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MCL coexpression mm9:462: Difference between revisions

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{{MCL_coexpression_mm9
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|gostat_on_MCL_coexpression=GO:0005856;cytoskeleton;0.0250868850449667;68089,11461,13169!GO:0003779;actin binding;0.0250868850449667;68089,13169!GO:0005885;Arp2/3 protein complex;0.0250868850449667;68089!GO:0043232;intracellular non-membrane-bound organelle;0.0250868850449667;68089,11461,13169!GO:0043228;non-membrane-bound organelle;0.0250868850449667;68089,11461,13169!GO:0008092;cytoskeletal protein binding;0.0250868850449667;68089,13169!GO:0042995;cell projection;0.0254891151896614;68089,13169!GO:0016601;Rac protein signal transduction;0.0316022499170498;13169!GO:0030041;actin filament polymerization;0.0318311073828121;68089!GO:0051015;actin filament binding;0.0404209655317858;13169!GO:0005737;cytoplasm;0.0476799831454238;66460,68089,11461,13169!GO:0001726;ruffle;0.0476799831454238;13169!GO:0051258;protein polymerization;0.0480569440756613;68089!GO:0008154;actin polymerization and/or depolymerization;0.0480569440756613;68089!
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|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0002384!1.70e-09!46;UBERON:0002193!8.41e-08!48;UBERON:0002405!8.41e-08!48;UBERON:0002390!3.02e-07!45;UBERON:0003061!3.02e-07!45
|tfbs_overrepresentation_for_novel_motifs=0.19013,0.0414522,0.984016,0.221468,0.325044,0.232532,0.823081,1.12446,0.439801,0.491359,0.26934,0.295134,1.1257,0.845901,0.713337,0,0.482714,0.094037,0.167127,0.599319,0.44813,0.115953,0.844218,0.0977158,0.176763,0.338177,0.156743,0.694761,0.793289,0.490013,0.237846,0.574932,2.80125,0.133454,0.714678,0.0966689,0.614421,0.292182,0.262298,0.0613737,0.656409,0.678575,0.599247,3.03418,0.950724,0.610939,0.41191,0.26128,0.304847,0.128181,0.467043,0.360991,0.466115,0.7073,0.723811,0.85924,1.33918,0.284741,0.611426,0.319396,0.556492,0.369066,0.215066,0.456979,0.330403,0.493315,0.854035,1.19441,1.36039,1.05011,0.158281,0.0523282,0.0088675,0.755651,0.0343898,0.297446,0.133371,0.401969,0.540754,0.148967,0.195767,0.498379,0.963084,0.177942,0.646739,0.0340059,0.0426811,0.107772,0.416206,1.35441,0.92132,0.6514,0.586758,0.102076,0.256377,0.49924,0.409982,0.589355,0.412133,0.217195,1.52818,0.574674,0.690844,0.467576,0.466632,0.241519,1.29324,0.716149,0.152257,0.147333,0.185018,0.692526,0.894157,0.273484,0.928143,0.315992,0.243544,1.19286,1.21499,1.50799,0.760792,0.438354,0.339713,0.40118,0.980682,0.544138,0.838247,0.580495,0.852575,0.10384,0.67485,0.617809,0.824167,0.332514,0.949083,0.11332,0.571001,0.24296,0.901468,1.71991,1.32292,0.85857,0.349901,0.584599,1.16552,0.679396,0.414644,1.68046,0.575158,0.327798,0.267549,0.00625462,0.708784,0.0677483,0.331737,0.786435,0.361851,0.115836,0.551917,0.570508,0.910663,0.645939,0.544546,0.539942,0.457889,0.869172,0.0869123,0.293837,0.393099
}}

Latest revision as of 15:20, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr11:5688483..5688563,+p1@Dbnl
Mm9::chr11:70465538..70465630,+p@chr11:70465538..70465630
+
Mm9::chr16:37882681..37882733,+p1@ENSMUST00000119947
Mm9::chr16:37883536..37883578,+p@chr16:37883536..37883578
+
Mm9::chr2:164286445..164286518,+p1@Sys1
Mm9::chr5:143665070..143665098,-p@chr5:143665070..143665098
-
Mm9::chr5:143665205..143665254,-p@chr5:143665205..143665254
-
Mm9::chr5:143665480..143665529,-p@chr5:143665480..143665529
-
Mm9::chr5:143666062..143666094,-p@chr5:143666062..143666094
-
Mm9::chr5:143666153..143666189,-p@chr5:143666153..143666189
-
Mm9::chr5:143666379..143666429,+p@chr5:143666379..143666429
+
Mm9::chr5:143666423..143666462,-p@chr5:143666423..143666462
-
Mm9::chr5:143667058..143667080,-p@chr5:143667058..143667080
-
Mm9::chr5:143668400..143668405,-p1@Actb
Mm9::chr5:38918434..38918452,-p@chr5:38918434..38918452
-
Mm9::chr6:113339103..113339107,+p1@Ttll3


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:0005856cytoskeleton0.0250868850449667
GO:0003779actin binding0.0250868850449667
GO:0005885Arp2/3 protein complex0.0250868850449667
GO:0043232intracellular non-membrane-bound organelle0.0250868850449667
GO:0043228non-membrane-bound organelle0.0250868850449667
GO:0008092cytoskeletal protein binding0.0250868850449667
GO:0042995cell projection0.0254891151896614
GO:0016601Rac protein signal transduction0.0316022499170498
GO:0030041actin filament polymerization0.0318311073828121
GO:0051015actin filament binding0.0404209655317858
GO:0005737cytoplasm0.0476799831454238
GO:0001726ruffle0.0476799831454238
GO:0051258protein polymerization0.0480569440756613
GO:0008154actin polymerization and/or depolymerization0.0480569440756613



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
somatic cell4.64e-24118
animal cell4.63e-22115
eukaryotic cell4.63e-22115
stem cell5.57e-1697
somatic stem cell6.27e-1591
multi fate stem cell6.27e-1591
motile cell1.10e-1254
embryonic cell7.01e-1070
connective tissue cell1.70e-0946
mesenchymal cell1.70e-0946
non-terminally differentiated cell1.85e-0949
hematopoietic lineage restricted progenitor cell5.66e-0825
neural cell3.03e-0743
ectodermal cell4.70e-0744
neurectodermal cell4.70e-0744
leukocyte6.26e-0717
nongranular leukocyte6.26e-0717

Uber Anatomy
Ontology termp-valuen
connective tissue1.70e-0946
hemolymphoid system8.41e-0848
immune system8.41e-0848
hematopoietic system3.02e-0745
blood island3.02e-0745


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)
MA0003.10.0557359
MA0004.10.221835
MA0006.10.344361
MA0007.10.210531
MA0009.10.599391
MA0014.10.0783947
MA0017.10.387005
MA0019.10.434009
MA0024.11.3747
MA0025.10.819843
MA0027.12.21717
MA0028.11.1993
MA0029.10.53905
MA0030.10.545058
MA0031.10.512616
MA0038.10.33811
MA0040.10.611015
MA0041.10.498821
MA0042.10.476352
MA0043.10.689898
MA0046.10.632833
MA0048.10.420794
MA0050.10.251816
MA0051.11.63616
MA0052.10.618515
MA0055.10.498225
MA0056.10
MA0057.10.381022
MA0058.10.464825
MA0059.10.161227
MA0060.10.223836
MA0061.10.267107
MA0063.10
MA0066.10.328887
MA0067.10.92691
MA0068.10.0798662
MA0069.12.54851
MA0070.10.609808
MA0071.10.70014
MA0072.10.601934
MA0073.10.00111286
MA0074.10.299171
MA0076.12.61276
MA0077.10.581866
MA0078.10.37382
MA0081.10.177433
MA0083.10.68915
MA0084.11.24749
MA0087.10.648637
MA0088.10.67791
MA0089.10
MA0090.10.196267
MA0091.10.231874
MA0092.10.196497
MA0093.10.11723
MA0095.10
MA0098.10
MA0100.10.289731
MA0101.10.167439
MA0103.10.128989
MA0105.10.128193
MA0106.10.380511
MA0107.10.125067
MA0108.21.15138
MA0109.10
MA0111.10.206727
MA0113.10.356344
MA0114.10.263654
MA0115.10.692537
MA0116.10.105729
MA0117.10.662171
MA0119.10.502046
MA0122.10.680832
MA0124.10.875485
MA0125.10.804312
MA0130.10
MA0131.10.43
MA0132.10
MA0133.10
MA0135.10.724328
MA0136.10.315568
MA0139.10.181201
MA0140.10.289637
MA0141.10.141822
MA0142.10.499475
MA0143.10.37032
MA0144.10.566612
MA0145.11.39384
MA0146.10.00479338
MA0147.10.0844713
MA0148.10.660829
MA0149.10.171305
MA0062.21.75994
MA0035.20.293466
MA0039.20.0402554
MA0138.20.423003
MA0002.21.11938
MA0137.20.852405
MA0104.20.0556953
MA0047.20.895806
MA0112.20.0491092
MA0065.20.0494003
MA0150.10.210447
MA0151.10
MA0152.10.896007
MA0153.10.740107
MA0154.10.676749
MA0155.10.0605786
MA0156.10.41693
MA0157.10.47062
MA0158.10
MA0159.10.626722
MA0160.10.23657
MA0161.10
MA0162.10.000977979
MA0163.10.00566486
MA0164.10.315868
MA0080.20.396013
MA0018.20.323932
MA0099.20.417463
MA0079.20.000116462
MA0102.21.29919
MA0258.10.24394
MA0259.10.0787033
MA0442.10
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