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MCL coexpression mm9:1425: Difference between revisions

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{{MCL_coexpression_mm9
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cilium biogenesis;0.0137063192827999;93840!GO:0007164;establishment of tissue polarity;0.0137063192827999;93840!GO:0001736;establishment of planar polarity;0.0137063192827999;93840!GO:0045197;establishment and/or maintenance of epithelial cell polarity;0.0137063192827999;93840!GO:0045176;apical protein localization;0.0137063192827999;93840!GO:0008105;asymmetric protein localization;0.0137063192827999;93840!GO:0035088;establishment and/or maintenance of apical/basal cell polarity;0.0137063192827999;93840!GO:0001738;morphogenesis of a polarized epithelium;0.0137063192827999;93840!GO:0042384;cilium biogenesis;0.0139543778698986;93840!GO:0001947;heart looping;0.0139543778698986;93840!GO:0007163;establishment and/or maintenance of cell polarity;0.0217411228203974;93840!GO:0003007;heart morphogenesis;0.0282255244932613;93840!GO:0001843;neural tube closure;0.028373652194394;93840!GO:0014020;primary neural tube formation;0.028373652194394;93840!GO:0030031;cell projection biogenesis;0.028373652194394;93840!GO:0016324;apical plasma membrane;0.028373652194394;93840!GO:0001841;neural tube formation;0.028373652194394;93840!GO:0001839;neural plate morphogenesis;0.028373652194394;93840!GO:0001840;neural plate development;0.028373652194394;93840!GO:0001838;embryonic epithelial tube formation;0.028373652194394;93840!GO:0021915;neural tube development;0.0308083974695856;93840!GO:0016331;morphogenesis of embryonic epithelium;0.0330202130454143;93840!GO:0045177;apical part of cell;0.0333115541741164;93840!GO:0002009;morphogenesis of an epithelium;0.0495929248956148;93840!GO:0007275;multicellular organismal 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|gostat_on_MCL_coexpression=GO:0035058;sensory cilium biogenesis;0.0137063192827999;93840!GO:0007164;establishment of tissue polarity;0.0137063192827999;93840!GO:0001736;establishment of planar polarity;0.0137063192827999;93840!GO:0045197;establishment and/or maintenance of epithelial cell polarity;0.0137063192827999;93840!GO:0045176;apical protein localization;0.0137063192827999;93840!GO:0008105;asymmetric protein localization;0.0137063192827999;93840!GO:0035088;establishment and/or maintenance of apical/basal cell polarity;0.0137063192827999;93840!GO:0001738;morphogenesis of a polarized epithelium;0.0137063192827999;93840!GO:0042384;cilium biogenesis;0.0139543778698986;93840!GO:0001947;heart looping;0.0139543778698986;93840!GO:0007163;establishment and/or maintenance of cell polarity;0.0217411228203974;93840!GO:0003007;heart morphogenesis;0.0282255244932613;93840!GO:0001843;neural tube closure;0.028373652194394;93840!GO:0014020;primary neural tube formation;0.028373652194394;93840!GO:0030031;cell projection biogenesis;0.028373652194394;93840!GO:0016324;apical plasma membrane;0.028373652194394;93840!GO:0001841;neural tube formation;0.028373652194394;93840!GO:0001839;neural plate morphogenesis;0.028373652194394;93840!GO:0001840;neural plate development;0.028373652194394;93840!GO:0001838;embryonic epithelial tube formation;0.028373652194394;93840!GO:0021915;neural tube development;0.0308083974695856;93840!GO:0016331;morphogenesis of embryonic epithelium;0.0330202130454143;93840!GO:0045177;apical part of cell;0.0333115541741164;93840!GO:0002009;morphogenesis of an epithelium;0.0495929248956148;93840!GO:0007275;multicellular organismal development;0.0495929248956148;93840,18071!
|ontology_enrichment_celltype=CL:0000221!3.18e-12!44;CL:0000133!3.18e-12!44;CL:0002319!1.16e-11!43;CL:0000540!2.94e-11!33;CL:0000047!2.94e-11!33;CL:0000031!2.94e-11!33;CL:0000404!2.94e-11!33;CL:0000117!3.18e-11!23;CL:0000337!3.18e-11!23;CL:0000055!1.99e-09!49;CL:0000393!1.10e-08!39;CL:0000211!1.10e-08!39
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0004121!1.79e-15!95;UBERON:0000924!1.79e-15!95;UBERON:0006601!1.79e-15!95;UBERON:0010371!1.44e-14!73;UBERON:0001017!6.25e-12!73;UBERON:0002346!6.42e-12!64;UBERON:0003075!6.42e-12!64;UBERON:0007284!6.42e-12!64;UBERON:0000468!9.94e-12!333;UBERON:0000922!1.38e-11!320;UBERON:0001016!5.35e-11!75;UBERON:0010314!3.34e-09!92;UBERON:0001049!8.90e-09!52;UBERON:0005068!8.90e-09!52;UBERON:0006241!8.90e-09!52;UBERON:0007135!8.90e-09!52;UBERON:0003056!1.19e-08!49;UBERON:0000073!1.28e-08!54
|tfbs_overrepresentation_for_novel_motifs=0.491922,0.819928,0.464605,0.535892,0.346849,0.550971,0.645383,0.691572,0.257202,0.0835344,0.599767,0.632897,1.28144,0.6581,0.364314,0,0.856992,0.338549,1.90111,0.86893,1.09054,0.713088,0.657163,0.345236,1.19059,0.686615,0.223823,0.572827,0.394364,0.534301,0.558142,0.960397,0.336199,0.204204,0.364821,0.144368,0.326478,0.629145,0.820134,1.37841,0.342638,0.56353,0.0995018,0.366415,0.659176,0.524258,0.77511,1.43855,0.284064,0.397446,0.839084,0.714419,0.174327,1.10437,1.12205,0.66551,0.406788,0.619643,0.21472,0.663395,0.939962,0.724164,0.269393,0.827522,0.677043,0.869046,1.2599,1.61148,0.935192,1.46355,1.1311,0.70565,0.11437,1.156,0.208101,1.08629,0.204132,0.763395,0.922432,0.430551,0.708505,0.874787,0.722675,0.240896,1.03903,0.0539203,0.220054,0.181203,0.780154,1.77427,1.33021,1.04409,0.973447,0.35304,0.2995,0.769162,0.244935,0.976308,0.775372,0.160254,1.56871,0.960112,1.08669,0.839694,0.838613,0.563071,0.8998,0.585058,0.435642,0.428007,1.21641,1.0885,0.431734,0.605144,1.33732,0.90315,0.0704207,0.53982,0.858327,0.322606,1.16147,0.805995,0.688501,0.762461,1.39185,2.13557,0.65384,0.966541,1.25836,0.356163,1.06946,0.52828,1.2285,0.679647,1.35909,0.106956,0.500709,0.564999,1.30952,2.14327,1.74232,1.26465,0.700956,0.971067,0.831964,0.564002,0.778321,2.10357,0.503174,0.348692,0.183562,0.0987301,1.10596,0.287383,1.62569,1.18867,0.71546,0.376898,0.48935,2.16235,1.31911,1.03816,0.926663,1.21135,0.82857,0.671017,0.325308,0.63125,2.24139
|tfbs_overrepresentation_jaspar=MA0003.1;2.22936,MA0004.1;0.536396,MA0006.1;0.359699,MA0007.1;0.52077,MA0009.1;0.987341,MA0014.1;0.304529,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;0.927235,MA0031.1;0.890871,MA0038.1;0.686534,MA0040.1;1.00009,MA0041.1;2.01886,MA0042.1;1.97265,MA0043.1;1.08567,MA0046.1;1.02391,MA0048.1;2.15574,MA0050.1;0.57678,MA0051.1;0.695779,MA0052.1;1.00829,MA0055.1;0.465302,MA0056.1;0,MA0057.1;2.76847,MA0058.1;0.436487,MA0059.1;0.449345,MA0060.1;1.38604,MA0061.1;0.307097,MA0063.1;0,MA0066.1;0.675169,MA0067.1;1.33603,MA0068.1;0.467569,MA0069.1;1.00864,MA0070.1;0.998765,MA0071.1;0.575909,MA0072.1;0.990133,MA0073.1;0.972762,MA0074.1;0.638014,MA0076.1;0.407465,MA0077.1;2.22096,MA0078.1;0.729877,MA0081.1;2.07288,MA0083.1;1.08487,MA0084.1;1.66561,MA0087.1;1.04109,MA0088.1;0.358337,MA0089.1;0,MA0090.1;3.19482,MA0091.1;0.55008,MA0092.1;1.25163,MA0093.1;0.379257,MA0095.1;0,MA0098.1;0,MA0100.1;0.626021,MA0101.1;1.16089,MA0103.1;0.398766,MA0105.1;1.09694,MA0106.1;0.737893,MA0107.1;1.0169,MA0108.2;0.824407,MA0109.1;0,MA0111.1;1.2824,MA0113.1;0.708789,MA0114.1;0.822296,MA0115.1;1.08851,MA0116.1;0.944657,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;0.658622,MA0139.1;2.74529,MA0140.1;0.625902,MA0141.1;0.419361,MA0142.1;0.876028,MA0143.1;0.725672,MA0144.1;0.829535,MA0145.1;0.761789,MA0146.1;0.635245,MA0147.1;0.320675,MA0148.1;0.553294,MA0149.1;0.464445,MA0062.2;0.204999,MA0035.2;0.630778,MA0039.2;1.39094,MA0138.2;0.788113,MA0002.2;0.246463,MA0137.2;0.416331,MA0104.2;0.261255,MA0047.2;0.685741,MA0112.2;0.37938,MA0065.2;1.81707,MA0150.1;0.520653,MA0151.1;0,MA0152.1;0.685852,MA0153.1;1.13945,MA0154.1;0.480757,MA0155.1;1.92909,MA0156.1;0.406559,MA0157.1;0.843181,MA0158.1;0,MA0159.1;1.58527,MA0160.1;0.556423,MA0161.1;0,MA0162.1;0.397553,MA0163.1;8.27119,MA0164.1;0.658997,MA0080.2;1.01893,MA0018.2;0.669032,MA0099.2;0.781628,MA0079.2;7.21796,MA0102.2;1.7182,MA0258.1;0.290587,MA0259.1;0.309517,MA0442.1;0
}}

Latest revision as of 16:54, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr1:173934582..173934589,-p@chr1:173934582..173934589
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Mm9::chr1:173934659..173934666,-p@chr1:173934659..173934666
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Mm9::chr1:173934671..173934684,-p@chr1:173934671..173934684
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Mm9::chr1:173957382..173957399,-p2@Vangl2
Mm9::chr1:173957400..173957444,-p1@Vangl2
Mm9::chr1:173987720..173987729,-p1@Nhlh1


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:0035058sensory cilium biogenesis0.0137063192827999
GO:0007164establishment of tissue polarity0.0137063192827999
GO:0001736establishment of planar polarity0.0137063192827999
GO:0045197establishment and/or maintenance of epithelial cell polarity0.0137063192827999
GO:0045176apical protein localization0.0137063192827999
GO:0008105asymmetric protein localization0.0137063192827999
GO:0035088establishment and/or maintenance of apical/basal cell polarity0.0137063192827999
GO:0001738morphogenesis of a polarized epithelium0.0137063192827999
GO:0042384cilium biogenesis0.0139543778698986
GO:0001947heart looping0.0139543778698986
GO:0007163establishment and/or maintenance of cell polarity0.0217411228203974
GO:0003007heart morphogenesis0.0282255244932613
GO:0001843neural tube closure0.028373652194394
GO:0014020primary neural tube formation0.028373652194394
GO:0030031cell projection biogenesis0.028373652194394
GO:0016324apical plasma membrane0.028373652194394
GO:0001841neural tube formation0.028373652194394
GO:0001839neural plate morphogenesis0.028373652194394
GO:0001840neural plate development0.028373652194394
GO:0001838embryonic epithelial tube formation0.028373652194394
GO:0021915neural tube development0.0308083974695856
GO:0016331morphogenesis of embryonic epithelium0.0330202130454143
GO:0045177apical part of cell0.0333115541741164
GO:0002009morphogenesis of an epithelium0.0495929248956148
GO:0007275multicellular organismal development0.0495929248956148



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>


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)
MA0003.12.22936
MA0004.10.536396
MA0006.10.359699
MA0007.10.52077
MA0009.10.987341
MA0014.10.304529
MA0017.10.387481
MA0019.10.800946
MA0024.10.942716
MA0025.11.22395
MA0027.12.64231
MA0028.10.370592
MA0029.10.920529
MA0030.10.927235
MA0031.10.890871
MA0038.10.686534
MA0040.11.00009
MA0041.12.01886
MA0042.11.97265
MA0043.11.08567
MA0046.11.02391
MA0048.12.15574
MA0050.10.57678
MA0051.10.695779
MA0052.11.00829
MA0055.10.465302
MA0056.10
MA0057.12.76847
MA0058.10.436487
MA0059.10.449345
MA0060.11.38604
MA0061.10.307097
MA0063.10
MA0066.10.675169
MA0067.11.33603
MA0068.10.467569
MA0069.11.00864
MA0070.10.998765
MA0071.10.575909
MA0072.10.990133
MA0073.10.972762
MA0074.10.638014
MA0076.10.407465
MA0077.12.22096
MA0078.10.729877
MA0081.12.07288
MA0083.11.08487
MA0084.11.66561
MA0087.11.04109
MA0088.10.358337
MA0089.10
MA0090.13.19482
MA0091.10.55008
MA0092.11.25163
MA0093.10.379257
MA0095.10
MA0098.10
MA0100.10.626021
MA0101.11.16089
MA0103.10.398766
MA0105.11.09694
MA0106.10.737893
MA0107.11.0169
MA0108.20.824407
MA0109.10
MA0111.11.2824
MA0113.10.708789
MA0114.10.822296
MA0115.11.08851
MA0116.10.944657
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
MA0136.10.658622
MA0139.12.74529
MA0140.10.625902
MA0141.10.419361
MA0142.10.876028
MA0143.10.725672
MA0144.10.829535
MA0145.10.761789
MA0146.10.635245
MA0147.10.320675
MA0148.10.553294
MA0149.10.464445
MA0062.20.204999
MA0035.20.630778
MA0039.21.39094
MA0138.20.788113
MA0002.20.246463
MA0137.20.416331
MA0104.20.261255
MA0047.20.685741
MA0112.20.37938
MA0065.21.81707
MA0150.10.520653
MA0151.10
MA0152.10.685852
MA0153.11.13945
MA0154.10.480757
MA0155.11.92909
MA0156.10.406559
MA0157.10.843181
MA0158.10
MA0159.11.58527
MA0160.10.556423
MA0161.10
MA0162.10.397553
MA0163.18.27119
MA0164.10.658997
MA0080.21.01893
MA0018.20.669032
MA0099.20.781628
MA0079.27.21796
MA0102.21.7182
MA0258.10.290587
MA0259.10.309517
MA0442.10
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