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MCL coexpression mm9:1808: Difference between revisions

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{{MCL_coexpression_mm9
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development;0.0357320503066181;15379!GO:0003700;transcription factor activity;0.0357320503066181;15379,18028!GO:0030902;hindbrain development;0.0357320503066181;18028!GO:0048513;organ development;0.0357320503066181;15379,18028!GO:0030324;lung development;0.0357320503066181;18028!GO:0030323;respiratory tube development;0.0357320503066181;18028!GO:0048731;system development;0.0357320503066181;15379,18028!GO:0006355;regulation of transcription, DNA-dependent;0.0357320503066181;15379,18028!GO:0006351;transcription, DNA-dependent;0.0357320503066181;15379,18028!GO:0032774;RNA biosynthetic process;0.0357320503066181;15379,18028!GO:0003677;DNA binding;0.0357320503066181;15379,18028!GO:0045449;regulation of transcription;0.0357320503066181;15379,18028!GO:0006006;glucose metabolic process;0.0357320503066181;15379!GO:0048856;anatomical structure development;0.0357320503066181;15379,18028!GO:0030900;forebrain development;0.0357320503066181;18028!GO:0019219;regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process;0.0357320503066181;15379,18028!GO:0006350;transcription;0.0357320503066181;15379,18028!GO:0010468;regulation of gene expression;0.0357320503066181;15379,18028!GO:0008285;negative regulation of cell proliferation;0.0357320503066181;18028!GO:0031323;regulation of cellular metabolic process;0.0357320503066181;15379,18028!GO:0007275;multicellular organismal development;0.0357320503066181;15379,18028!GO:0019222;regulation of metabolic process;0.0357320503066181;15379,18028!GO:0019318;hexose metabolic process;0.0357320503066181;15379!GO:0006260;DNA replication;0.0357320503066181;18028!GO:0005996;monosaccharide metabolic process;0.0357320503066181;15379!GO:0016070;RNA metabolic process;0.0357320503066181;15379,18028!GO:0007420;brain development;0.0465151027743479;18028!GO:0010467;gene expression;0.0465151027743479;15379,18028!GO:0035295;tube development;0.0465151027743479;18028!GO:0003676;nucleic acid binding;0.0465151027743479;15379,18028!GO:0032502;developmental process;0.0479441086384382;15379,18028!GO:0007417;central nervous system development;0.0491106509337442;18028!GO:0006139;nucleobase, nucleoside, nucleotide and nucleic acid metabolic process;0.0491106509337442;15379,18028!GO:0044262;cellular carbohydrate metabolic process;0.0497486728019959;15379!GO:0006066;alcohol metabolic 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|gostat_on_MCL_coexpression=GO:0007492;endoderm development;0.0357320503066181;15379!GO:0003700;transcription factor activity;0.0357320503066181;15379,18028!GO:0030902;hindbrain development;0.0357320503066181;18028!GO:0048513;organ development;0.0357320503066181;15379,18028!GO:0030324;lung development;0.0357320503066181;18028!GO:0030323;respiratory tube development;0.0357320503066181;18028!GO:0048731;system development;0.0357320503066181;15379,18028!GO:0006355;regulation of transcription, DNA-dependent;0.0357320503066181;15379,18028!GO:0006351;transcription, DNA-dependent;0.0357320503066181;15379,18028!GO:0032774;RNA biosynthetic process;0.0357320503066181;15379,18028!GO:0003677;DNA binding;0.0357320503066181;15379,18028!GO:0045449;regulation of transcription;0.0357320503066181;15379,18028!GO:0006006;glucose metabolic process;0.0357320503066181;15379!GO:0048856;anatomical structure development;0.0357320503066181;15379,18028!GO:0030900;forebrain development;0.0357320503066181;18028!GO:0019219;regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process;0.0357320503066181;15379,18028!GO:0006350;transcription;0.0357320503066181;15379,18028!GO:0010468;regulation of gene expression;0.0357320503066181;15379,18028!GO:0008285;negative regulation of cell proliferation;0.0357320503066181;18028!GO:0031323;regulation of cellular metabolic process;0.0357320503066181;15379,18028!GO:0007275;multicellular organismal development;0.0357320503066181;15379,18028!GO:0019222;regulation of metabolic process;0.0357320503066181;15379,18028!GO:0019318;hexose metabolic process;0.0357320503066181;15379!GO:0006260;DNA replication;0.0357320503066181;18028!GO:0005996;monosaccharide metabolic process;0.0357320503066181;15379!GO:0016070;RNA metabolic process;0.0357320503066181;15379,18028!GO:0007420;brain development;0.0465151027743479;18028!GO:0010467;gene expression;0.0465151027743479;15379,18028!GO:0035295;tube development;0.0465151027743479;18028!GO:0003676;nucleic acid binding;0.0465151027743479;15379,18028!GO:0032502;developmental process;0.0479441086384382;15379,18028!GO:0007417;central nervous system development;0.0491106509337442;18028!GO:0006139;nucleobase, nucleoside, nucleotide and nucleic acid metabolic process;0.0491106509337442;15379,18028!GO:0044262;cellular carbohydrate metabolic process;0.0497486728019959;15379!GO:0006066;alcohol metabolic process;0.0497486728019959;15379!
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|ontology_enrichment_uberon=UBERON:0002107!9.29e-18!22;UBERON:0007499!9.29e-18!22;UBERON:0006925!9.29e-18!22;UBERON:0009497!9.29e-18!22;UBERON:0000015!9.29e-18!22;UBERON:0002423!9.29e-18!22;UBERON:0006235!9.29e-18!22;UBERON:0008835!9.29e-18!22;UBERON:0003894!9.29e-18!22;UBERON:0004161!9.29e-18!22;UBERON:0008836!9.29e-18!22;UBERON:0009854!1.35e-16!23;UBERON:0009856!1.35e-16!23;UBERON:0002365!1.46e-14!25;UBERON:0002330!1.46e-14!25;UBERON:0001264!4.34e-12!12;UBERON:0000949!1.63e-09!72;UBERON:0000466!1.68e-07!79;UBERON:0002075!7.90e-07!19
|tfbs_overrepresentation_for_novel_motifs=0.557864,0.293744,0.529553,0.603273,0.406364,0.618805,0.715644,0.812379,0.310789,0.115752,0.668936,0.702872,0.812978,0.728641,1.90904,0,0.930881,0.397593,0.283802,0.545768,0.489529,0.874994,0.727684,0.404661,1.32977,0.757752,0.274609,1.54767,0.456327,0.227599,0.626183,1.03545,0.395107,0.253145,0.425309,0.454919,2.66119,0.699032,0.360612,0.328675,0.401916,0.631725,0.134724,0.426986,0.0637209,0.591277,0.847828,0.658142,0.370501,1.16276,0.912738,1.84811,0.220111,1.18062,1.19842,0.73621,0.469329,1.64777,0.26467,1.74061,1.01481,1.86856,0.865544,0.901018,0.747985,0.943088,1.33705,1.68977,1.00999,1.54147,0.509047,0.30684,0.152094,1.23259,0.257421,0.245132,0.253065,0.835925,0.997094,0.494135,0.308173,0.948899,0.794502,0.293164,2.51921,1.99513,0.297068,1.20595,0.852952,1.85284,1.40768,1.11989,1.04863,0.412897,0.356133,0.3366,0.297538,1.05152,0.848095,0.590368,0.384901,1.03517,1.16282,0.913356,0.91226,3.77118,0.97421,0.653843,0.499439,2.13274,0.550229,1.16464,0.495367,0.674448,1.41481,0.399936,1.64321,0.607321,0.932233,0.380707,1.23809,0.879184,0.759676,0.834976,1.46955,1.00091,0.724289,1.04166,1.33551,1.06895,1.14546,0.595426,1.3055,0.750642,1.43666,0.143464,0.566955,0.633235,1.3869,2.2222,1.82084,1.34183,0.772375,1.04623,0.905521,0.632211,0.851091,2.18247,0.569503,0.408309,2.65584,1.33841,1.18223,0.343194,0.749664,1.26545,0.787153,0.438007,0.555203,0.566652,1.39653,1.11392,1.00137,0.547782,0.90208,0.741834,0.997706,0.701187,0.191104
|tfbs_overrepresentation_jaspar=MA0003.1;0.989123,MA0004.1;2.50003,MA0006.1;0.419915,MA0007.1;2.44791,MA0009.1;1.06266,MA0014.1;0.736185,MA0017.1;0.449113,MA0019.1;0.874061,MA0024.1;1.01759,MA0025.1;1.30092,MA0027.1;2.72141,MA0028.1;0.43138,MA0029.1;0.995171,MA0030.1;1.00195,MA0031.1;0.965177,MA0038.1;0.757669,MA0040.1;1.07552,MA0041.1;0.522007,MA0042.1;0.507715,MA0043.1;1.1618,MA0046.1;1.09955,MA0048.1;1.7574,MA0050.1;0.645342,MA0051.1;0.767098,MA0052.1;1.08379,MA0055.1;4.09564,MA0056.1;0,MA0057.1;0.562607,MA0058.1;2.16203,MA0059.1;3.25322,MA0060.1;0.881183,MA0061.1;0.364227,MA0063.1;0,MA0066.1;0.746072,MA0067.1;1.41352,MA0068.1;4.059,MA0069.1;1.08414,MA0070.1;1.07418,MA0071.1;0.644448,MA0072.1;1.06547,MA0073.1;16.3563,MA0074.1;0.708108,MA0076.1;0.470037,MA0077.1;1.04318,MA0078.1;0.801834,MA0081.1;0.53877,MA0083.1;1.16099,MA0084.1;1.74401,MA0087.1;1.11687,MA0088.1;1.42769,MA0089.1;0,MA0090.1;2.38058,MA0091.1;0.617887,MA0092.1;0.567278,MA0093.1;1.96218,MA0095.1;0,MA0098.1;0,MA0100.1;0.695835,MA0101.1;0.523409,MA0103.1;0.460936,MA0105.1;0.248108,MA0106.1;0.809991,MA0107.1;0.454197,MA0108.2;0.897859,MA0109.1;0,MA0111.1;0.582193,MA0113.1;0.780358,MA0114.1;0.361633,MA0115.1;1.16466,MA0116.1;0.419688,MA0117.1;1.13165,MA0119.1;0.524046,MA0122.1;1.15196,MA0124.1;1.35963,MA0125.1;1.28445,MA0130.1;0,MA0131.1;0.869325,MA0132.1;0,MA0133.1;0,MA0135.1;1.19898,MA0136.1;0.729175,MA0139.1;0.8026,MA0140.1;0.695713,MA0141.1;0.482463,MA0142.1;0.950155,MA0143.1;0.797553,MA0144.1;0.956957,MA0145.1;0.476962,MA0146.1;1.24854,MA0147.1;1.75115,MA0148.1;0.621195,MA0149.1;0.529387,MA0062.2;0.254018,MA0035.2;0.700704,MA0039.2;4.4018,MA0138.2;0.861035,MA0002.2;0.809945,MA0137.2;0.479301,MA0104.2;1.52809,MA0047.2;0.75686,MA0112.2;0.157681,MA0065.2;0.158101,MA0150.1;0.587557,MA0151.1;0,MA0152.1;0.756973,MA0153.1;1.21594,MA0154.1;0.203217,MA0155.1;0.173445,MA0156.1;0.469089,MA0157.1;0.91689,MA0158.1;0,MA0159.1;0.389847,MA0160.1;0.624415,MA0161.1;0,MA0162.1;3.09272,MA0163.1;1.29282,MA0164.1;0.729558,MA0080.2;0.455167,MA0018.2;1.75252,MA0099.2;0.854449,MA0079.2;5.51,MA0102.2;1.79669,MA0258.1;0.346619,MA0259.1;2.5756,MA0442.1;0
}}

Latest revision as of 17:31, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr4:82151500..82151505,-p11@Nfib
Mm9::chr9:74709664..74709671,+p6@Onecut1
Mm9::chr9:74709682..74709691,+p3@Onecut1
Mm9::chr9:74709695..74709722,+p1@Onecut1
Mm9::chr9:74714281..74714296,+p5@Onecut1


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:0007492endoderm development0.0357320503066181
GO:0003700transcription factor activity0.0357320503066181
GO:0030902hindbrain development0.0357320503066181
GO:0048513organ development0.0357320503066181
GO:0030324lung development0.0357320503066181
GO:0030323respiratory tube development0.0357320503066181
GO:0048731system development0.0357320503066181
GO:0006355regulation of transcription, DNA-dependent0.0357320503066181
GO:0006351transcription, DNA-dependent0.0357320503066181
GO:0032774RNA biosynthetic process0.0357320503066181
GO:0003677DNA binding0.0357320503066181
GO:0045449regulation of transcription0.0357320503066181
GO:0006006glucose metabolic process0.0357320503066181
GO:0048856anatomical structure development0.0357320503066181
GO:0030900forebrain development0.0357320503066181
GO:0019219regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process0.0357320503066181
GO:0006350transcription0.0357320503066181
GO:0010468regulation of gene expression0.0357320503066181
GO:0008285negative regulation of cell proliferation0.0357320503066181
GO:0031323regulation of cellular metabolic process0.0357320503066181
GO:0007275multicellular organismal development0.0357320503066181
GO:0019222regulation of metabolic process0.0357320503066181
GO:0019318hexose metabolic process0.0357320503066181
GO:0006260DNA replication0.0357320503066181
GO:0005996monosaccharide metabolic process0.0357320503066181
GO:0016070RNA metabolic process0.0357320503066181
GO:0007420brain development0.0465151027743479
GO:0010467gene expression0.0465151027743479
GO:0035295tube development0.0465151027743479
GO:0003676nucleic acid binding0.0465151027743479
GO:0032502developmental process0.0479441086384382
GO:0007417central nervous system development0.0491106509337442
GO:0006139nucleobase, nucleoside, nucleotide and nucleic acid metabolic process0.0491106509337442
GO:0044262cellular carbohydrate metabolic process0.0497486728019959
GO:0006066alcohol metabolic process0.0497486728019959



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
liver9.29e-1822
epithelial sac9.29e-1822
digestive gland9.29e-1822
epithelium of foregut-midgut junction9.29e-1822
anatomical boundary9.29e-1822
hepatobiliary system9.29e-1822
foregut-midgut junction9.29e-1822
hepatic diverticulum9.29e-1822
liver primordium9.29e-1822
septum transversum9.29e-1822
liver bud9.29e-1822
digestive tract diverticulum1.35e-1623
sac1.35e-1623
exocrine gland1.46e-1425
exocrine system1.46e-1425
pancreas4.34e-1212
endocrine system1.63e-0972
immaterial anatomical entity1.68e-0779
viscus7.90e-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)
MA0003.10.989123
MA0004.12.50003
MA0006.10.419915
MA0007.12.44791
MA0009.11.06266
MA0014.10.736185
MA0017.10.449113
MA0019.10.874061
MA0024.11.01759
MA0025.11.30092
MA0027.12.72141
MA0028.10.43138
MA0029.10.995171
MA0030.11.00195
MA0031.10.965177
MA0038.10.757669
MA0040.11.07552
MA0041.10.522007
MA0042.10.507715
MA0043.11.1618
MA0046.11.09955
MA0048.11.7574
MA0050.10.645342
MA0051.10.767098
MA0052.11.08379
MA0055.14.09564
MA0056.10
MA0057.10.562607
MA0058.12.16203
MA0059.13.25322
MA0060.10.881183
MA0061.10.364227
MA0063.10
MA0066.10.746072
MA0067.11.41352
MA0068.14.059
MA0069.11.08414
MA0070.11.07418
MA0071.10.644448
MA0072.11.06547
MA0073.116.3563
MA0074.10.708108
MA0076.10.470037
MA0077.11.04318
MA0078.10.801834
MA0081.10.53877
MA0083.11.16099
MA0084.11.74401
MA0087.11.11687
MA0088.11.42769
MA0089.10
MA0090.12.38058
MA0091.10.617887
MA0092.10.567278
MA0093.11.96218
MA0095.10
MA0098.10
MA0100.10.695835
MA0101.10.523409
MA0103.10.460936
MA0105.10.248108
MA0106.10.809991
MA0107.10.454197
MA0108.20.897859
MA0109.10
MA0111.10.582193
MA0113.10.780358
MA0114.10.361633
MA0115.11.16466
MA0116.10.419688
MA0117.11.13165
MA0119.10.524046
MA0122.11.15196
MA0124.11.35963
MA0125.11.28445
MA0130.10
MA0131.10.869325
MA0132.10
MA0133.10
MA0135.11.19898
MA0136.10.729175
MA0139.10.8026
MA0140.10.695713
MA0141.10.482463
MA0142.10.950155
MA0143.10.797553
MA0144.10.956957
MA0145.10.476962
MA0146.11.24854
MA0147.11.75115
MA0148.10.621195
MA0149.10.529387
MA0062.20.254018
MA0035.20.700704
MA0039.24.4018
MA0138.20.861035
MA0002.20.809945
MA0137.20.479301
MA0104.21.52809
MA0047.20.75686
MA0112.20.157681
MA0065.20.158101
MA0150.10.587557
MA0151.10
MA0152.10.756973
MA0153.11.21594
MA0154.10.203217
MA0155.10.173445
MA0156.10.469089
MA0157.10.91689
MA0158.10
MA0159.10.389847
MA0160.10.624415
MA0161.10
MA0162.13.09272
MA0163.11.29282
MA0164.10.729558
MA0080.20.455167
MA0018.21.75252
MA0099.20.854449
MA0079.25.51
MA0102.21.79669
MA0258.10.346619
MA0259.12.5756
MA0442.10
Retrieved from "http://f5-webapp4.gsc.riken.jp/resource_browser/index.php?title=MCL_coexpression_mm9:1808&oldid=3073807"