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MCL coexpression mm9:2433: Difference between revisions

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{{MCL_coexpression_mm9
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epithelial cell differentiation;0.00876544222422034;27428!GO:0002066;columnar/cuboidal epithelial cell development;0.00876544222422034;27428!GO:0002064;epithelial cell development;0.0204498970139181;27428!GO:0007399;nervous system development;0.0228906919482546;27428,20347!GO:0030855;epithelial cell differentiation;0.0306781855020501;27428!GO:0001843;neural tube closure;0.0306781855020501;27428!GO:0014020;primary neural tube formation;0.0306781855020501;27428!GO:0022603;regulation of anatomical structure morphogenesis;0.0306781855020501;27428!GO:0008360;regulation of cell shape;0.0306781855020501;27428!GO:0022604;regulation of cell morphogenesis;0.0306781855020501;27428!GO:0016324;apical plasma membrane;0.0306781855020501;27428!GO:0001841;neural tube formation;0.0306781855020501;27428!GO:0001839;neural plate morphogenesis;0.0306781855020501;27428!GO:0001840;neural plate development;0.0306781855020501;27428!GO:0001838;embryonic epithelial tube formation;0.0306781855020501;27428!GO:0005912;adherens junction;0.0306781855020501;27428!GO:0021915;neural tube development;0.0306781855020501;27428!GO:0016331;morphogenesis of embryonic epithelium;0.0306781855020501;27428!GO:0048731;system development;0.0306781855020501;27428,20347!GO:0045177;apical part of cell;0.0306781855020501;27428!GO:0048869;cellular developmental process;0.0306781855020501;27428,20347!GO:0030154;cell differentiation;0.0306781855020501;27428,20347!GO:0043296;apical junction complex;0.032791165650253;27428!GO:0016327;apicolateral plasma membrane;0.032791165650253;27428!GO:0048856;anatomical structure development;0.0348025444443735;27428,20347!GO:0002009;morphogenesis of an epithelium;0.0403686812337117;27428!GO:0007275;multicellular organismal development;0.0403686812337117;27428,20347!GO:0035239;tube morphogenesis;0.0448085718115091;27428!GO:0005911;intercellular junction;0.0448085718115091;27428!GO:0030036;actin cytoskeleton organization and 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|gostat_on_MCL_coexpression=GO:0002065;columnar/cuboidal epithelial cell differentiation;0.00876544222422034;27428!GO:0002066;columnar/cuboidal epithelial cell development;0.00876544222422034;27428!GO:0002064;epithelial cell development;0.0204498970139181;27428!GO:0007399;nervous system development;0.0228906919482546;27428,20347!GO:0030855;epithelial cell differentiation;0.0306781855020501;27428!GO:0001843;neural tube closure;0.0306781855020501;27428!GO:0014020;primary neural tube formation;0.0306781855020501;27428!GO:0022603;regulation of anatomical structure morphogenesis;0.0306781855020501;27428!GO:0008360;regulation of cell shape;0.0306781855020501;27428!GO:0022604;regulation of cell morphogenesis;0.0306781855020501;27428!GO:0016324;apical plasma membrane;0.0306781855020501;27428!GO:0001841;neural tube formation;0.0306781855020501;27428!GO:0001839;neural plate morphogenesis;0.0306781855020501;27428!GO:0001840;neural plate development;0.0306781855020501;27428!GO:0001838;embryonic epithelial tube formation;0.0306781855020501;27428!GO:0005912;adherens junction;0.0306781855020501;27428!GO:0021915;neural tube development;0.0306781855020501;27428!GO:0016331;morphogenesis of embryonic epithelium;0.0306781855020501;27428!GO:0048731;system development;0.0306781855020501;27428,20347!GO:0045177;apical part of cell;0.0306781855020501;27428!GO:0048869;cellular developmental process;0.0306781855020501;27428,20347!GO:0030154;cell differentiation;0.0306781855020501;27428,20347!GO:0043296;apical junction complex;0.032791165650253;27428!GO:0016327;apicolateral plasma membrane;0.032791165650253;27428!GO:0048856;anatomical structure development;0.0348025444443735;27428,20347!GO:0002009;morphogenesis of an epithelium;0.0403686812337117;27428!GO:0007275;multicellular organismal development;0.0403686812337117;27428,20347!GO:0035239;tube morphogenesis;0.0448085718115091;27428!GO:0005911;intercellular junction;0.0448085718115091;27428!GO:0030036;actin cytoskeleton organization and biogenesis;0.0448085718115091;27428!GO:0030029;actin filament-based process;0.046446441539182;27428!
|ontology_enrichment_celltype=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0005409!1.26e-21!47;UBERON:0000160!2.99e-19!31;UBERON:0000344!2.26e-09!15;UBERON:0001242!1.45e-08!13;UBERON:0000060!1.45e-08!13;UBERON:0001262!1.45e-08!13;UBERON:0004786!1.45e-08!13;UBERON:0000468!5.67e-08!333;UBERON:0004923!1.56e-07!24;UBERON:0000922!3.31e-07!320
|tfbs_overrepresentation_for_novel_motifs=0.641384,0.801438,1.48646,0.688265,0.483253,0.704257,0.803568,0.370124,0.381467,0.949265,1.78549,0.790506,0.96877,0.81685,0.502646,0,1.02248,0.473993,0.928768,0.24402,0.570433,0.197567,1.90943,0.481455,0.620553,0.846564,0.342316,0.727368,0.535752,0.290745,0.711848,1.12823,1.18815,0.318879,1.2563,0.623685,2.02937,0.786577,0.434783,0.40068,0.478558,1.70641,0.544696,0.504971,0.66772,0.675898,0.938241,0.744678,0.49007,0.539131,1.0041,0.875451,0.771943,1.2746,1.29252,0.82458,0.549352,0.776619,0.331485,0.822375,1.10737,2.05242,0.39557,0.992216,0.8366,1.03484,1.43193,1.78579,1.1025,3.57191,0.590754,0.377213,1.12016,1.32691,4.24297,0.310084,0.854076,0.926147,1.08947,0.575233,0.37865,1.04072,0.884013,0.362446,1.20828,2.44772,1.90208,1.4408,0.943446,1.94914,1.50286,1.21342,1.14153,0.490141,0.430015,0.409166,0.367176,1.14445,0.938512,0.264911,0.460566,1.12793,1.25667,1.00472,1.00361,0.717061,1.06633,0.740267,0.580757,4.72443,0.633483,1.25851,0.576517,0.7614,1.51002,0.476467,2.70806,0.692434,1.02384,1.15537,1.33244,0.970073,0.848526,0.925183,1.56496,1.09333,0.812403,1.13449,1.43038,0.493609,1.23918,0.680176,1.40022,0.839311,1.53196,0.569254,0.650785,0.719099,1.482,2.31884,1.91709,1.43673,0.861473,1.1391,0.996781,0.718046,0.941555,2.27909,0.653418,0.485304,1.4513,0.542121,1.27621,0.416214,0.838313,1.35996,0.87653,0.516549,0.63863,0.650472,1.49167,1.20739,1.09379,0.630949,0.993294,0.830321,0.459159,0.788782,0.589293
}}

Latest revision as of 18:31, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr5:93326982..93327000,+p6@Shroom3
Mm9::chr5:93327007..93327078,+p3@Shroom3
Mm9::chr5:93327079..93327101,+p5@Shroom3
Mm9::chr9:107507626..107507662,-p2@Sema3b


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:0002065columnar/cuboidal epithelial cell differentiation0.00876544222422034
GO:0002066columnar/cuboidal epithelial cell development0.00876544222422034
GO:0002064epithelial cell development0.0204498970139181
GO:0007399nervous system development0.0228906919482546
GO:0030855epithelial cell differentiation0.0306781855020501
GO:0001843neural tube closure0.0306781855020501
GO:0014020primary neural tube formation0.0306781855020501
GO:0022603regulation of anatomical structure morphogenesis0.0306781855020501
GO:0008360regulation of cell shape0.0306781855020501
GO:0022604regulation of cell morphogenesis0.0306781855020501
GO:0016324apical plasma membrane0.0306781855020501
GO:0001841neural tube formation0.0306781855020501
GO:0001839neural plate morphogenesis0.0306781855020501
GO:0001840neural plate development0.0306781855020501
GO:0001838embryonic epithelial tube formation0.0306781855020501
GO:0005912adherens junction0.0306781855020501
GO:0021915neural tube development0.0306781855020501
GO:0016331morphogenesis of embryonic epithelium0.0306781855020501
GO:0048731system development0.0306781855020501
GO:0045177apical part of cell0.0306781855020501
GO:0048869cellular developmental process0.0306781855020501
GO:0030154cell differentiation0.0306781855020501
GO:0043296apical junction complex0.032791165650253
GO:0016327apicolateral plasma membrane0.032791165650253
GO:0048856anatomical structure development0.0348025444443735
GO:0002009morphogenesis of an epithelium0.0403686812337117
GO:0007275multicellular organismal development0.0403686812337117
GO:0035239tube morphogenesis0.0448085718115091
GO:0005911intercellular junction0.0448085718115091
GO:0030036actin cytoskeleton organization and biogenesis0.0448085718115091
GO:0030029actin filament-based process0.046446441539182



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
gastrointestinal system1.26e-2147
intestine2.99e-1931
mucosa2.26e-0915
intestinal mucosa1.45e-0813
anatomical wall1.45e-0813
wall of intestine1.45e-0813
gastrointestinal system mucosa1.45e-0813
multi-cellular organism5.67e-08333
organ component layer1.56e-0724
embryo3.31e-07320


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)
MA0003.14.15047
MA0004.10.6888
MA0006.10.497533
MA0007.10.672186
MA0009.11.15569
MA0014.10.981995
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
MA0058.10.581673
MA0059.10.59559
MA0060.14.83418
MA0061.11.95592
MA0063.10
MA0066.10.834648
MA0067.11.50873
MA0068.10.256913
MA0069.11.17737
MA0070.11.16732
MA0071.10.73062
MA0072.11.15853
MA0073.10.112167
MA0074.10.795862
MA0076.10.550092
MA0077.11.13603
MA0078.10.891476
MA0081.10.621611
MA0083.11.25482
MA0084.11.84013
MA0087.11.21037
MA0088.11.1032
MA0089.10
MA0090.10.650768
MA0091.10.703314
MA0092.10.651119
MA0093.10.519148
MA0095.10
MA0098.10
MA0100.10.783305
MA0101.11.47308
MA0103.10.540576
MA0105.12.31605
MA0106.10.899777
MA0107.11.3208
MA0108.20.989014
MA0109.10
MA0111.10.666525
MA0113.10.869608
MA0114.10.43587
MA0115.11.25852
MA0116.12.15201
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
MA0142.13.87354
MA0143.13.39515
MA0144.10.439506
MA0145.10.21199
MA0146.11.07887
MA0147.10.453952
MA0148.10.706718
MA0149.10.611881
MA0062.20.319836
MA0035.20.788288
MA0039.20.238019
MA0138.20.951653
MA0002.20.368961
MA0137.20.559766
MA0104.21.0034
MA0047.20.845655
MA0112.20.608441
MA0065.20.609584
MA0150.10.67206
MA0151.10
MA0152.10.84577
MA0153.11.31015
MA0154.10.728853
MA0155.10.650923
MA0156.10.549102
MA0157.11.0083
MA0158.10
MA0159.10.465802
MA0160.10.71003
MA0161.10
MA0162.10.704935
MA0163.10.327769
MA0164.10.817786
MA0080.20.534538
MA0018.20.828253
MA0099.20.944966
MA0079.20.00774881
MA0102.21.8929
MA0258.10.419871
MA0259.10.441366
MA0442.10
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