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MCL coexpression mm9:230: Difference between revisions

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|ontology_enrichment_uberon=UBERON:0000055!7.96e-09!5;UBERON:0007500!7.96e-09!5;UBERON:0001981!7.96e-09!5;UBERON:0002049!7.96e-09!5;UBERON:0007798!7.96e-09!5;UBERON:0004537!7.96e-09!5;UBERON:0006965!7.96e-09!5;UBERON:0004535!7.39e-08!23;UBERON:0001009!7.39e-08!23;UBERON:0000947!8.48e-08!4;UBERON:0001637!8.48e-08!4;UBERON:0004573!8.48e-08!4;UBERON:0003509!8.48e-08!4;UBERON:0004571!8.48e-08!4;UBERON:0010191!8.48e-08!4;UBERON:0004572!8.48e-08!4;UBERON:0001134!3.37e-07!9;UBERON:0002036!3.37e-07!9;UBERON:0002385!3.37e-07!9;UBERON:0000486!3.37e-07!9;UBERON:0007503!3.37e-07!9;UBERON:0001015!3.37e-07!9;UBERON:0002329!3.37e-07!9;UBERON:0003082!3.37e-07!9;UBERON:0003059!3.37e-07!9;UBERON:0007282!3.37e-07!9;UBERON:0004290!3.37e-07!9;UBERON:0009618!3.37e-07!9
|ontology_enrichment_uberon=UBERON:0000055!7.96e-09!5;UBERON:0007500!7.96e-09!5;UBERON:0001981!7.96e-09!5;UBERON:0002049!7.96e-09!5;UBERON:0007798!7.96e-09!5;UBERON:0004537!7.96e-09!5;UBERON:0006965!7.96e-09!5;UBERON:0004535!7.39e-08!23;UBERON:0001009!7.39e-08!23;UBERON:0000947!8.48e-08!4;UBERON:0001637!8.48e-08!4;UBERON:0004573!8.48e-08!4;UBERON:0003509!8.48e-08!4;UBERON:0004571!8.48e-08!4;UBERON:0010191!8.48e-08!4;UBERON:0004572!8.48e-08!4;UBERON:0001134!3.37e-07!9;UBERON:0002036!3.37e-07!9;UBERON:0002385!3.37e-07!9;UBERON:0000486!3.37e-07!9;UBERON:0007503!3.37e-07!9;UBERON:0001015!3.37e-07!9;UBERON:0002329!3.37e-07!9;UBERON:0003082!3.37e-07!9;UBERON:0003059!3.37e-07!9;UBERON:0007282!3.37e-07!9;UBERON:0004290!3.37e-07!9;UBERON:0009618!3.37e-07!9
|tfbs_overrepresentation_for_novel_motifs=0.366787,0.216627,0.581563,0.203424,0.14741,0.219188,0.328638,0.233506,0.256774,0.12786,0.576186,1.07742,0.23408,0.10597,0.33605,0,0.627265,0.482728,0.199105,1.00578,0.481886,0.343542,0.105521,0.503491,0.332802,0.765668,0.0913482,0.24292,0.404553,0.305597,0.226861,0.792615,0.276494,0.0691052,0.0135241,0.110361,0.0441231,0.308579,0.213707,1.30512,0.495389,0.862948,0.288836,0.171902,0.148651,1.14545,0.973401,0.554379,0.546725,0.411843,0.208313,0.829508,0.604815,0.401722,0.415953,0.35415,1.04143,1.03552,0.440709,0.351437,0.276833,0.852206,0.466197,0.582136,0.369084,0.227914,0.531135,0.84881,0.273438,0.711943,0.286688,0.131131,0.0527354,0.443654,0.0732621,0.00626798,0.250244,0.48752,0.730734,0.263889,0.413735,0.231745,0.430279,0.556545,0.350386,0.00985002,0.00228134,0.306125,0.171806,1.00305,0.592345,0.354286,0.301061,1.12775,0.580528,0.0788096,1.40646,0.818915,0.168969,0.708158,2.13844,0.291331,0.387634,0.208705,0.599006,0.0652131,0.24871,0.0737572,0.112458,0.0250628,0.153706,0.389069,0.109434,0.587433,0.598607,0.489574,0.0471447,0.792614,0.629331,0.249404,0.448157,0.187467,0.121031,0.16141,0.647114,0.267084,0.103935,0.296009,0.529818,0.814978,0.374039,1.16136,0.504302,0.116549,0.617878,0.627319,0.382576,0.234302,0.574183,1.36129,0.972535,0.535229,0.798421,0.299317,0.588876,0.233214,0.170717,1.32235,0.0447643,0.0552603,0.472109,0.0144808,0.402997,0.334377,0.116068,0.470737,0.420387,1.26068,0.648801,0.0439242,0.582585,0.349717,0.267404,0.151572,0.583725,0.361253,0.254696,0.0934613,0.128219
|tfbs_overrepresentation_for_novel_motifs=0.366787,0.216627,0.581563,0.203424,0.14741,0.219188,0.328638,0.233506,0.256774,0.12786,0.576186,1.07742,0.23408,0.10597,0.33605,0,0.627265,0.482728,0.199105,1.00578,0.481886,0.343542,0.105521,0.503491,0.332802,0.765668,0.0913482,0.24292,0.404553,0.305597,0.226861,0.792615,0.276494,0.0691052,0.0135241,0.110361,0.0441231,0.308579,0.213707,1.30512,0.495389,0.862948,0.288836,0.171902,0.148651,1.14545,0.973401,0.554379,0.546725,0.411843,0.208313,0.829508,0.604815,0.401722,0.415953,0.35415,1.04143,1.03552,0.440709,0.351437,0.276833,0.852206,0.466197,0.582136,0.369084,0.227914,0.531135,0.84881,0.273438,0.711943,0.286688,0.131131,0.0527354,0.443654,0.0732621,0.00626798,0.250244,0.48752,0.730734,0.263889,0.413735,0.231745,0.430279,0.556545,0.350386,0.00985002,0.00228134,0.306125,0.171806,1.00305,0.592345,0.354286,0.301061,1.12775,0.580528,0.0788096,1.40646,0.818915,0.168969,0.708158,2.13844,0.291331,0.387634,0.208705,0.599006,0.0652131,0.24871,0.0737572,0.112458,0.0250628,0.153706,0.389069,0.109434,0.587433,0.598607,0.489574,0.0471447,0.792614,0.629331,0.249404,0.448157,0.187467,0.121031,0.16141,0.647114,0.267084,0.103935,0.296009,0.529818,0.814978,0.374039,1.16136,0.504302,0.116549,0.617878,0.627319,0.382576,0.234302,0.574183,1.36129,0.972535,0.535229,0.798421,0.299317,0.588876,0.233214,0.170717,1.32235,0.0447643,0.0552603,0.472109,0.0144808,0.402997,0.334377,0.116068,0.470737,0.420387,1.26068,0.648801,0.0439242,0.582585,0.349717,0.267404,0.151572,0.583725,0.361253,0.254696,0.0934613,0.128219
|tfbs_overrepresentation_jaspar=MA0003.1;0.00601349,MA0004.1;1.19361,MA0006.1;0.0127788,MA0007.1;0.41953,MA0009.1;0.311311,MA0014.1;0.00777527,MA0017.1;0.0781308,MA0019.1;0.542303,MA0024.1;0.2788,MA0025.1;0.500436,MA0027.1;1.85482,MA0028.1;0.349965,MA0029.1;0.263093,MA0030.1;0.267807,MA0031.1;0.242604,MA0038.1;0.120029,MA0040.1;0.32081,MA0041.1;1.72879,MA0042.1;1.64691,MA0043.1;0.386827,MA0046.1;0.338806,MA0048.1;0.235372,MA0050.1;0.24732,MA0051.1;0.786554,MA0052.1;0.872393,MA0055.1;0.0272514,MA0056.1;0,MA0057.1;0.455095,MA0058.1;1.60488,MA0059.1;0.859481,MA0060.1;0.165672,MA0061.1;0.103274,MA0063.1;0,MA0066.1;0.114312,MA0067.1;0.597474,MA0068.1;0.12269,MA0069.1;0.327233,MA0070.1;0.856383,MA0071.1;0.0701355,MA0072.1;0.313384,MA0073.1;3.3155,MA0074.1;1.0937,MA0076.1;0.0915916,MA0077.1;0.297113,MA0078.1;0.142992,MA0081.1;0.03619,MA0083.1;0.386189,MA0084.1;0.899737,MA0087.1;0.351973,MA0088.1;0.0219501,MA0089.1;0,MA0090.1;0.168659,MA0091.1;0.475676,MA0092.1;0.0441077,MA0093.1;1.27399,MA0095.1;0,MA0098.1;0,MA0100.1;0.631746,MA0101.1;0.13112,MA0103.1;0.0855935,MA0105.1;0.0643847,MA0106.1;0.451394,MA0107.1;0.0812941,MA0108.2;0.577424,MA0109.1;0,MA0111.1;0.048616,MA0113.1;0.411312,MA0114.1;0.100825,MA0115.1;0.389079,MA0116.1;0.54868,MA0117.1;0.363331,MA0119.1;0.131636,MA0122.1;0.987913,MA0124.1;0.550539,MA0125.1;0.486591,MA0130.1;0,MA0131.1;0.181514,MA0132.1;0,MA0133.1;0,MA0135.1;0.4164,MA0136.1;0.106221,MA0139.1;0.0148967,MA0140.1;0.304632,MA0141.1;0.100135,MA0142.1;0.656918,MA0143.1;1.38097,MA0144.1;0.613691,MA0145.1;0.0596805,MA0146.1;0.00743003,MA0147.1;0.245652,MA0148.1;0.221662,MA0149.1;0.915423,MA0062.2;0.00742176,MA0035.2;0.641981,MA0039.2;0.0143379,MA0138.2;0.523377,MA0002.2;1.10185,MA0137.2;0.0979218,MA0104.2;0.26672,MA0047.2;0.119626,MA0112.2;0.0278415,MA0065.2;0.11193,MA0150.1;1.13124,MA0151.1;0,MA0152.1;0.763936,MA0153.1;0.430089,MA0154.1;0.510612,MA0155.1;1.38532,MA0156.1;0.0909568,MA0157.1;0.605995,MA0158.1;0,MA0159.1;0.129147,MA0160.1;0.225012,MA0161.1;0,MA0162.1;0.0480644,MA0163.1;0.803239,MA0164.1;1.16107,MA0080.2;0.0819057,MA0018.2;0.111278,MA0099.2;0.172684,MA0079.2;0.374537,MA0102.2;0.949579,MA0258.1;0.0291367,MA0259.1;0.224435,MA0442.1;0
}}
}}

Revision as of 11:24, 23 January 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr11:16801833..16801838,+p@chr11:16801833..16801838
+
Mm9::chr11:50416871..50416882,+p5@Adamts2
Mm9::chr11:86417559..86417568,+p@chr11:86417559..86417568
+
Mm9::chr13:113253807..113253846,+p4@Il6st
Mm9::chr13:119579287..119579292,+p@chr13:119579287..119579292
+
Mm9::chr13:49704496..49704539,+p3@Ogn
Mm9::chr13:96374858..96374868,-p@chr13:96374858..96374868
-
Mm9::chr14:48268074..48268102,+p@chr14:48268074..48268102
+
Mm9::chr15:6824231..6824248,-p2@Osmr
Mm9::chr17:14813242..14813246,-p@chr17:14813242..14813246
-
Mm9::chr17:14831089..14831106,-p1@Thbs2
Mm9::chr17:29227828..29227839,-p@chr17:29227828..29227839
-
Mm9::chr17:6106908..6106922,+p5@Tulp4
Mm9::chr17:75577989..75578000,+p11@Ltbp1
Mm9::chr17:75578018..75578028,+p14@Ltbp1
Mm9::chr17:75578058..75578071,+p8@Ltbp1
Mm9::chr17:75578115..75578134,+p9@Ltbp1
Mm9::chr17:75578137..75578164,+p2@Ltbp1
Mm9::chr17:75578174..75578196,+p7@Ltbp1
Mm9::chr17:75578287..75578301,+p5@Ltbp1
Mm9::chr17:87506961..87507024,+p1@Socs5
Mm9::chr17:87507025..87507042,+p3@Socs5
Mm9::chr17:87544959..87544962,+p@chr17:87544959..87544962
+
Mm9::chr1:127573864..127573879,+p10@Gpr39
Mm9::chr1:127574253..127574264,+p@chr1:127574253..127574264
+
Mm9::chr1:165243978..165243992,-p9@Prrx1
Mm9::chr2:113589030..113589077,-p@chr2:113589030..113589077
-
Mm9::chr2:117938827..117938841,+p@chr2:117938827..117938841
+
Mm9::chr2:117943977..117944000,+p@chr2:117943977..117944000
+
Mm9::chr2:178190171..178190178,+p@chr2:178190171..178190178
+
Mm9::chr5:114822634..114822665,-p9@Kctd10
Mm9::chr7:90893343..90893363,-p@chr7:90893343..90893363
-
Mm9::chr7:90894306..90894354,-p2@Il16
Mm9::chr7:91081998..91082010,-p@chr7:91081998..91082010
-
Mm9::chr7:91235004..91235019,-p1@9930013L23Rik
Mm9::chr8:34997222..34997224,-p@chr8:34997222..34997224
-
Mm9::chr9:96632690..96632703,-p20@Zbtb38


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:0044421extracellular region part0.0263871369384338
GO:0045625regulation of T-helper 1 cell differentiation0.0386373874983721
GO:0045627positive regulation of T-helper 1 cell differentiation0.0386373874983721
GO:0004924oncostatin-M receptor activity0.0386373874983721
GO:0004896hematopoietin/interferon-class (D200-domain) cytokine receptor activity0.0386373874983721
GO:0005102receptor binding0.0386373874983721
GO:0005515protein binding0.0386373874983721
GO:0007167enzyme linked receptor protein signaling pathway0.0386373874983721
GO:0005578proteinaceous extracellular matrix0.0386373874983721
GO:0045629negative regulation of T-helper 2 cell differentiation0.0386373874983721
GO:0045624positive regulation of T-helper cell differentiation0.0386373874983721
GO:0007178transmembrane receptor protein serine/threonine kinase signaling pathway0.0386373874983721
GO:0007166cell surface receptor linked signal transduction0.0386373874983721
GO:0009966regulation of signal transduction0.0386373874983721
GO:0009968negative regulation of signal transduction0.0386373874983721
GO:0045628regulation of T-helper 2 cell differentiation0.0386373874983721
GO:0045063T-helper 1 cell differentiation0.0386373874983721
GO:0017074procollagen N-endopeptidase activity0.0386373874983721
GO:0045623negative regulation of T-helper cell differentiation0.0386373874983721
GO:0045064T-helper 2 cell differentiation0.041147959075257
GO:0008593regulation of Notch signaling pathway0.041147959075257
GO:0045622regulation of T-helper cell differentiation0.041147959075257
GO:0007165signal transduction0.041147959075257
GO:0005615extracellular space0.041147959075257
GO:0042092T-helper 2 type immune response0.0476555594886153
GO:0007154cell communication0.0476555594886153
GO:0050920regulation of chemotaxis0.0476555594886153
GO:0050926regulation of positive chemotaxis0.0476555594886153
GO:0050921positive regulation of chemotaxis0.0476555594886153
GO:0005154epidermal growth factor receptor binding0.0476555594886153
GO:0050927positive regulation of positive chemotaxis0.0476555594886153
GO:0050930induction of positive chemotaxis0.0476555594886153
GO:0002294CD4-positive, alpha-beta T cell differentiation during immune response0.0476555594886153
GO:0042088T-helper 1 type immune response0.0476555594886153
GO:0002286T cell activation during immune response0.0476555594886153
GO:0002292T cell differentiation during immune response0.0476555594886153
GO:0042093T-helper cell differentiation0.0476555594886153
GO:0019894kinesin binding0.0476555594886153
GO:0002285lymphocyte activation during immune response0.0476555594886153
GO:0002293alpha-beta T cell differentiation during immune response0.0476555594886153
GO:0050918positive chemotaxis0.0476555594886153
GO:0051605protein maturation via proteolysis0.0499379591277511
GO:0002366leukocyte activation during immune response0.0499379591277511
GO:0002263cell activation during immune response0.0499379591277511



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
mesodermal cell2.04e-127
muscle precursor cell2.12e-116
contractile cell2.12e-116
muscle cell2.12e-116
myoblast2.12e-116
multi-potent skeletal muscle stem cell3.37e-079


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)
MA0003.10.00601349
MA0004.11.19361
MA0006.10.0127788
MA0007.10.41953
MA0009.10.311311
MA0014.10.00777527
MA0017.10.0781308
MA0019.10.542303
MA0024.10.2788
MA0025.10.500436
MA0027.11.85482
MA0028.10.349965
MA0029.10.263093
MA0030.10.267807
MA0031.10.242604
MA0038.10.120029
MA0040.10.32081
MA0041.11.72879
MA0042.11.64691
MA0043.10.386827
MA0046.10.338806
MA0048.10.235372
MA0050.10.24732
MA0051.10.786554
MA0052.10.872393
MA0055.10.0272514
MA0056.10
MA0057.10.455095
MA0058.11.60488
MA0059.10.859481
MA0060.10.165672
MA0061.10.103274
MA0063.10
MA0066.10.114312
MA0067.10.597474
MA0068.10.12269
MA0069.10.327233
MA0070.10.856383
MA0071.10.0701355
MA0072.10.313384
MA0073.13.3155
MA0074.11.0937
MA0076.10.0915916
MA0077.10.297113
MA0078.10.142992
MA0081.10.03619
MA0083.10.386189
MA0084.10.899737
MA0087.10.351973
MA0088.10.0219501
MA0089.10
MA0090.10.168659
MA0091.10.475676
MA0092.10.0441077
MA0093.11.27399
MA0095.10
MA0098.10
MA0100.10.631746
MA0101.10.13112
MA0103.10.0855935
MA0105.10.0643847
MA0106.10.451394
MA0107.10.0812941
MA0108.20.577424
MA0109.10
MA0111.10.048616
MA0113.10.411312
MA0114.10.100825
MA0115.10.389079
MA0116.10.54868
MA0117.10.363331
MA0119.10.131636
MA0122.10.987913
MA0124.10.550539
MA0125.10.486591
MA0130.10
MA0131.10.181514
MA0132.10
MA0133.10
MA0135.10.4164
MA0136.10.106221
MA0139.10.0148967
MA0140.10.304632
MA0141.10.100135
MA0142.10.656918
MA0143.11.38097
MA0144.10.613691
MA0145.10.0596805
MA0146.10.00743003
MA0147.10.245652
MA0148.10.221662
MA0149.10.915423
MA0062.20.00742176
MA0035.20.641981
MA0039.20.0143379
MA0138.20.523377
MA0002.21.10185
MA0137.20.0979218
MA0104.20.26672
MA0047.20.119626
MA0112.20.0278415
MA0065.20.11193
MA0150.11.13124
MA0151.10
MA0152.10.763936
MA0153.10.430089
MA0154.10.510612
MA0155.11.38532
MA0156.10.0909568
MA0157.10.605995
MA0158.10
MA0159.10.129147
MA0160.10.225012
MA0161.10
MA0162.10.0480644
MA0163.10.803239
MA0164.11.16107
MA0080.20.0819057
MA0018.20.111278
MA0099.20.172684
MA0079.20.374537
MA0102.20.949579
MA0258.10.0291367
MA0259.10.224435
MA0442.10
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