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MCL coexpression mm9:2011: Difference between revisions

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{{MCL_coexpression_mm9
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specification process;0.0067782216449032;15412,103889!GO:0005667;transcription factor complex;0.0067782216449032;15412,103889!GO:0043565;sequence-specific DNA binding;0.0067782216449032;15412,103889!GO:0048103;somatic stem cell division;0.0067782216449032;15412!GO:0009887;organ morphogenesis;0.0067782216449032;15412,103889!GO:0044451;nucleoplasm part;0.0067782216449032;15412,103889!GO:0005654;nucleoplasm;0.0067782216449032;15412,103889!GO:0017145;stem cell division;0.0067782216449032;15412!GO:0031981;nuclear lumen;0.00771427592729887;15412,103889!GO:0031974;membrane-enclosed lumen;0.00803070639851947;15412,103889!GO:0043233;organelle lumen;0.00803070639851947;15412,103889!GO:0003700;transcription factor activity;0.00888194999068237;15412,103889!GO:0044428;nuclear part;0.012010296484892;15412,103889!GO:0009653;anatomical structure morphogenesis;0.0144897618126466;15412,103889!GO:0048513;organ development;0.0192494362873099;15412,103889!GO:0043234;protein complex;0.0244547895776987;15412,103889!GO:0048731;system development;0.0244547895776987;15412,103889!GO:0006355;regulation of transcription, DNA-dependent;0.0244547895776987;15412,103889!GO:0006351;transcription, DNA-dependent;0.0244547895776987;15412,103889!GO:0032774;RNA biosynthetic process;0.0244547895776987;15412,103889!GO:0003677;DNA binding;0.0244547895776987;15412,103889!GO:0045449;regulation of transcription;0.0244547895776987;15412,103889!GO:0048856;anatomical structure development;0.0244547895776987;15412,103889!GO:0019219;regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process;0.0244547895776987;15412,103889!GO:0006350;transcription;0.0244547895776987;15412,103889!GO:0032991;macromolecular complex;0.0244547895776987;15412,103889!GO:0010468;regulation of gene expression;0.0244698493575507;15412,103889!GO:0031323;regulation of cellular metabolic process;0.0255699535665104;15412,103889!GO:0007275;multicellular organismal 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|gostat_on_MCL_coexpression=GO:0007389;pattern specification process;0.0067782216449032;15412,103889!GO:0005667;transcription factor complex;0.0067782216449032;15412,103889!GO:0043565;sequence-specific DNA binding;0.0067782216449032;15412,103889!GO:0048103;somatic stem cell division;0.0067782216449032;15412!GO:0009887;organ morphogenesis;0.0067782216449032;15412,103889!GO:0044451;nucleoplasm part;0.0067782216449032;15412,103889!GO:0005654;nucleoplasm;0.0067782216449032;15412,103889!GO:0017145;stem cell division;0.0067782216449032;15412!GO:0031981;nuclear lumen;0.00771427592729887;15412,103889!GO:0031974;membrane-enclosed lumen;0.00803070639851947;15412,103889!GO:0043233;organelle lumen;0.00803070639851947;15412,103889!GO:0003700;transcription factor activity;0.00888194999068237;15412,103889!GO:0044428;nuclear part;0.012010296484892;15412,103889!GO:0009653;anatomical structure morphogenesis;0.0144897618126466;15412,103889!GO:0048513;organ development;0.0192494362873099;15412,103889!GO:0043234;protein complex;0.0244547895776987;15412,103889!GO:0048731;system development;0.0244547895776987;15412,103889!GO:0006355;regulation of transcription, DNA-dependent;0.0244547895776987;15412,103889!GO:0006351;transcription, DNA-dependent;0.0244547895776987;15412,103889!GO:0032774;RNA biosynthetic process;0.0244547895776987;15412,103889!GO:0003677;DNA binding;0.0244547895776987;15412,103889!GO:0045449;regulation of transcription;0.0244547895776987;15412,103889!GO:0048856;anatomical structure development;0.0244547895776987;15412,103889!GO:0019219;regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process;0.0244547895776987;15412,103889!GO:0006350;transcription;0.0244547895776987;15412,103889!GO:0032991;macromolecular complex;0.0244547895776987;15412,103889!GO:0010468;regulation of gene expression;0.0244698493575507;15412,103889!GO:0031323;regulation of cellular metabolic process;0.0255699535665104;15412,103889!GO:0007275;multicellular organismal development;0.0256627453421236;15412,103889!GO:0019222;regulation of metabolic process;0.0256627453421236;15412,103889!GO:0016070;RNA metabolic process;0.0261632524006471;15412,103889!GO:0044446;intracellular organelle part;0.0263378390366999;15412,103889!GO:0044422;organelle part;0.0263378390366999;15412,103889!GO:0010467;gene expression;0.0341625144397291;15412,103889!GO:0003676;nucleic acid binding;0.0348072197631174;15412,103889!GO:0032502;developmental process;0.0360426389896548;15412,103889!GO:0051301;cell division;0.0372330122993926;15412!GO:0006139;nucleobase, nucleoside, nucleotide and nucleic acid metabolic process;0.0372330122993926;15412,103889!GO:0050794;regulation of cellular process;0.041722885145668;15412,103889!
|ontology_enrichment_celltype=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0005177!1.18e-13!79;UBERON:0002100!1.87e-13!90;UBERON:0009569!1.71e-11!66;UBERON:0000489!1.30e-10!21;UBERON:0005157!5.85e-10!20;UBERON:0002048!5.36e-09!14;UBERON:0000117!5.36e-09!14;UBERON:0000171!5.36e-09!14;UBERON:0000170!5.36e-09!14;UBERON:0005597!5.36e-09!14;UBERON:0000118!5.36e-09!14;UBERON:0005178!2.58e-08!17;UBERON:0005181!2.58e-08!17;UBERON:0002224!2.58e-08!17;UBERON:0000915!2.58e-08!17;UBERON:0008947!2.58e-08!17;UBERON:0003258!2.58e-08!17;UBERON:0005153!5.99e-08!17;UBERON:0002113!2.04e-07!14;UBERON:0003918!2.04e-07!14;UBERON:0011143!2.04e-07!14;UBERON:0005095!2.04e-07!14;UBERON:0007687!2.04e-07!14;UBERON:0000464!6.60e-07!57;UBERON:0001008!8.92e-07!19
|tfbs_overrepresentation_for_novel_motifs=0.641384,2.54893,0.612053,0.688265,0.483253,0.704257,0.803568,0.370124,0.381467,0.162942,0.755749,0.790506,0.96877,0.81685,0.502646,0,1.02248,0.473993,0.352304,0.683591,0.570433,1.08884,0.815872,0.481455,0.620553,0.846564,0.342316,0.727368,1.32554,0.290745,0.711848,1.12823,1.18815,0.318879,0.503207,4.18064,0.460474,0.786577,0.434783,2.7359,0.478558,0.717547,0.185353,0.504971,0.325217,0.675898,0.938241,0.744678,0.162985,0.539131,1.0041,0.875451,0.282443,1.2746,1.29252,0.82458,0.549352,0.776619,0.331485,0.822375,1.10737,0.885556,0.39557,0.992216,0.8366,1.03484,1.43193,1.78579,1.1025,1.63712,0.590754,0.377213,0.205546,1.32691,0.323563,0.310084,0.318792,0.926147,1.08947,0.575233,0.37865,1.04072,3.3855,0.362446,1.20828,0.11855,0.129654,0.290918,0.943446,1.94914,1.50286,1.21342,1.14153,1.22838,0.430015,1.05366,0.367176,2.57928,0.938512,2.8889,0.460566,1.12793,1.25667,1.00472,1.00361,0.717061,1.06633,0.740267,1.42067,1.4032,0.633483,1.25851,0.576517,0.7614,1.51002,1.1991,0.442329,0.692434,1.02384,2.01478,1.33244,0.970073,0.848526,0.925183,1.56496,1.09333,0.812403,1.13449,1.43038,0.493609,1.23918,0.680176,1.40022,0.839311,1.53196,0.569254,0.650785,0.719099,1.482,2.31884,1.91709,1.43673,0.861473,1.1391,0.996781,0.718046,0.941555,2.27909,0.653418,0.485304,0.293812,0.184289,1.27621,0.416214,0.838313,1.35996,0.87653,0.516549,0.63863,0.650472,3.27965,1.20739,2.47662,0.630949,0.993294,0.830321,1.16191,0.788782,0.0824127
|tfbs_overrepresentation_jaspar=MA0003.1;0.0356887,MA0004.1;0.6888,MA0006.1;0.497533,MA0007.1;0.672186,MA0009.1;1.15569,MA0014.1;1.46333,MA0017.1;0.528196,MA0019.1;0.964875,MA0024.1;1.11019,MA0025.1;1.39562,MA0027.1;2.81824,MA0028.1;0.509589,MA0029.1;1.08753,MA0030.1;1.09438,MA0031.1;1.05719,MA0038.1;0.846479,MA0040.1;1.16866,MA0041.1;0.604221,MA0042.1;0.589368,MA0043.1;1.25564,MA0046.1;1.1929,MA0048.1;0.266382,MA0050.1;0.731539,MA0051.1;0.856094,MA0052.1;1.17701,MA0055.1;0.125758,MA0056.1;0,MA0057.1;0.251896,MA0058.1;1.4226,MA0059.1;0.59559,MA0060.1;1.04037,MA0061.1;1.11761,MA0063.1;0,MA0066.1;0.834648,MA0067.1;1.50873,MA0068.1;5.66365,MA0069.1;1.17737,MA0070.1;4.25739,MA0071.1;0.73062,MA0072.1;1.15853,MA0073.1;4.40992,MA0074.1;0.795862,MA0076.1;0.550092,MA0077.1;1.13603,MA0078.1;0.891476,MA0081.1;0.621611,MA0083.1;1.25482,MA0084.1;1.84013,MA0087.1;1.21037,MA0088.1;1.73268,MA0089.1;0,MA0090.1;0.650768,MA0091.1;0.703314,MA0092.1;0.651119,MA0093.1;1.29026,MA0095.1;0,MA0098.1;0,MA0100.1;0.783305,MA0101.1;0.605676,MA0103.1;0.540576,MA0105.1;4.16446,MA0106.1;0.899777,MA0107.1;0.533522,MA0108.2;0.989014,MA0109.1;0,MA0111.1;0.666525,MA0113.1;0.869608,MA0114.1;0.43587,MA0115.1;1.25852,MA0116.1;0.497293,MA0117.1;1.22527,MA0119.1;0.606338,MA0122.1;1.24573,MA0124.1;1.45461,MA0125.1;1.37907,MA0130.1;0,MA0131.1;0.960068,MA0132.1;0,MA0133.1;0,MA0135.1;1.29308,MA0136.1;0.817395,MA0139.1;0.365453,MA0140.1;0.78318,MA0141.1;0.563066,MA0142.1;1.04199,MA0143.1;0.887119,MA0144.1;0.439506,MA0145.1;0.21199,MA0146.1;0.313734,MA0147.1;0.453952,MA0148.1;0.706718,MA0149.1;0.611881,MA0062.2;0.319836,MA0035.2;0.788288,MA0039.2;0.731226,MA0138.2;0.951653,MA0002.2;0.368961,MA0137.2;0.559766,MA0104.2;0.386166,MA0047.2;0.845655,MA0112.2;0.211985,MA0065.2;1.14711,MA0150.1;0.67206,MA0151.1;0,MA0152.1;0.84577,MA0153.1;1.31015,MA0154.1;0.263609,MA0155.1;0.650923,MA0156.1;0.549102,MA0157.1;1.0083,MA0158.1;0,MA0159.1;0.465802,MA0160.1;0.71003,MA0161.1;0,MA0162.1;0.704935,MA0163.1;6.91304,MA0164.1;0.817786,MA0080.2;1.32296,MA0018.2;0.828253,MA0099.2;0.944966,MA0079.2;10.9523,MA0102.2;1.8929,MA0258.1;0.419871,MA0259.1;0.441366,MA0442.1;0
}}

Latest revision as of 17:51, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr11:96180069..96180089,+p3@Hoxb4
Mm9::chr11:96213264..96213282,+p5@Hoxb2
Mm9::chr11:96213288..96213332,+p6@Hoxb2
Mm9::chr11:96213434..96213452,+p7@Hoxb2


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 process0.0067782216449032
GO:0005667transcription factor complex0.0067782216449032
GO:0043565sequence-specific DNA binding0.0067782216449032
GO:0048103somatic stem cell division0.0067782216449032
GO:0009887organ morphogenesis0.0067782216449032
GO:0044451nucleoplasm part0.0067782216449032
GO:0005654nucleoplasm0.0067782216449032
GO:0017145stem cell division0.0067782216449032
GO:0031981nuclear lumen0.00771427592729887
GO:0031974membrane-enclosed lumen0.00803070639851947
GO:0043233organelle lumen0.00803070639851947
GO:0003700transcription factor activity0.00888194999068237
GO:0044428nuclear part0.012010296484892
GO:0009653anatomical structure morphogenesis0.0144897618126466
GO:0048513organ development0.0192494362873099
GO:0043234protein complex0.0244547895776987
GO:0048731system development0.0244547895776987
GO:0006355regulation of transcription, DNA-dependent0.0244547895776987
GO:0006351transcription, DNA-dependent0.0244547895776987
GO:0032774RNA biosynthetic process0.0244547895776987
GO:0003677DNA binding0.0244547895776987
GO:0045449regulation of transcription0.0244547895776987
GO:0048856anatomical structure development0.0244547895776987
GO:0019219regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process0.0244547895776987
GO:0006350transcription0.0244547895776987
GO:0032991macromolecular complex0.0244547895776987
GO:0010468regulation of gene expression0.0244698493575507
GO:0031323regulation of cellular metabolic process0.0255699535665104
GO:0007275multicellular organismal development0.0256627453421236
GO:0019222regulation of metabolic process0.0256627453421236
GO:0016070RNA metabolic process0.0261632524006471
GO:0044446intracellular organelle part0.0263378390366999
GO:0044422organelle part0.0263378390366999
GO:0010467gene expression0.0341625144397291
GO:0003676nucleic acid binding0.0348072197631174
GO:0032502developmental process0.0360426389896548
GO:0051301cell division0.0372330122993926
GO:0006139nucleobase, nucleoside, nucleotide and nucleic acid metabolic process0.0372330122993926
GO:0050794regulation of cellular process0.041722885145668



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
trunk region element1.18e-1379
trunk1.87e-1390
subdivision of trunk1.71e-1166
cavitated compound organ1.30e-1021
epithelial fold5.85e-1020
lung5.36e-0914
respiratory tube5.36e-0914
respiration organ5.36e-0914
pair of lungs5.36e-0914
lung primordium5.36e-0914
lung bud5.36e-0914
thoracic cavity element2.58e-0817
thoracic segment organ2.58e-0817
thoracic cavity2.58e-0817
thoracic segment of trunk2.58e-0817
respiratory primordium2.58e-0817
endoderm of foregut2.58e-0817
epithelial bud5.99e-0817
kidney2.04e-0714
kidney mesenchyme2.04e-0714
upper urinary tract2.04e-0714
kidney rudiment2.04e-0714
kidney field2.04e-0714
anatomical space6.60e-0757
renal system8.92e-0719


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)
MA0003.10.0356887
MA0004.10.6888
MA0006.10.497533
MA0007.10.672186
MA0009.11.15569
MA0014.11.46333
MA0017.10.528196
MA0019.10.964875
MA0024.11.11019
MA0025.11.39562
MA0027.12.81824
MA0028.10.509589
MA0029.11.08753
MA0030.11.09438
MA0031.11.05719
MA0038.10.846479
MA0040.11.16866
MA0041.10.604221
MA0042.10.589368
MA0043.11.25564
MA0046.11.1929
MA0048.10.266382
MA0050.10.731539
MA0051.10.856094
MA0052.11.17701
MA0055.10.125758
MA0056.10
MA0057.10.251896
MA0058.11.4226
MA0059.10.59559
MA0060.11.04037
MA0061.11.11761
MA0063.10
MA0066.10.834648
MA0067.11.50873
MA0068.15.66365
MA0069.11.17737
MA0070.14.25739
MA0071.10.73062
MA0072.11.15853
MA0073.14.40992
MA0074.10.795862
MA0076.10.550092
MA0077.11.13603
MA0078.10.891476
MA0081.10.621611
MA0083.11.25482
MA0084.11.84013
MA0087.11.21037
MA0088.11.73268
MA0089.10
MA0090.10.650768
MA0091.10.703314
MA0092.10.651119
MA0093.11.29026
MA0095.10
MA0098.10
MA0100.10.783305
MA0101.10.605676
MA0103.10.540576
MA0105.14.16446
MA0106.10.899777
MA0107.10.533522
MA0108.20.989014
MA0109.10
MA0111.10.666525
MA0113.10.869608
MA0114.10.43587
MA0115.11.25852
MA0116.10.497293
MA0117.11.22527
MA0119.10.606338
MA0122.11.24573
MA0124.11.45461
MA0125.11.37907
MA0130.10
MA0131.10.960068
MA0132.10
MA0133.10
MA0135.11.29308
MA0136.10.817395
MA0139.10.365453
MA0140.10.78318
MA0141.10.563066
MA0142.11.04199
MA0143.10.887119
MA0144.10.439506
MA0145.10.21199
MA0146.10.313734
MA0147.10.453952
MA0148.10.706718
MA0149.10.611881
MA0062.20.319836
MA0035.20.788288
MA0039.20.731226
MA0138.20.951653
MA0002.20.368961
MA0137.20.559766
MA0104.20.386166
MA0047.20.845655
MA0112.20.211985
MA0065.21.14711
MA0150.10.67206
MA0151.10
MA0152.10.84577
MA0153.11.31015
MA0154.10.263609
MA0155.10.650923
MA0156.10.549102
MA0157.11.0083
MA0158.10
MA0159.10.465802
MA0160.10.71003
MA0161.10
MA0162.10.704935
MA0163.16.91304
MA0164.10.817786
MA0080.21.32296
MA0018.20.828253
MA0099.20.944966
MA0079.210.9523
MA0102.21.8929
MA0258.10.419871
MA0259.10.441366
MA0442.10
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