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MCL coexpression mm9:2956: Difference between revisions

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{{MCL_coexpression_mm9|gostat_on_MCL_coexpression=GO:0007389;pattern specification process;0.00803872071608881;15427,209448!GO:0005667;transcription factor complex;0.00803872071608881;15427,209448!GO:0043565;sequence-specific DNA binding;0.00803872071608881;15427,209448!GO:0009887;organ morphogenesis;0.00803872071608881;15427,209448!GO:0044451;nucleoplasm part;0.00803872071608881;15427,209448!GO:0005654;nucleoplasm;0.00803872071608881;15427,209448!GO:0031981;nuclear lumen;0.00963684767822337;15427,209448!GO:0031974;membrane-enclosed lumen;0.00963684767822337;15427,209448!GO:0043233;organelle lumen;0.00963684767822337;15427,209448!GO:0003700;transcription factor activity;0.0104645519890221;15427,209448!GO:0044428;nuclear part;0.0139359142684202;15427,209448!GO:0009653;anatomical structure morphogenesis;0.0165973635308497;15427,209448!GO:0048513;organ development;0.0218070536961134;15427,209448!GO:0043234;protein complex;0.0259469384460429;15427,209448!GO:0048731;system development;0.0259469384460429;15427,209448!GO:0006355;regulation of transcription, DNA-dependent;0.0259469384460429;15427,209448!GO:0006351;transcription, DNA-dependent;0.0259469384460429;15427,209448!GO:0032774;RNA biosynthetic process;0.0259469384460429;15427,209448!GO:0003677;DNA binding;0.0259469384460429;15427,209448!GO:0045449;regulation of transcription;0.0259469384460429;15427,209448!GO:0048856;anatomical structure development;0.0259469384460429;15427,209448!GO:0019219;regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process;0.0259469384460429;15427,209448!GO:0006350;transcription;0.0259469384460429;15427,209448!GO:0032991;macromolecular complex;0.0259469384460429;15427,209448!GO:0010468;regulation of gene expression;0.0259469384460429;15427,209448!GO:0031323;regulation of cellular metabolic process;0.0269958749702859;15427,209448!GO:0007275;multicellular organismal development;0.0269958749702859;15427,209448!GO:0019222;regulation of metabolic process;0.0269958749702859;15427,209448!GO:0016070;RNA metabolic process;0.0274591125508986;15427,209448!GO:0044446;intracellular organelle part;0.0275272898319057;15427,209448!GO:0044422;organelle part;0.0275272898319057;15427,209448!GO:0016563;transcription activator activity;0.0327528128633795;15427!GO:0010467;gene expression;0.0345577832018417;15427,209448!GO:0003676;nucleic acid binding;0.0351794894932043;15427,209448!GO:0032502;developmental process;0.0363983845173449;15427,209448!GO:0006139;nucleobase, nucleoside, nucleotide and nucleic acid metabolic process;0.0385869400193705;15427,209448!GO:0050794;regulation of cellular process;0.0431785730303571;15427,209448!}}
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DNA-dependent;0.0259469384460429;15427,209448!GO:0006351;transcription, DNA-dependent;0.0259469384460429;15427,209448!GO:0032774;RNA biosynthetic process;0.0259469384460429;15427,209448!GO:0003677;DNA binding;0.0259469384460429;15427,209448!GO:0045449;regulation of transcription;0.0259469384460429;15427,209448!GO:0048856;anatomical structure development;0.0259469384460429;15427,209448!GO:0019219;regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process;0.0259469384460429;15427,209448!GO:0006350;transcription;0.0259469384460429;15427,209448!GO:0032991;macromolecular complex;0.0259469384460429;15427,209448!GO:0010468;regulation of gene expression;0.0259469384460429;15427,209448!GO:0031323;regulation of cellular metabolic process;0.0269958749702859;15427,209448!GO:0007275;multicellular organismal development;0.0269958749702859;15427,209448!GO:0019222;regulation of metabolic process;0.0269958749702859;15427,209448!GO:0016070;RNA metabolic process;0.0274591125508986;15427,209448!GO:0044446;intracellular organelle part;0.0275272898319057;15427,209448!GO:0044422;organelle part;0.0275272898319057;15427,209448!GO:0016563;transcription activator activity;0.0327528128633795;15427!GO:0010467;gene expression;0.0345577832018417;15427,209448!GO:0003676;nucleic acid binding;0.0351794894932043;15427,209448!GO:0032502;developmental process;0.0363983845173449;15427,209448!GO:0006139;nucleobase, nucleoside, nucleotide and nucleic acid metabolic process;0.0385869400193705;15427,209448!GO:0050794;regulation of cellular process;0.0431785730303571;15427,209448!|ontology_enrichment_celltype=|ontology_enrichment_disease=|ontology_enrichment_uberon=UBERON:0000489!9.30e-14!21;UBERON:0002113!1.53e-09!14;UBERON:0003918!1.53e-09!14;UBERON:0011143!1.53e-09!14;UBERON:0005095!1.53e-09!14;UBERON:0007687!1.53e-09!14;UBERON:0000991!3.82e-08!18;UBERON:0005564!3.82e-08!18;UBERON:0006554!4.15e-08!18;UBERON:0005156!1.19e-07!26;UBERON:0000990!1.19e-07!26;UBERON:0001008!2.11e-07!19;UBERON:0004176!2.18e-07!17;UBERON:0009196!2.18e-07!17;UBERON:0009117!2.18e-07!17;UBERON:0003133!6.73e-07!24;UBERON:0002240!7.16e-07!6;UBERON:0005174!7.16e-07!6;UBERON:0001137!7.16e-07!6|tfbs_overrepresentation_for_novel_motifs=0.752782,0.193418,0.722405,0.801166,0.587814,0.81763,0.919454,0.467321,0.479531,0.66329,0.870507,0.906098,0.467629,0.933025,0.608226,0,1.14208,1.41496,0.448066,0.328717,0.679146,0.275782,0.932027,0.585919,1.73474,0.963352,0.437236,0.841386,0.64294,0.380786,0.825437,1.24901,0.575271,0.411696,0.608816,0.872889,0.563758,0.902078,0.536514,1.24975,0.582863,0.831295,0.261619,0.610669,0.156582,0.788421,1.05665,0.859154,0.235354,0.646474,1.12346,0.99279,0.371606,1.3966,1.41464,0.940919,0.657156,0.891887,0.425455,2.16101,1.22795,1.00308,0.494668,1.11142,0.953187,1.15459,1.55483,1.90983,1.22303,1.7608,0.700291,0.474956,0.284975,1.44925,1.882,0.402065,0.411601,1.04436,1.20986,0.684144,0.476502,1.16055,1.00151,1.16164,1.32978,0.181575,0.195254,2.64303,1.06194,2.07346,1.62608,1.33496,1.26245,0.595071,0.531443,0.509215,0.464141,1.26539,1.05692,0.352122,0.563856,1.24872,1.37854,1.12409,1.12297,0.830796,1.18646,0.854628,0.689894,0.681267,0.744607,1.38039,0.685481,0.876299,1.63327,0.580657,0.609576,0.805461,1.14346,0.559153,1.45481,1.08896,0.965352,1.04338,1.68841,1.21376,2.14021,1.25534,1.55328,0.598722,1.36093,0.792832,1.52297,0.955954,1.65529,0.273451,0.762499,1.94441,1.60513,2.44352,2.04137,1.55966,0.978551,1.26,1.11604,0.831808,1.06002,2.40374,0.765221,0.589976,0.38417,0.260379,1.39822,0.516739,0.954936,1.48249,0.993889,0.622823,0.749933,0.762177,1.61484,1.32889,1.21423,0.741984,2.51458,2.17757,0.562367,0.904334,0.135528|tfbs_overrepresentation_jaspar=MA0003.1;0.245953,MA0004.1;1.8803,MA0006.1;0.60285,MA0007.1;0.784593,MA0009.1;1.27673,MA0014.1;0.416365,MA0017.1;0.635031,MA0019.1;1.08369,MA0024.1;1.23079,MA0025.1;1.51835,MA0027.1;2.9431,MA0028.1;0.61552,MA0029.1;1.20789,MA0030.1;1.21482,MA0031.1;1.17722,MA0038.1;0.963265,MA0040.1;1.28983,MA0041.1;0.714279,MA0042.1;0.69885,MA0043.1;1.3775,MA0046.1;1.31428,MA0048.1;0.353763,MA0050.1;0.845669,MA0051.1;0.973068,MA0052.1;1.29825,MA0055.1;0.190475,MA0056.1;0,MA0057.1;3.35395,MA0058.1;2.77886,MA0059.1;0.705317,MA0060.1;2.1699,MA0061.1;0.5406,MA0063.1;0,MA0066.1;0.951196,MA0067.1;1.63197,MA0068.1;2.46203,MA0069.1;1.29861,MA0070.1;1.28847,MA0071.1;0.844726,MA0072.1;1.2796,MA0073.1;0.25258,MA0074.1;2.10566,MA0076.1;0.657929,MA0077.1;1.2569,MA0078.1;1.0091,MA0081.1;0.732313,MA0083.1;1.37668,MA0084.1;1.96428,MA0087.1;1.33189,MA0088.1;0.27999,MA0089.1;0,MA0090.1;0.762482,MA0091.1;0.816659,MA0092.1;0.762845,MA0093.1;2.57012,MA0095.1;0,MA0098.1;0,MA0100.1;0.89873,MA0101.1;0.71579,MA0103.1;0.647985,MA0105.1;1.84392,MA0106.1;1.01755,MA0107.1;0.640607,MA0108.2;1.10817,MA0109.1;0,MA0111.1;0.778753,MA0113.1;0.986839,MA0114.1;0.537669,MA0115.1;1.38041,MA0116.1;0.602598,MA0117.1;1.34691,MA0119.1;0.716476,MA0122.1;1.36752,MA0124.1;1.57762,MA0125.1;1.5017,MA0130.1;0,MA0131.1;1.07881,MA0132.1;0,MA0133.1;0,MA0135.1;1.4152,MA0136.1;0.933582,MA0139.1;0.462282,MA0140.1;2.07913,MA0141.1;0.671467,MA0142.1;1.16183,MA0143.1;1.00467,MA0144.1;2.29766,MA0145.1;0.292366,MA0146.1;0.151124,MA0147.1;0.556853,MA0148.1;0.820161,MA0149.1;0.722227,MA0062.2;0.412742,MA0035.2;0.903829,MA0039.2;0.0481552,MA0138.2;1.07027,MA0002.2;0.466067,MA0137.2;2.70616,MA0104.2;1.21648,MA0047.2;0.962424,MA0112.2;0.29236,MA0065.2;0.292912,MA0150.1;0.784464,MA0151.1;0,MA0152.1;0.962542,MA0153.1;1.43238,MA0154.1;0.35067,MA0155.1;0.840842,MA0156.1;0.656895,MA0157.1;1.12772,MA0158.1;0,MA0159.1;0.569393,MA0160.1;0.823568,MA0161.1;0,MA0162.1;0.166722,MA0163.1;0.477233,MA0164.1;0.933981,MA0080.2;0.64167,MA0018.2;0.944669,MA0099.2;1.06348,MA0079.2;7.93563,MA0102.2;2.01714,MA0258.1;0.520639,MA0259.1;0.543506,MA0442.1;0}}

Latest revision as of 19:21, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr15:102797288..102797302,+p1@Hoxc10
Mm9::chr15:102812013..102812029,+p@chr15:102812013..102812029
+
Mm9::chr15:102812035..102812072,+p@chr15:102812035..102812072
+


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:0007389pattern specification process0.00803872071608881
GO:0005667transcription factor complex0.00803872071608881
GO:0043565sequence-specific DNA binding0.00803872071608881
GO:0009887organ morphogenesis0.00803872071608881
GO:0044451nucleoplasm part0.00803872071608881
GO:0005654nucleoplasm0.00803872071608881
GO:0031981nuclear lumen0.00963684767822337
GO:0031974membrane-enclosed lumen0.00963684767822337
GO:0043233organelle lumen0.00963684767822337
GO:0003700transcription factor activity0.0104645519890221
GO:0044428nuclear part0.0139359142684202
GO:0009653anatomical structure morphogenesis0.0165973635308497
GO:0048513organ development0.0218070536961134
GO:0043234protein complex0.0259469384460429
GO:0048731system development0.0259469384460429
GO:0006355regulation of transcription, DNA-dependent0.0259469384460429
GO:0006351transcription, DNA-dependent0.0259469384460429
GO:0032774RNA biosynthetic process0.0259469384460429
GO:0003677DNA binding0.0259469384460429
GO:0045449regulation of transcription0.0259469384460429
GO:0048856anatomical structure development0.0259469384460429
GO:0019219regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process0.0259469384460429
GO:0006350transcription0.0259469384460429
GO:0032991macromolecular complex0.0259469384460429
GO:0010468regulation of gene expression0.0259469384460429
GO:0031323regulation of cellular metabolic process0.0269958749702859
GO:0007275multicellular organismal development0.0269958749702859
GO:0019222regulation of metabolic process0.0269958749702859
GO:0016070RNA metabolic process0.0274591125508986
GO:0044446intracellular organelle part0.0275272898319057
GO:0044422organelle part0.0275272898319057
GO:0016563transcription activator activity0.0327528128633795
GO:0010467gene expression0.0345577832018417
GO:0003676nucleic acid binding0.0351794894932043
GO:0032502developmental process0.0363983845173449
GO:0006139nucleobase, nucleoside, nucleotide and nucleic acid metabolic process0.0385869400193705
GO:0050794regulation of cellular process0.0431785730303571



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
cavitated compound organ9.30e-1421
kidney1.53e-0914
kidney mesenchyme1.53e-0914
upper urinary tract1.53e-0914
kidney rudiment1.53e-0914
kidney field1.53e-0914
gonad3.82e-0818
gonad primordium3.82e-0818
urinary system structure4.15e-0818
reproductive structure1.19e-0726
reproductive system1.19e-0726
renal system2.11e-0719
external genitalia2.18e-0717
indifferent external genitalia2.18e-0717
indifferent gonad2.18e-0717
reproductive organ6.73e-0724
spinal cord7.16e-076
dorsal region element7.16e-076
dorsum7.16e-076


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)
MA0003.10.245953
MA0004.11.8803
MA0006.10.60285
MA0007.10.784593
MA0009.11.27673
MA0014.10.416365
MA0017.10.635031
MA0019.11.08369
MA0024.11.23079
MA0025.11.51835
MA0027.12.9431
MA0028.10.61552
MA0029.11.20789
MA0030.11.21482
MA0031.11.17722
MA0038.10.963265
MA0040.11.28983
MA0041.10.714279
MA0042.10.69885
MA0043.11.3775
MA0046.11.31428
MA0048.10.353763
MA0050.10.845669
MA0051.10.973068
MA0052.11.29825
MA0055.10.190475
MA0056.10
MA0057.13.35395
MA0058.12.77886
MA0059.10.705317
MA0060.12.1699
MA0061.10.5406
MA0063.10
MA0066.10.951196
MA0067.11.63197
MA0068.12.46203
MA0069.11.29861
MA0070.11.28847
MA0071.10.844726
MA0072.11.2796
MA0073.10.25258
MA0074.12.10566
MA0076.10.657929
MA0077.11.2569
MA0078.11.0091
MA0081.10.732313
MA0083.11.37668
MA0084.11.96428
MA0087.11.33189
MA0088.10.27999
MA0089.10
MA0090.10.762482
MA0091.10.816659
MA0092.10.762845
MA0093.12.57012
MA0095.10
MA0098.10
MA0100.10.89873
MA0101.10.71579
MA0103.10.647985
MA0105.11.84392
MA0106.11.01755
MA0107.10.640607
MA0108.21.10817
MA0109.10
MA0111.10.778753
MA0113.10.986839
MA0114.10.537669
MA0115.11.38041
MA0116.10.602598
MA0117.11.34691
MA0119.10.716476
MA0122.11.36752
MA0124.11.57762
MA0125.11.5017
MA0130.10
MA0131.11.07881
MA0132.10
MA0133.10
MA0135.11.4152
MA0136.10.933582
MA0139.10.462282
MA0140.12.07913
MA0141.10.671467
MA0142.11.16183
MA0143.11.00467
MA0144.12.29766
MA0145.10.292366
MA0146.10.151124
MA0147.10.556853
MA0148.10.820161
MA0149.10.722227
MA0062.20.412742
MA0035.20.903829
MA0039.20.0481552
MA0138.21.07027
MA0002.20.466067
MA0137.22.70616
MA0104.21.21648
MA0047.20.962424
MA0112.20.29236
MA0065.20.292912
MA0150.10.784464
MA0151.10
MA0152.10.962542
MA0153.11.43238
MA0154.10.35067
MA0155.10.840842
MA0156.10.656895
MA0157.11.12772
MA0158.10
MA0159.10.569393
MA0160.10.823568
MA0161.10
MA0162.10.166722
MA0163.10.477233
MA0164.10.933981
MA0080.20.64167
MA0018.20.944669
MA0099.21.06348
MA0079.27.93563
MA0102.22.01714
MA0258.10.520639
MA0259.10.543506
MA0442.10
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