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MCL coexpression mm9:326: Difference between revisions

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{{MCL_coexpression_mm9
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regulation of DNA replication;0.0402497060598641;13874!GO:0004360;glutamine-fructose-6-phosphate transaminase (isomerizing) activity;0.0402497060598641;14584!GO:0045741;positive regulation of epidermal growth factor receptor activity;0.0402497060598641;13874!GO:0005588;collagen type V;0.0402497060598641;12832!GO:0045840;positive regulation of mitosis;0.0402497060598641;13874!GO:0048661;positive regulation of smooth muscle cell proliferation;0.0402497060598641;13874!GO:0048660;regulation of smooth muscle cell proliferation;0.0402497060598641;13874!GO:0051054;positive regulation of DNA metabolic process;0.0402497060598641;13874!GO:0007176;regulation of epidermal growth factor receptor activity;0.0402497060598641;13874!GO:0045742;positive regulation of epidermal growth factor receptor signaling pathway;0.0425893257526012;13874!GO:0005583;fibrillar collagen;0.0425893257526012;12832!GO:0030036;actin cytoskeleton organization and biogenesis;0.0425893257526012;11641,80837!GO:0048659;smooth muscle cell proliferation;0.0425893257526012;13874!GO:0030029;actin filament-based process;0.0425893257526012;11641,80837!GO:0045410;positive regulation of interleukin-6 biosynthetic process;0.0425893257526012;13874!GO:0042058;regulation of epidermal growth factor receptor signaling pathway;0.0425893257526012;13874!GO:0004720;protein-lysine 6-oxidase activity;0.0425893257526012;94352!GO:0008284;positive regulation of cell proliferation;0.0433274084684527;13874,11535!GO:0005154;epidermal growth factor receptor binding;0.0444475374244391;13874!GO:0051018;protein kinase A 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|gostat_on_MCL_coexpression=GO:0045740;positive regulation of DNA replication;0.0402497060598641;13874!GO:0004360;glutamine-fructose-6-phosphate transaminase (isomerizing) activity;0.0402497060598641;14584!GO:0045741;positive regulation of epidermal growth factor receptor activity;0.0402497060598641;13874!GO:0005588;collagen type V;0.0402497060598641;12832!GO:0045840;positive regulation of mitosis;0.0402497060598641;13874!GO:0048661;positive regulation of smooth muscle cell proliferation;0.0402497060598641;13874!GO:0048660;regulation of smooth muscle cell proliferation;0.0402497060598641;13874!GO:0051054;positive regulation of DNA metabolic process;0.0402497060598641;13874!GO:0007176;regulation of epidermal growth factor receptor activity;0.0402497060598641;13874!GO:0045742;positive regulation of epidermal growth factor receptor signaling pathway;0.0425893257526012;13874!GO:0005583;fibrillar collagen;0.0425893257526012;12832!GO:0030036;actin cytoskeleton organization and biogenesis;0.0425893257526012;11641,80837!GO:0048659;smooth muscle cell proliferation;0.0425893257526012;13874!GO:0030029;actin filament-based process;0.0425893257526012;11641,80837!GO:0045410;positive regulation of interleukin-6 biosynthetic process;0.0425893257526012;13874!GO:0042058;regulation of epidermal growth factor receptor signaling pathway;0.0425893257526012;13874!GO:0004720;protein-lysine 6-oxidase activity;0.0425893257526012;94352!GO:0008284;positive regulation of cell proliferation;0.0433274084684527;13874,11535!GO:0005154;epidermal growth factor receptor binding;0.0444475374244391;13874!GO:0051018;protein kinase A binding;0.0482467528778367;11641!
|ontology_enrichment_celltype=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0004535!9.60e-12!23;UBERON:0001009!9.60e-12!23;UBERON:0004872!5.89e-10!33;UBERON:0007100!2.75e-09!18;UBERON:0000948!2.75e-09!18;UBERON:0005498!2.75e-09!18;UBERON:0004140!2.75e-09!18;UBERON:0009881!2.75e-09!18;UBERON:0004141!2.75e-09!18;UBERON:0003084!2.75e-09!18;UBERON:0007005!2.75e-09!18;UBERON:0004139!2.75e-09!18;UBERON:0004291!2.75e-09!18
|tfbs_overrepresentation_for_novel_motifs=0.653885,1.55144,0.282026,0.376992,0.968363,0.794046,0.1827,0.339268,0.364548,0.135725,0.469093,0.174808,0.171442,0.19087,0.672427,0,0.333505,0.933534,0.300991,0.553915,0.234822,1.56119,0.190264,0.340076,0.292091,0.209658,0.481302,0.429523,0.438605,0.332722,0.13045,0.416414,0.923713,0.641376,0.166509,0.586878,0.0315753,0.172462,0.0255429,0.670706,0.335087,0.416106,0.464587,1.0513,0.87772,1.19916,0.271716,0.45352,0.356355,0.201733,1.54421,0.228569,0.310742,1.33224,0.554419,0.195691,0.464683,0.498914,0.98814,0.194311,1.0329,0.235329,0.205288,0.310832,0.20328,0.342909,0.678037,2.30344,0.395762,0.867464,0.0740354,0.180319,0.0258637,0.584436,1.65593,0.87597,0.234136,0.263199,1.00174,0.883217,0.18222,0.347414,0.234292,0.0604242,0.48244,0.0253614,0.214763,1.07036,0.275409,1.16606,0.74267,0.486763,0.427209,0.994482,0.255947,0.699836,0.332811,0.429584,0.271907,1.20965,0.0315985,0.416179,0.523506,0.320141,0.855238,0.133214,0.961759,0.145827,0.246199,0.510198,0.0921762,0.525078,0.518312,0.477109,0.749248,0.600735,0.170096,0.120391,0.334542,0.125121,0.589296,0.294572,0.210922,0.262524,0.800032,1.00844,0.551377,0.421488,0.67664,0.647397,0.508573,0.73944,0.649498,0.205008,0.769462,0.057122,0.328991,0.418217,0.723554,1.52843,1.13499,0.682379,0.219341,0.425235,0.843813,0.825793,0.274066,1.4892,1.65642,0.346748,0.542902,0.101696,0.540306,0.724307,1.11557,0.613593,0.229288,0.179236,0.647931,0.673649,0.732404,0.481698,0.388835,0.631413,0.311631,0.578243,1.26634,0.173777,0.84207
}}

Latest revision as of 15:06, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr11:49607659..49607686,+p1@Gfpt2
Mm9::chr12:76409326..76409345,+p4@Rhoj
Mm9::chr14:70008967..70008981,+p1@Loxl2
Mm9::chr1:45499562..45499597,-p@chr1:45499562..45499597
-
Mm9::chr1:45559410..45559413,-p@chr1:45559410..45559413
-
Mm9::chr1:45559901..45559916,-p1@Col5a2
Mm9::chr2:27806885..27806899,+p@chr2:27806885..27806899
+
Mm9::chr4:57858149..57858160,+p5@Akap2
Mm9::chr5:91503323..91503334,+p2@Ereg
Mm9::chr6:91162781..91162792,+p2@Fbln2
Mm9::chr6:91162793..91162838,+p1@Fbln2
Mm9::chr6:91162853..91162864,+p3@Fbln2
Mm9::chr6:91183204..91183213,+p@chr6:91183204..91183213
+
Mm9::chr6:91183472..91183486,+p@chr6:91183472..91183486
+
Mm9::chr6:91183490..91183501,+p@chr6:91183490..91183501
+
Mm9::chr6:91183746..91183762,+p@chr6:91183746..91183762
+
Mm9::chr6:91183788..91183800,+p@chr6:91183788..91183800
+
Mm9::chr6:91183906..91183958,-p@chr6:91183906..91183958
-
Mm9::chr6:91184210..91184231,+p@chr6:91184210..91184231
+
Mm9::chr6:91184284..91184295,+p@chr6:91184284..91184295
+
Mm9::chr6:91222095..91222107,+p@chr6:91222095..91222107
+
Mm9::chr7:105639067..105639106,+p@chr7:105639067..105639106
+
Mm9::chr7:117771164..117771180,+p1@Adm
Mm9::chr7:117772048..117772059,+p@chr7:117772048..117772059
+
Mm9::chr7:26573654..26573729,-p1@Axl


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:0045740positive regulation of DNA replication0.0402497060598641
GO:0004360glutamine-fructose-6-phosphate transaminase (isomerizing) activity0.0402497060598641
GO:0045741positive regulation of epidermal growth factor receptor activity0.0402497060598641
GO:0005588collagen type V0.0402497060598641
GO:0045840positive regulation of mitosis0.0402497060598641
GO:0048661positive regulation of smooth muscle cell proliferation0.0402497060598641
GO:0048660regulation of smooth muscle cell proliferation0.0402497060598641
GO:0051054positive regulation of DNA metabolic process0.0402497060598641
GO:0007176regulation of epidermal growth factor receptor activity0.0402497060598641
GO:0045742positive regulation of epidermal growth factor receptor signaling pathway0.0425893257526012
GO:0005583fibrillar collagen0.0425893257526012
GO:0030036actin cytoskeleton organization and biogenesis0.0425893257526012
GO:0048659smooth muscle cell proliferation0.0425893257526012
GO:0030029actin filament-based process0.0425893257526012
GO:0045410positive regulation of interleukin-6 biosynthetic process0.0425893257526012
GO:0042058regulation of epidermal growth factor receptor signaling pathway0.0425893257526012
GO:0004720protein-lysine 6-oxidase activity0.0425893257526012
GO:0008284positive regulation of cell proliferation0.0433274084684527
GO:0005154epidermal growth factor receptor binding0.0444475374244391
GO:0051018protein kinase A binding0.0482467528778367



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>


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)
MA0003.10.0978048
MA0004.10.118549
MA0006.10.161227
MA0007.11.73673
MA0009.11.11793
MA0014.10.110955
MA0017.10.190692
MA0019.10.290797
MA0024.11.03781
MA0025.10.645374
MA0027.12.02409
MA0028.10.0452573
MA0029.10.383872
MA0030.11.01026
MA0031.10.946067
MA0038.10.209603
MA0040.10.449452
MA0041.10.0795363
MA0042.10.0734808
MA0043.10.522621
MA0046.10.469568
MA0048.10.918827
MA0050.10.141024
MA0051.11.81275
MA0052.10.456356
MA0055.10.600243
MA0056.10
MA0057.10.390656
MA0058.10.0704409
MA0059.10.0759876
MA0060.10.0191397
MA0061.10.269352
MA0063.10
MA0066.10.20204
MA0067.10.748059
MA0068.10.246947
MA0069.10.456647
MA0070.10.448343
MA0071.10.140522
MA0072.10.44111
MA0073.10.0586171
MA0074.10.526923
MA0076.10.0586682
MA0077.10.422739
MA0078.10.672666
MA0081.10.293354
MA0083.10.521922
MA0084.11.0607
MA0087.10.484199
MA0088.11.00693
MA0089.10
MA0090.10.32897
MA0091.10.125983
MA0092.11.11922
MA0093.10.0482497
MA0095.10
MA0098.10
MA0100.10.508591
MA0101.10.274567
MA0103.10.447794
MA0105.10.61924
MA0106.10.685785
MA0107.10.196036
MA0108.20.830865
MA0109.10
MA0111.11.71244
MA0113.11.86061
MA0114.10.265028
MA0115.10.525089
MA0116.10.0415661
MA0117.10.496768
MA0119.10.275337
MA0122.10.514153
MA0124.11.66708
MA0125.10.630583
MA0130.10
MA0131.10.287321
MA0132.10
MA0133.10
MA0135.10.554905
MA0136.10.191208
MA0139.11.5573
MA0140.10.170444
MA0141.10.846766
MA0142.10.34839
MA0143.10.236381
MA0144.11.17278
MA0145.10.414538
MA0146.10.485808
MA0147.10.0299713
MA0148.10.127756
MA0149.10.0827548
MA0062.20.00745981
MA0035.20.173482
MA0039.20.37693
MA0138.22.15544
MA0002.20.336716
MA0137.20.223304
MA0104.20.0744814
MA0047.20.601531
MA0112.20.831988
MA0065.20.0291578
MA0150.10.110236
MA0151.10
MA0152.10.209147
MA0153.10.569763
MA0154.10.140391
MA0155.10.0945236
MA0156.10.464199
MA0157.10.863107
MA0158.10
MA0159.10.313465
MA0160.10.807296
MA0161.10
MA0162.10.00177304
MA0163.10.112891
MA0164.10.559407
MA0080.20.197063
MA0018.20.197998
MA0099.20.276491
MA0079.20.0137477
MA0102.21.11159
MA0258.10.240529
MA0259.10.113327
MA0442.10
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