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MCL coexpression mm9:1224: Difference between revisions

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{{MCL_coexpression_mm9
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activator activity;0.003266495597277;216445!GO:0008047;enzyme activator activity;0.003266495597277;216445!GO:0030695;GTPase regulator activity;0.0045733790285238;216445!GO:0043087;regulation of GTPase activity;0.0471714856983727;!|ontology_enrichment_celltype=CL:0000838!3.60e-15!12;CL:0000791!2.56e-14!9;CL:0000789!2.56e-14!9;CL:0002420!2.56e-14!9;CL:0002419!2.56e-14!9;CL:0000790!2.56e-14!9;CL:0000542!8.73e-14!13;CL:0000051!8.73e-14!13;CL:0000084!9.67e-14!11;CL:0000827!9.67e-14!11;CL:0000624!1.40e-12!8;CL:0002031!3.96e-12!25;CL:0000988!2.24e-11!32;CL:0002032!2.24e-11!32;CL:0000037!2.24e-11!32;CL:0000566!2.24e-11!32;CL:0000837!2.24e-11!32;CL:0002242!1.11e-10!16;CL:0000738!6.82e-10!17;CL:0002087!6.82e-10!17;CL:0000893!1.36e-09!6;CL:0002489!1.36e-09!6;CL:0000898!1.36e-09!6;CL:0000809!1.36e-09!6;CL:0000810!1.36e-09!6;CL:0000895!1.36e-09!6;CL:0000808!1.36e-09!6;CL:0000894!1.36e-09!6;CL:0000806!1.36e-09!6;CL:0000807!1.36e-09!6;CL:0000805!1.36e-09!6;CL:0002425!1.36e-09!6;CL:0002436!1.36e-09!6;CL:0002427!1.36e-09!6;CL:0002428!1.36e-09!6;CL:0002429!1.36e-09!6;CL:0002433!1.36e-09!6;CL:0002431!1.36e-09!6;CL:0002432!1.36e-09!6|ontology_enrichment_disease=|ontology_enrichment_uberon=UBERON:0004177!1.90e-28!29;UBERON:0005057!1.90e-28!29;UBERON:0002370!9.87e-26!23;UBERON:0000974!9.87e-26!23;UBERON:0004807!9.87e-26!23;UBERON:0005058!9.87e-26!23;UBERON:0003351!9.87e-26!23;UBERON:0009113!9.87e-26!23;UBERON:0003295!9.87e-26!23;UBERON:0009722!9.87e-26!23;UBERON:0005562!9.87e-26!23;UBERON:0007690!9.87e-26!23;UBERON:0002193!3.85e-25!48;UBERON:0002405!3.85e-25!48;UBERON:0006562!2.08e-24!24;UBERON:0003408!2.08e-24!24;UBERON:0001557!2.08e-24!24;UBERON:0001042!2.08e-24!24;UBERON:0008814!2.08e-24!24;UBERON:0009145!2.08e-24!24;UBERON:0002390!2.75e-23!45;UBERON:0003061!2.75e-23!45;UBERON:0000065!1.57e-22!41;UBERON:0000077!2.44e-22!35;UBERON:0001004!8.28e-22!42;UBERON:0000072!4.99e-21!27;UBERON:0000063!1.64e-16!35;UBERON:0007811!2.62e-14!36;UBERON:0001041!1.09e-11!80;UBERON:0000153!4.60e-11!43;UBERON:0005911!2.31e-10!69;UBERON:0003081!6.51e-10!87;UBERON:0003929!1.72e-07!55;UBERON:0001007!7.88e-07!116;UBERON:0001555!7.88e-07!116;UBERON:0007026!7.88e-07!116|tfbs_overrepresentation_for_novel_motifs=1.23219,0.0600685,0.464605,0.535892,0.346849,0.550971,0.645383,1.28052,0.257202,0.283981,0.599767,0.632897,0.692139,0.6581,0.955327,0,0.856992,0.338549,0.656199,0.442204,0.426133,0.108444,0.657163,0.91309,0.472505,0.686615,0.223823,0.572827,0.394364,0.181062,0.558142,0.960397,0.336199,0.589948,0.364821,0.0363535,0.326478,0.629145,0.303703,0.27383,0.342638,0.56353,1.11416,0.366415,0.161543,0.524258,0.77511,0.589246,0.284064,0.397446,0.839084,0.714419,0.517905,1.10437,1.12205,0.66551,0.406788,0.619643,0.21472,0.663395,0.939962,0.724164,0.742129,0.827522,0.677043,0.869046,1.2599,1.61148,0.935192,1.46355,0.444872,0.253541,0.11437,1.156,0.208101,0.19692,0.204132,0.763395,0.922432,0.430551,0.254777,0.874787,1.71704,0.240896,1.03903,0.0539203,4.27671,0.181203,0.780154,1.77427,1.33021,1.04409,0.973447,0.35304,0.2995,0.281222,0.244935,2.23779,0.775372,0.938145,0.326561,0.960112,1.08669,0.839694,0.838613,0.563071,0.8998,1.42973,0.435642,0.428007,1.21641,1.0885,1.10269,0.605144,1.33732,0.340765,0.0704207,0.53982,0.858327,0.322606,1.16147,0.805995,0.688501,0.762461,1.39185,0.926209,0.65384,0.966541,1.25836,0.356163,1.06946,0.52828,1.2285,0.679647,1.35909,0.106956,0.500709,0.564999,1.30952,2.14327,1.74232,1.26465,0.700956,0.971067,1.94251,0.564002,0.778321,2.10357,0.503174,0.348692,0.183562,0.0987301,1.10596,0.287383,0.678689,1.18867,0.71546,0.376898,0.48935,0.500417,1.31911,1.03816,0.926663,0.482185,0.82857,0.671017,0.325308,0.63125,0.0323861|tfbs_overrepresentation_jaspar=MA0003.1;0.00973143,MA0004.1;0.536396,MA0006.1;0.945134,MA0007.1;3.28487,MA0009.1;0.987341,MA0014.1;0.12867,MA0017.1;0.387481,MA0019.1;0.800946,MA0024.1;0.942716,MA0025.1;1.22395,MA0027.1;2.64231,MA0028.1;0.370592,MA0029.1;0.920529,MA0030.1;3.5196,MA0031.1;2.06331,MA0038.1;0.686534,MA0040.1;1.00009,MA0041.1;0.457338,MA0042.1;0.443591,MA0043.1;1.08567,MA0046.1;1.02391,MA0048.1;0.161427,MA0050.1;0.57678,MA0051.1;0.695779,MA0052.1;1.00829,MA0055.1;0.465302,MA0056.1;0,MA0057.1;0.149949,MA0058.1;0.436487,MA0059.1;1.14076,MA0060.1;0.275911,MA0061.1;0.307097,MA0063.1;0,MA0066.1;0.675169,MA0067.1;1.33603,MA0068.1;0.153907,MA0069.1;1.00864,MA0070.1;0.998765,MA0071.1;0.575909,MA0072.1;0.990133,MA0073.1;1.22055,MA0074.1;0.638014,MA0076.1;0.407465,MA0077.1;0.968053,MA0078.1;0.729877,MA0081.1;0.473489,MA0083.1;1.08487,MA0084.1;1.66561,MA0087.1;1.04109,MA0088.1;0.358337,MA0089.1;0,MA0090.1;0.500693,MA0091.1;0.55008,MA0092.1;0.501022,MA0093.1;0.379257,MA0095.1;0,MA0098.1;0,MA0100.1;0.626021,MA0101.1;2.02339,MA0103.1;0.398766,MA0105.1;0.199622,MA0106.1;0.737893,MA0107.1;1.79828,MA0108.2;0.824407,MA0109.1;0,MA0111.1;0.515457,MA0113.1;0.708789,MA0114.1;0.304661,MA0115.1;1.08851,MA0116.1;0.359483,MA0117.1;1.05576,MA0119.1;0.459301,MA0122.1;1.07591,MA0124.1;1.28237,MA0125.1;1.20757,MA0130.1;0,MA0131.1;0.796279,MA0132.1;0,MA0133.1;0,MA0135.1;1.1226,MA0136.1;1.58388,MA0139.1;0.243463,MA0140.1;0.625902,MA0141.1;0.419361,MA0142.1;0.876028,MA0143.1;0.725672,MA0144.1;1.502,MA0145.1;0.119202,MA0146.1;0.0392287,MA0147.1;0.320675,MA0148.1;0.553294,MA0149.1;0.464445,MA0062.2;1.11803,MA0035.2;0.630778,MA0039.2;0.00481054,MA0138.2;0.788113,MA0002.2;2.76558,MA0137.2;0.416331,MA0104.2;0.261255,MA0047.2;0.685741,MA0112.2;0.37938,MA0065.2;0.119561,MA0150.1;1.29346,MA0151.1;0,MA0152.1;0.685852,MA0153.1;1.13945,MA0154.1;0.159217,MA0155.1;0.132921,MA0156.1;1.04798,MA0157.1;1.96555,MA0158.1;0,MA0159.1;0.331229,MA0160.1;0.556423,MA0161.1;0,MA0162.1;0.0465447,MA0163.1;0.0423021,MA0164.1;0.658997,MA0080.2;1.80146,MA0018.2;0.669032,MA0099.2;0.781628,MA0079.2;0.000341844,MA0102.2;1.7182,MA0258.1;0.790457,MA0259.1;0.309517,MA0442.1;0}}
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|gostat_on_MCL_coexpression=GO:0005096;GTPase activator activity;0.003266495597277;216445!GO:0008047;enzyme activator activity;0.003266495597277;216445!GO:0030695;GTPase regulator activity;0.0045733790285238;216445!GO:0043087;regulation of GTPase activity;0.0471714856983727;!
}}

Latest revision as of 16:35, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr10:126759057..126759082,+p8@Arhgap9
Mm9::chr11:106022022..106022035,-p11@Limd2
Mm9::chr4:120647785..120647794,-p@chr4:120647785..120647794
-
Mm9::chr4:120648011..120648037,-p6@Smap2
Mm9::chr4:120648047..120648070,-p5@Smap2
Mm9::chr4:120648071..120648079,-p8@Smap2


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:0005096GTPase activator activity0.003266495597277
GO:0008047enzyme activator activity0.003266495597277
GO:0030695GTPase regulator activity0.0045733790285238
GO:0043087regulation of GTPase activity0.0471714856983727



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>cell_data<br>uberon_data<br><br>

Cell Type
Ontology termp-valuen
lymphoid lineage restricted progenitor cell3.60e-1512
mature alpha-beta T cell2.56e-149
alpha-beta T cell2.56e-149
immature T cell2.56e-149
mature T cell2.56e-149
immature alpha-beta T cell2.56e-149
lymphocyte8.73e-1413
common lymphoid progenitor8.73e-1413
T cell9.67e-1411
pro-T cell9.67e-1411
CD4-positive, alpha-beta T cell1.40e-128
hematopoietic lineage restricted progenitor cell3.96e-1225
hematopoietic cell2.24e-1132
hematopoietic oligopotent progenitor cell2.24e-1132
hematopoietic stem cell2.24e-1132
angioblastic mesenchymal cell2.24e-1132
hematopoietic multipotent progenitor cell2.24e-1132
nucleate cell1.11e-1016
leukocyte6.82e-1017
nongranular leukocyte6.82e-1017
thymocyte1.36e-096
double negative thymocyte1.36e-096
naive T cell1.36e-096
double-positive, alpha-beta thymocyte1.36e-096
CD4-positive, alpha-beta thymocyte1.36e-096
naive thymus-derived CD4-positive, alpha-beta T cell1.36e-096
DN4 thymocyte1.36e-096
DN1 thymic pro-T cell1.36e-096
DN2 thymocyte1.36e-096
DN3 thymocyte1.36e-096
immature single positive thymocyte1.36e-096
early T lineage precursor1.36e-096
mature CD4 single-positive thymocyte1.36e-096
resting double-positive thymocyte1.36e-096
double-positive blast1.36e-096
CD69-positive double-positive thymocyte1.36e-096
CD69-positive, CD4-positive single-positive thymocyte1.36e-096
CD4-positive, CD8-intermediate double-positive thymocyte1.36e-096
CD24-positive, CD4 single-positive thymocyte1.36e-096

Uber Anatomy
Ontology termp-valuen
hemopoietic organ1.90e-2829
immune organ1.90e-2829
thymus9.87e-2623
neck9.87e-2623
respiratory system epithelium9.87e-2623
hemolymphoid system gland9.87e-2623
pharyngeal epithelium9.87e-2623
thymic region9.87e-2623
pharyngeal gland9.87e-2623
entire pharyngeal arch endoderm9.87e-2623
thymus primordium9.87e-2623
early pharyngeal endoderm9.87e-2623
hemolymphoid system3.85e-2548
immune system3.85e-2548
pharynx2.08e-2424
gland of gut2.08e-2424
upper respiratory tract2.08e-2424
chordate pharynx2.08e-2424
pharyngeal arch system2.08e-2424
pharyngeal region of foregut2.08e-2424
hematopoietic system2.75e-2345
blood island2.75e-2345
respiratory tract1.57e-2241
mixed endoderm/mesoderm-derived structure2.44e-2235
respiratory system8.28e-2242
segment of respiratory tract4.99e-2127
organ segment1.64e-1635
craniocervical region2.62e-1436
foregut1.09e-1180
anterior region of body4.60e-1143
endo-epithelium2.31e-1069
lateral plate mesoderm6.51e-1087
gut epithelium1.72e-0755
digestive system7.88e-07116
digestive tract7.88e-07116
primitive gut7.88e-07116


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)
MA0003.10.00973143
MA0004.10.536396
MA0006.10.945134
MA0007.13.28487
MA0009.10.987341
MA0014.10.12867
MA0017.10.387481
MA0019.10.800946
MA0024.10.942716
MA0025.11.22395
MA0027.12.64231
MA0028.10.370592
MA0029.10.920529
MA0030.13.5196
MA0031.12.06331
MA0038.10.686534
MA0040.11.00009
MA0041.10.457338
MA0042.10.443591
MA0043.11.08567
MA0046.11.02391
MA0048.10.161427
MA0050.10.57678
MA0051.10.695779
MA0052.11.00829
MA0055.10.465302
MA0056.10
MA0057.10.149949
MA0058.10.436487
MA0059.11.14076
MA0060.10.275911
MA0061.10.307097
MA0063.10
MA0066.10.675169
MA0067.11.33603
MA0068.10.153907
MA0069.11.00864
MA0070.10.998765
MA0071.10.575909
MA0072.10.990133
MA0073.11.22055
MA0074.10.638014
MA0076.10.407465
MA0077.10.968053
MA0078.10.729877
MA0081.10.473489
MA0083.11.08487
MA0084.11.66561
MA0087.11.04109
MA0088.10.358337
MA0089.10
MA0090.10.500693
MA0091.10.55008
MA0092.10.501022
MA0093.10.379257
MA0095.10
MA0098.10
MA0100.10.626021
MA0101.12.02339
MA0103.10.398766
MA0105.10.199622
MA0106.10.737893
MA0107.11.79828
MA0108.20.824407
MA0109.10
MA0111.10.515457
MA0113.10.708789
MA0114.10.304661
MA0115.11.08851
MA0116.10.359483
MA0117.11.05576
MA0119.10.459301
MA0122.11.07591
MA0124.11.28237
MA0125.11.20757
MA0130.10
MA0131.10.796279
MA0132.10
MA0133.10
MA0135.11.1226
MA0136.11.58388
MA0139.10.243463
MA0140.10.625902
MA0141.10.419361
MA0142.10.876028
MA0143.10.725672
MA0144.11.502
MA0145.10.119202
MA0146.10.0392287
MA0147.10.320675
MA0148.10.553294
MA0149.10.464445
MA0062.21.11803
MA0035.20.630778
MA0039.20.00481054
MA0138.20.788113
MA0002.22.76558
MA0137.20.416331
MA0104.20.261255
MA0047.20.685741
MA0112.20.37938
MA0065.20.119561
MA0150.11.29346
MA0151.10
MA0152.10.685852
MA0153.11.13945
MA0154.10.159217
MA0155.10.132921
MA0156.11.04798
MA0157.11.96555
MA0158.10
MA0159.10.331229
MA0160.10.556423
MA0161.10
MA0162.10.0465447
MA0163.10.0423021
MA0164.10.658997
MA0080.21.80146
MA0018.20.669032
MA0099.20.781628
MA0079.20.000341844
MA0102.21.7182
MA0258.10.790457
MA0259.10.309517
MA0442.10
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