metabolic process0.00286419718910655
GO:0016043cellular component organization and biogenesis0.00562950163876434
GO:0043229intracellular organelle0.00562950163876434
GO:0043226organelle0.00562950163876434
GO:0005843cytosolic small ribosomal subunit (sensu Eukaryota)0.00765632666923851
GO:0019843rRNA binding0.0121575059345522
GO:0044424intracellular part0.0148822751252279
GO:0015935small ribosomal subunit0.0148822751252279
GO:0005622intracellular0.0173222684612825
GO:0033279ribosomal subunit0.0288723918971308
GO:0005730nucleolus0.0481465775613396



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><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)
MA0003.10.601088
MA0004.10.67248
MA0006.10.756673
MA0007.10.227553
MA0009.10.623671
MA0014.10.457814
MA0017.10.420732
MA0019.10.456268
MA0024.10.582844
MA0025.10.845702
MA0027.12.24512
MA0028.13.99822
MA0029.10.562703
MA0030.10.568779
MA0031.10.535959
MA0038.10.358622
MA0040.10.635404
MA0041.10.536212
MA0042.10.172351
MA0043.11.70101
MA0046.10.657417
MA0048.10.0239691
MA0050.10.743895
MA0051.10.366328
MA0052.10.642973
MA0055.10.00245735
MA0056.10
MA0057.10.0903541
MA0058.10.968034
MA0059.10.522737
MA0060.10.071412
MA0061.10.295622
MA0063.10
MA0066.10.921885
MA0067.10.953264
MA0068.10.0945752
MA0069.10.643292
MA0070.10.634186
MA0071.10.742345
MA0072.10.626238
MA0073.13.61478e-05
MA0074.10.318792
MA0076.14.33051
MA0077.10.605975
MA0078.10.395048
MA0081.10.56362
MA0083.10.714187
MA0084.11.27474
MA0087.10.673355
MA0088.10.499348
MA0089.10
MA0090.10.610307
MA0091.10.24961
MA0092.10.610874
MA0093.10.40751
MA0095.10
MA0098.10
MA0100.10.309116
MA0101.10.182791
MA0103.10.14251
MA0105.10.0373599
MA0106.10.401864
MA0107.10.138378
MA0108.20.476838
MA0109.10
MA0111.10.223614
MA0113.10.377232
MA0114.10.609093
MA0115.10.717599
MA0116.10.37608
MA0117.10.686999
MA0119.10.183219
MA0122.10.705806
MA0124.10.901619
MA0125.10.830088
MA0130.10
MA0131.11.14691
MA0132.10
MA0133.10
MA0135.10.749615
MA0136.11.60065
MA0139.10.20466
MA0140.10.30902
MA0141.10.155997
MA0142.10.522654
MA0143.10.391481
MA0144.10.617592
MA0145.10.0124347
MA0146.10.383608
MA0147.10.31605
MA0148.10.252062
MA0149.10.18682
MA0062.26.49285
MA0035.20.312946
MA0039.20.242567
MA0138.20.445088
MA0002.20.796194
MA0137.20.467774
MA0104.20.229221
MA0047.20.357963
MA0112.20.160225
MA0065.20.160972
MA0150.10.227466
MA0151.10
MA0152.10.358055
MA0153.10.765498
MA0154.10.10034
MA0155.10.0157857
MA0156.11.42296
MA0157.10.493416
MA0158.10
MA0159.11.12623
MA0160.10.254455
MA0161.10
MA0162.10.170606
MA0163.10.0289848
MA0164.10.335886
MA0080.20.430071
MA0018.20.91064
MA0099.20.439458
MA0079.20.00035791
MA0102.21.32652
MA0258.10.572032
MA0259.10.621948
MA0442.10
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