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MCL coexpression mm9:391: Difference between revisions

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{{MCL_coexpression_mm9
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0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.978748387393722,1.00433070349492,0.142671721075526,0.0997909775761048,0,0.0481920468563092,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0403878614760544,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0|gostat_on_MCL_coexpression=GO:0048863;stem cell differentiation;2.7667001875512e-06;18999,18119,71950!GO:0048864;stem cell development;0.000451023744568524;18999,18119!GO:0019827;stem cell maintenance;0.000451023744568524;18999,18119!GO:0042074;cell migration involved in gastrulation;0.000630972040384902;13590,18119!GO:0045596;negative regulation of cell differentiation;0.000948523766910004;18999,18119,71950!GO:0045120;pronucleus;0.00124038586237459;21432,73708!GO:0051093;negative regulation of developmental process;0.00124038586237459;18999,18119,71950!GO:0008083;growth factor activity;0.00304482699284934;320202,13590,18119!GO:0045595;regulation of cell differentiation;0.00304482699284934;18999,18119,71950!GO:0009790;embryonic development;0.00342597435615527;13590,73708,18119,71950!GO:0005125;cytokine activity;0.00670187390332782;320202,13590,18119!GO:0007389;pattern specification process;0.00788911411822714;13590,18119,71950!GO:0050793;regulation of developmental process;0.00788911411822714;18999,18119,71950!GO:0001714;endodermal cell fate specification;0.00788911411822714;71950!GO:0042664;negative regulation of endodermal cell fate specification;0.00788911411822714;71950!GO:0002085;repression of premature neural plate formation;0.00788911411822714;18119!GO:0030718;germ-line stem cell maintenance;0.00788911411822714;18999!GO:0042663;regulation of endodermal cell fate specification;0.00788911411822714;71950!GO:0004577;N-acetylglucosaminyldiphosphodolichol N-acetylglucosaminyltransferase activity;0.00788911411822714;67574!GO:0007369;gastrulation;0.00835616358503614;13590,18119!GO:0032502;developmental process;0.00842780921854488;378430,320202,13590,73708,18999,18119,71950!GO:0032501;multicellular organismal process;0.0105943426963285;18796,13590,320202,378430,73708,12877,71950,18119!GO:0007275;multicellular organismal development;0.010703428565192;378430,320202,13590,73708,18119,71950!GO:0001711;endodermal cell fate commitment;0.010703428565192;71950!GO:0042659;regulation of cell fate specification;0.010703428565192;71950!GO:0010453;regulation of cell fate commitment;0.010703428565192;71950!GO:0009996;negative regulation of cell fate specification;0.010703428565192;71950!GO:0010454;negative regulation of cell fate commitment;0.010703428565192;71950!GO:0048523;negative regulation of cellular process;0.0116737389182239;13590,18999,18119,71950!GO:0009952;anterior/posterior pattern formation;0.012727101419578;13590,18119!GO:0045165;cell fate commitment;0.0138066231261762;18119,71950!GO:0048519;negative regulation of biological process;0.0138066231261762;13590,18999,18119,71950!GO:0030259;lipid glycosylation;0.0176185544395488;67574!GO:0001940;male pronucleus;0.0176185544395488;73708!GO:0006417;regulation of translation;0.0196990255106665;378430,12877!GO:0048505;regulation of timing of cell differentiation;0.0196990255106665;18119!GO:0040034;regulation of development, heterochronic;0.0196990255106665;18119!GO:0001939;female pronucleus;0.0196990255106665;73708!GO:0031326;regulation of cellular biosynthetic process;0.0211316487213253;378430,12877!GO:0005160;transforming growth factor beta receptor binding;0.0218905462024405;320202!GO:0040016;embryonic cleavage;0.0218905462024405;73708!GO:0003002;regionalization;0.0218905462024405;13590,18119!GO:0009889;regulation of biosynthetic process;0.0237110789038901;378430,12877!GO:0007130;synaptonemal complex assembly;0.0238035645283384;12877!GO:0065007;biological regulation;0.0271473139901545;378430,320202,13590,12877,18999,18119,71950!GO:0017145;stem cell division;0.0288307489318434;71950!GO:0005102;receptor binding;0.0288307489318434;320202,13590,18119!GO:0009948;anterior/posterior axis specification;0.0342471769361994;13590!GO:0007129;synapsis;0.0365870750233847;12877!GO:0001947;heart looping;0.0406109439809507;18119!GO:0048168;regulation of neuronal synaptic plasticity;0.0406109439809507;12877!GO:0050794;regulation of cellular process;0.0406109439809507;378430,13590,12877,18999,18119,71950!GO:0051246;regulation of protein metabolic process;0.0413016207316092;378430,12877!GO:0051301;cell division;0.0419009446029893;73708,71950!GO:0009798;axis 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|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0000991!3.01e-25!18;UBERON:0005564!3.01e-25!18;UBERON:0000473!1.18e-22!14;UBERON:0003135!3.54e-21!15;UBERON:0003101!6.98e-20!16;UBERON:0000079!6.98e-20!16;UBERON:0003133!4.99e-19!24;UBERON:0004176!9.72e-19!17;UBERON:0009196!9.72e-19!17;UBERON:0009117!9.72e-19!17;UBERON:0005156!1.37e-17!26;UBERON:0000990!1.37e-17!26;UBERON:0002323!1.93e-12!37;UBERON:0004458!1.93e-12!37;UBERON:0003886!4.04e-12!38;UBERON:0002553!8.16e-12!39;UBERON:0000464!3.90e-08!57
|tfbs_overrepresentation_for_novel_motifs=0.149902,0.201919,0.133309,1.01095,0.0709145,0.551286,0.254787,1.28332,0.596432,0.0396053,0.221763,1.27358,0.0322096,0.73029,0.271754,0,0.42315,0.0671461,0.514215,0.245228,0.358501,0.685027,0.263535,0.527336,0.138033,0.285776,0.486875,0.202945,0.0941661,0.884629,0.562931,0.512187,0.0660956,0.424507,0.970517,0.0928537,0.0618293,0.242872,0.194199,0.364515,0.0689912,0.196576,0.249206,0.578047,0.459119,0.170437,0.355451,0.214351,0.32395,0.317394,0.408111,0.307229,0.167462,0.641205,0.657376,0.269785,0.100694,0.23598,1.48719,0.268198,0.494318,0.314847,0.354886,0.398468,0.278491,1.10617,0.785371,1.12243,0.490165,0.979213,0.386078,0.0340869,0.0244677,0.6886,0.710851,0.018158,1.40751,0.914794,0.479091,0.113666,0.138314,0.438213,0.31368,0.123739,0.582029,0.0422746,0.020087,0.0686434,0.359539,1.2816,0.851763,0.586575,0.523661,0.256716,0.189143,0.380698,0.555715,0.526183,0.355664,0.498538,0.483457,0.511936,0.625103,0.408622,0.407717,0.196264,0.459578,0.607107,0.116526,0.112248,0.44617,0.626748,0.366686,0.225582,0.858505,0.516755,0.0274913,0.180644,0.424276,0.820725,0.693645,0.380657,0.287218,0.345253,0.910454,0.482363,0.261058,0.517583,0.783932,1.40627,0.609469,0.173056,0.75595,0.280468,0.879201,0.277969,0.471259,0.197578,0.832159,1.64606,1.25025,0.789841,0.296788,0.521565,0.402166,0.196898,0.358053,1.60668,0.156941,0.250986,0.360841,0.0560078,0.642658,0.174823,0.765783,0.718834,0.829911,1.01394,0.453591,0.155206,0.841238,0.581248,0.482758,0.143905,0.39934,0.273933,0.220881,0.244407,0.0148726
|tfbs_overrepresentation_jaspar=MA0003.1;0.263084,MA0004.1;0.527785,MA0006.1;0.265566,MA0007.1;0.168178,MA0009.1;0.535932,MA0014.1;1.59389,MA0017.1;2.13316,MA0019.1;0.982191,MA0024.1;0.496718,MA0025.1;0.751694,MA0027.1;2.14278,MA0028.1;0.0821841,MA0029.1;0.477444,MA0030.1;0.483253,MA0031.1;0.451927,MA0038.1;1.42188,MA0040.1;0.547233,MA0041.1;0.404719,MA0042.1;0.384176,MA0043.1;0.624178,MA0046.1;0.568473,MA0048.1;0.0108253,MA0050.1;0.205672,MA0051.1;0.2928,MA0052.1;0.554531,MA0055.1;0.018284,MA0056.1;0,MA0057.1;0.454273,MA0058.1;0.117003,MA0059.1;0.124358,MA0060.1;0.0417645,MA0061.1;0.0537092,MA0063.1;0,MA0066.1;0.759694,MA0067.1;0.857286,MA0068.1;4.91593,MA0069.1;0.554839,MA0070.1;0.54606,MA0071.1;0.20507,MA0072.1;0.538403,MA0073.1;20.239,MA0074.1;1.28764,MA0076.1;0.101055,MA0077.1;0.518913,MA0078.1;0.319336,MA0081.1;0.429201,MA0083.1;0.623446,MA0084.1;1.1752,MA0087.1;0.583879,MA0088.1;1.29308,MA0089.1;0,MA0090.1;0.471234,MA0091.1;1.65596,MA0092.1;2.11049,MA0093.1;0.609251,MA0095.1;0,MA0098.1;0,MA0100.1;0.2406,MA0101.1;0.12981,MA0103.1;0.657254,MA0105.1;0.213264,MA0106.1;0.325663,MA0107.1;0.310214,MA0108.2;1.02466,MA0109.1;0,MA0111.1;0.494436,MA0113.1;0.302851,MA0114.1;1.62985,MA0115.1;2.57401,MA0116.1;3.9252,MA0117.1;0.597086,MA0119.1;0.130171,MA0122.1;0.615314,MA0124.1;0.80652,MA0125.1;0.736412,MA0130.1;0,MA0131.1;0.372683,MA0132.1;0,MA0133.1;0,MA0135.1;0.657882,MA0136.1;0.731186,MA0139.1;0.299978,MA0140.1;0.240513,MA0141.1;1.16831,MA0142.1;0.439269,MA0143.1;0.847878,MA0144.1;0.19926,MA0145.1;0.0269479,MA0146.1;0.104944,MA0147.1;0.0593437,MA0148.1;0.555053,MA0149.1;1.33466,MA0062.2;0.0201154,MA0035.2;0.244063,MA0039.2;4.43285,MA0138.2;0.366012,MA0002.2;0.886864,MA0137.2;0.701055,MA0104.2;0.145321,MA0047.2;0.285109,MA0112.2;0.326529,MA0065.2;2.16879,MA0150.1;0.168102,MA0151.1;0,MA0152.1;0.285194,MA0153.1;0.67335,MA0154.1;5.67232,MA0155.1;0.601417,MA0156.1;0.676622,MA0157.1;0.411541,MA0158.1;0,MA0159.1;0.0638985,MA0160.1;2.38263,MA0161.1;0,MA0162.1;1.18735,MA0163.1;2.69172,MA0164.1;1.34551,MA0080.2;0.643629,MA0018.2;0.272436,MA0099.2;0.360735,MA0079.2;9.83678,MA0102.2;1.22663,MA0258.1;0.401444,MA0259.1;0.201267,MA0442.1;0
}}

Latest revision as of 15:13, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr10:60881031..60881037,+p1@Nodal
Mm9::chr12:106460922..106460932,-p1@Tcl1
Mm9::chr12:106460944..106460955,-p2@Tcl1
Mm9::chr16:48281766..48281778,+p@chr16:48281766..48281778
+
Mm9::chr17:35642973..35642994,+p2@Pou5f1
Mm9::chr17:35642997..35643014,+p1@Pou5f1
Mm9::chr1:182823238..182823239,+p1@Lefty2
Mm9::chr1:182865168..182865172,+p2@Lefty1
Mm9::chr2:118541186..118541194,-p@chr2:118541186..118541194
-
Mm9::chr2:165635739..165635747,+p@chr2:165635739..165635747
+
Mm9::chr2:25621051..25621055,+p1@Lcn3
Mm9::chr6:122576436..122576438,+p1@Dppa3
Mm9::chr6:122657610..122657626,+p1@Nanog
p1@Nanogpd
Mm9::chr7:19572867..19572873,+p1@Nanos2
Mm9::chr7:88599637..88599650,-p4@Cpeb1
Mm9::chr9:78215959..78215971,-p1@Dppa5a
Mm9::chr9:78215974..78215984,-p2@Dppa5a
Mm9::chr9:78215998..78216003,-p3@Dppa5a
Mm9::chrX:140770330..140770374,+p5@Alg13


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:0048863stem cell differentiation2.7667001875512e-06
GO:0048864stem cell development0.000451023744568524
GO:0019827stem cell maintenance0.000451023744568524
GO:0042074cell migration involved in gastrulation0.000630972040384902
GO:0045596negative regulation of cell differentiation0.000948523766910004
GO:0045120pronucleus0.00124038586237459
GO:0051093negative regulation of developmental process0.00124038586237459
GO:0008083growth factor activity0.00304482699284934
GO:0045595regulation of cell differentiation0.00304482699284934
GO:0009790embryonic development0.00342597435615527
GO:0005125cytokine activity0.00670187390332782
GO:0007389pattern specification process0.00788911411822714
GO:0050793regulation of developmental process0.00788911411822714
GO:0001714endodermal cell fate specification0.00788911411822714
GO:0042664negative regulation of endodermal cell fate specification0.00788911411822714
GO:0002085repression of premature neural plate formation0.00788911411822714
GO:0030718germ-line stem cell maintenance0.00788911411822714
GO:0042663regulation of endodermal cell fate specification0.00788911411822714
GO:0004577N-acetylglucosaminyldiphosphodolichol N-acetylglucosaminyltransferase activity0.00788911411822714
GO:0007369gastrulation0.00835616358503614
GO:0032502developmental process0.00842780921854488
GO:0032501multicellular organismal process0.0105943426963285
GO:0007275multicellular organismal development0.010703428565192
GO:0001711endodermal cell fate commitment0.010703428565192
GO:0042659regulation of cell fate specification0.010703428565192
GO:0010453regulation of cell fate commitment0.010703428565192
GO:0009996negative regulation of cell fate specification0.010703428565192
GO:0010454negative regulation of cell fate commitment0.010703428565192
GO:0048523negative regulation of cellular process0.0116737389182239
GO:0009952anterior/posterior pattern formation0.012727101419578
GO:0045165cell fate commitment0.0138066231261762
GO:0048519negative regulation of biological process0.0138066231261762
GO:0030259lipid glycosylation0.0176185544395488
GO:0001940male pronucleus0.0176185544395488
GO:0006417regulation of translation0.0196990255106665
GO:0048505regulation of timing of cell differentiation0.0196990255106665
GO:0040034regulation of development, heterochronic0.0196990255106665
GO:0001939female pronucleus0.0196990255106665
GO:0031326regulation of cellular biosynthetic process0.0211316487213253
GO:0005160transforming growth factor beta receptor binding0.0218905462024405
GO:0040016embryonic cleavage0.0218905462024405
GO:0003002regionalization0.0218905462024405
GO:0009889regulation of biosynthetic process0.0237110789038901
GO:0007130synaptonemal complex assembly0.0238035645283384
GO:0065007biological regulation0.0271473139901545
GO:0017145stem cell division0.0288307489318434
GO:0005102receptor binding0.0288307489318434
GO:0009948anterior/posterior axis specification0.0342471769361994
GO:0007129synapsis0.0365870750233847
GO:0001947heart looping0.0406109439809507
GO:0048168regulation of neuronal synaptic plasticity0.0406109439809507
GO:0050794regulation of cellular process0.0406109439809507
GO:0051246regulation of protein metabolic process0.0413016207316092
GO:0051301cell division0.0419009446029893
GO:0009798axis specification0.0461078486046946



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
gonad3.01e-2518
gonad primordium3.01e-2518
testis1.18e-2214
male reproductive organ3.54e-2115
male organism6.98e-2016
male reproductive system6.98e-2016
reproductive organ4.99e-1924
external genitalia9.72e-1917
indifferent external genitalia9.72e-1917
indifferent gonad9.72e-1917
reproductive structure1.37e-1726
reproductive system1.37e-1726
body cavity1.93e-1237
body cavity or lining1.93e-1237
body cavity precursor4.04e-1238
anatomical cavity8.16e-1239
anatomical space3.90e-0857


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)
MA0003.10.263084
MA0004.10.527785
MA0006.10.265566
MA0007.10.168178
MA0009.10.535932
MA0014.11.59389
MA0017.12.13316
MA0019.10.982191
MA0024.10.496718
MA0025.10.751694
MA0027.12.14278
MA0028.10.0821841
MA0029.10.477444
MA0030.10.483253
MA0031.10.451927
MA0038.11.42188
MA0040.10.547233
MA0041.10.404719
MA0042.10.384176
MA0043.10.624178
MA0046.10.568473
MA0048.10.0108253
MA0050.10.205672
MA0051.10.2928
MA0052.10.554531
MA0055.10.018284
MA0056.10
MA0057.10.454273
MA0058.10.117003
MA0059.10.124358
MA0060.10.0417645
MA0061.10.0537092
MA0063.10
MA0066.10.759694
MA0067.10.857286
MA0068.14.91593
MA0069.10.554839
MA0070.10.54606
MA0071.10.20507
MA0072.10.538403
MA0073.120.239
MA0074.11.28764
MA0076.10.101055
MA0077.10.518913
MA0078.10.319336
MA0081.10.429201
MA0083.10.623446
MA0084.11.1752
MA0087.10.583879
MA0088.11.29308
MA0089.10
MA0090.10.471234
MA0091.11.65596
MA0092.12.11049
MA0093.10.609251
MA0095.10
MA0098.10
MA0100.10.2406
MA0101.10.12981
MA0103.10.657254
MA0105.10.213264
MA0106.10.325663
MA0107.10.310214
MA0108.21.02466
MA0109.10
MA0111.10.494436
MA0113.10.302851
MA0114.11.62985
MA0115.12.57401
MA0116.13.9252
MA0117.10.597086
MA0119.10.130171
MA0122.10.615314
MA0124.10.80652
MA0125.10.736412
MA0130.10
MA0131.10.372683
MA0132.10
MA0133.10
MA0135.10.657882
MA0136.10.731186
MA0139.10.299978
MA0140.10.240513
MA0141.11.16831
MA0142.10.439269
MA0143.10.847878
MA0144.10.19926
MA0145.10.0269479
MA0146.10.104944
MA0147.10.0593437
MA0148.10.555053
MA0149.11.33466
MA0062.20.0201154
MA0035.20.244063
MA0039.24.43285
MA0138.20.366012
MA0002.20.886864
MA0137.20.701055
MA0104.20.145321
MA0047.20.285109
MA0112.20.326529
MA0065.22.16879
MA0150.10.168102
MA0151.10
MA0152.10.285194
MA0153.10.67335
MA0154.15.67232
MA0155.10.601417
MA0156.10.676622
MA0157.10.411541
MA0158.10
MA0159.10.0638985
MA0160.12.38263
MA0161.10
MA0162.11.18735
MA0163.12.69172
MA0164.11.34551
MA0080.20.643629
MA0018.20.272436
MA0099.20.360735
MA0079.29.83678
MA0102.21.22663
MA0258.10.401444
MA0259.10.201267
MA0442.10
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