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MCL coexpression mm9:162: Difference between revisions

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{{MCL_coexpression_mm9|gostat_on_MCL_coexpression=GO:0006629;lipid metabolic process;0.0277682095850798;14245,26458,64291,11430!GO:0031529;ruffle organization and biogenesis;0.0277682095850798;14245!GO:0030948;negative regulation of vascular endothelial growth factor receptor signaling pathway;0.0277682095850798;16840!GO:0009966;regulation of signal transduction;0.0277682095850798;16840,53972,56508!GO:0032868;response to insulin stimulus;0.0277682095850798;14245!GO:0043434;response to peptide hormone stimulus;0.0277682095850798;14245!GO:0032870;cellular response to hormone stimulus;0.0277682095850798;14245!GO:0032869;cellular response to insulin stimulus;0.0277682095850798;14245!GO:0042579;microbody;0.0277682095850798;26458,11430!GO:0005777;peroxisome;0.0277682095850798;26458,11430!GO:0031532;actin cytoskeleton reorganization;0.0371242313547847;14245!GO:0005085;guanyl-nucleotide exchange factor activity;0.039670377237159;53972,56508!GO:0003997;acyl-CoA oxidase activity;0.039670377237159;11430!GO:0051056;regulation of small GTPase mediated signal transduction;0.039670377237159;53972,56508!GO:0044255;cellular lipid metabolic process;0.0425148821081574;26458,64291,11430!GO:0030947;regulation of vascular endothelial growth factor receptor signaling pathway;0.0425148821081574;16840!GO:0008195;phosphatidate phosphatase activity;0.048003657065088;14245!}}
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metabolic process;0.0277682095850798;14245,26458,64291,11430!GO:0031529;ruffle organization and biogenesis;0.0277682095850798;14245!GO:0030948;negative regulation of vascular endothelial growth factor receptor signaling pathway;0.0277682095850798;16840!GO:0009966;regulation of signal transduction;0.0277682095850798;16840,53972,56508!GO:0032868;response to insulin stimulus;0.0277682095850798;14245!GO:0043434;response to peptide hormone stimulus;0.0277682095850798;14245!GO:0032870;cellular response to hormone stimulus;0.0277682095850798;14245!GO:0032869;cellular response to insulin stimulus;0.0277682095850798;14245!GO:0042579;microbody;0.0277682095850798;26458,11430!GO:0005777;peroxisome;0.0277682095850798;26458,11430!GO:0031532;actin cytoskeleton reorganization;0.0371242313547847;14245!GO:0005085;guanyl-nucleotide exchange factor activity;0.039670377237159;53972,56508!GO:0003997;acyl-CoA oxidase activity;0.039670377237159;11430!GO:0051056;regulation of small GTPase mediated signal transduction;0.039670377237159;53972,56508!GO:0044255;cellular lipid metabolic process;0.0425148821081574;26458,64291,11430!GO:0030947;regulation of vascular endothelial growth factor receptor signaling pathway;0.0425148821081574;16840!GO:0008195;phosphatidate phosphatase activity;0.048003657065088;14245!|ontology_enrichment_celltype=CL:0000181!2.48e-24!5;CL:0000417!2.48e-24!5;CL:0000668!2.48e-24!5;CL:0000412!2.48e-24!5;CL:0000182!2.48e-24!5;CL:0000057!7.41e-09!1;CL:0000632!7.41e-09!1|ontology_enrichment_disease=|ontology_enrichment_uberon=UBERON:0002107!1.33e-32!22;UBERON:0007499!1.33e-32!22;UBERON:0006925!1.33e-32!22;UBERON:0009497!1.33e-32!22;UBERON:0000015!1.33e-32!22;UBERON:0002423!1.33e-32!22;UBERON:0006235!1.33e-32!22;UBERON:0008835!1.33e-32!22;UBERON:0003894!1.33e-32!22;UBERON:0004161!1.33e-32!22;UBERON:0008836!1.33e-32!22;UBERON:0009854!3.71e-31!23;UBERON:0009856!3.71e-31!23;UBERON:0002365!1.30e-28!25;UBERON:0002330!1.30e-28!25;UBERON:0005256!1.44e-15!45;UBERON:0003914!7.19e-15!47;UBERON:0005172!3.14e-14!49;UBERON:0005173!3.14e-14!49;UBERON:0002417!3.14e-14!49;UBERON:0000916!3.14e-14!49;UBERON:0003929!1.39e-12!55;UBERON:0002368!1.83e-11!60;UBERON:0003104!2.92e-11!61;UBERON:0009142!2.92e-11!61;UBERON:0002530!1.64e-10!65;UBERON:0000490!2.44e-10!66;UBERON:0009569!2.44e-10!66;UBERON:0005911!7.53e-10!69;UBERON:0000949!2.12e-09!72;UBERON:0000466!1.75e-08!79;UBERON:0005177!1.75e-08!79;UBERON:0001041!2.30e-08!80;UBERON:0002100!2.52e-07!90|tfbs_overrepresentation_for_novel_motifs=0.03128,0.000937455,0.0721634,0.27151,0.183219,0.508242,0.108081,0.147931,0.00935984,0.00296501,0.0793816,0.463631,0.0450167,0.0280835,0.726945,0,0.302987,0.810122,0.544594,0.0790777,0.369478,0.0666561,0.0278872,1.10166,0.172466,0.0344857,0.832128,0.339237,0.00930338,0.0726037,0.0575697,0.138901,0.163159,0.068805,0.0220356,0.0010894,0.0341499,0.0972905,0.613351,8.95973e-05,0.436335,0.160718,0.386605,1.90518,0.0516313,0.120832,0.471989,0.371549,1.21561,0.662539,0.282905,0.0415347,0.103707,0.222347,0.233728,0.122329,0.957121,0.228138,0.21871,0.02921,0.803006,0.0441965,1.00793,0.0785999,0.130925,0.316837,0.878384,0.616867,0.39734,0.49015,0.00303626,0.877871,3.06024e-05,0.256208,0.0025184,0.0588386,0.514177,0.451021,0.381241,0.228992,0.887801,0.0980457,0.381206,0.316263,0.182353,2.73636e-07,0.176041,0.0728382,0.0614341,0.763142,0.382871,0.185328,0.447132,0.669745,0.103622,1.36652,0.332808,0.450945,0.0598324,0.00430426,0.146075,0.429522,0.211201,0.0833891,0.282384,0.160216,0.109249,0.363181,0.0026512,0.00236174,0.544025,0.609261,1.77356,0.0825035,0.388387,0.82329,4.61157e-05,0.0492808,0.304507,0.235581,0.720321,1.88074,1.79775,0.782921,0.431518,0.385979,0.816461,0.142099,0.328524,0.327252,0.581258,0.258441,2.28341,0.312955,0.40544,0.00552151,0.86415,1.16029,0.366944,1.11117,0.733971,0.33317,0.149737,0.44397,0.0803297,2.42971,0.477804,1.07297,0.874955,0.10175,0.00954725,1.4487e-06,0.635304,0.0428318,0.311503,0.278572,0.369352,0.390885,0.352838,0.00630371,0.374299,0.181844,0.121963,0.336402,0.572331,0.872987,0.0335404,0.243554,1.3843e-06|tfbs_overrepresentation_jaspar=MA0003.1;1.38858e-12,MA0004.1;1.025,MA0006.1;0.0545783,MA0007.1;0.245853,MA0009.1;0.46576,MA0014.1;6.60087e-08,MA0017.1;1.41868,MA0019.1;0.519556,MA0024.1;0.12989,MA0025.1;2.26713,MA0027.1;1.59941,MA0028.1;0.000883268,MA0029.1;0.118998,MA0030.1;0.775333,MA0031.1;1.15283,MA0038.1;0.925152,MA0040.1;0.483091,MA0041.1;0.459147,MA0042.1;0.254235,MA0043.1;1.13973,MA0046.1;0.992857,MA0048.1;0.122836,MA0050.1;0.580263,MA0051.1;0.956711,MA0052.1;0.494368,MA0055.1;0.0220108,MA0056.1;0,MA0057.1;0.000945085,MA0058.1;0.398282,MA0059.1;0.0620265,MA0060.1;0.641135,MA0061.1;0.456037,MA0063.1;0,MA0066.1;0.560747,MA0067.1;0.387388,MA0068.1;0.102868,MA0069.1;0.164922,MA0070.1;0.934729,MA0071.1;0.868643,MA0072.1;0.469536,MA0073.1;0.0142121,MA0074.1;0.474988,MA0076.1;0.00170201,MA0077.1;0.142892,MA0078.1;0.174236,MA0081.1;0.17383,MA0083.1;0.210065,MA0084.1;0.664822,MA0087.1;0.183562,MA0088.1;0.0733481,MA0089.1;0,MA0090.1;1.53357,MA0091.1;0.146366,MA0092.1;0.380367,MA0093.1;1.06324,MA0095.1;0,MA0098.1;0,MA0100.1;0.236549,MA0101.1;0.463214,MA0103.1;0.463373,MA0105.1;0.17048,MA0106.1;0.717683,MA0107.1;0.0808299,MA0108.2;0.266897,MA0109.1;0,MA0111.1;0.112742,MA0113.1;0.358538,MA0114.1;2.25916,MA0115.1;1.14661,MA0116.1;0.00530013,MA0117.1;0.192271,MA0119.1;0.286362,MA0122.1;0.204518,MA0124.1;0.346379,MA0125.1;0.793271,MA0130.1;0,MA0131.1;0.237396,MA0132.1;0,MA0133.1;0,MA0135.1;1.23006,MA0136.1;0.521849,MA0139.1;0.0184675,MA0140.1;1.06816,MA0141.1;1.67225,MA0142.1;0.667303,MA0143.1;0.68599,MA0144.1;1.95706,MA0145.1;0.0100079,MA0146.1;5.69442e-05,MA0147.1;0.230754,MA0148.1;1.8881,MA0149.1;0.0039909,MA0062.2;0.000564861,MA0035.2;2.44148,MA0039.2;6.99506e-09,MA0138.2;0.0641537,MA0002.2;0.229976,MA0137.2;2.01645,MA0104.2;0.107492,MA0047.2;1.7827,MA0112.2;0.010006,MA0065.2;0.741795,MA0150.1;0.245658,MA0151.1;0,MA0152.1;0.922839,MA0153.1;0.68621,MA0154.1;0.0101745,MA0155.1;0.00842769,MA0156.1;0.038486,MA0157.1;1.50123,MA0158.1;0,MA0159.1;0.564224,MA0160.1;0.153045,MA0161.1;0,MA0162.1;2.26037e-05,MA0163.1;3.42301e-05,MA0164.1;0.282353,MA0080.2;0.0816674,MA0018.2;0.124921,MA0099.2;0.48382,MA0079.2;0,MA0102.2;0.712096,MA0258.1;0.0451601,MA0259.1;0.0605653,MA0442.1;0}}

Latest revision as of 14:48, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr10:111032948..111032961,+p@chr10:111032948..111032961
+
Mm9::chr10:67599952..67599956,-p@chr10:67599952..67599956
-
Mm9::chr11:116050856..116050864,-p15@Acox1
Mm9::chr11:16642247..16642283,-p@chr11:16642247..16642283
-
Mm9::chr12:16596529..16596541,-p2@Lpin1
Mm9::chr12:33455718..33455731,-p@chr12:33455718..33455731
-
Mm9::chr12:33455776..33455786,-p@chr12:33455776..33455786
-
Mm9::chr12:76700319..76700320,-p@chr12:76700319..76700320
-
Mm9::chr13:24420892..24420904,-p@chr13:24420892..24420904
-
Mm9::chr13:24420993..24421016,-p@chr13:24420993..24421016
-
Mm9::chr13:24422074..24422087,-p@chr13:24422074..24422087
-
Mm9::chr14:41917607..41917623,+p@chr14:41917607..41917623
+
Mm9::chr14:80041947..80041958,-p5@Lect1
Mm9::chr16:23981309..23981342,-p@chr16:23981309..23981342
-
Mm9::chr16:43236088..43236099,+p43@Zbtb20
Mm9::chr18:12801105..12801118,+p@chr18:12801105..12801118
+
Mm9::chr18:13018649..13018664,-p15@Osbpl1a
Mm9::chr18:13018706..13018744,-p10@Osbpl1a
Mm9::chr18:75825791..75825811,-p@chr18:75825791..75825811
-
Mm9::chr19:44079718..44079719,-p@chr19:44079718..44079719
-
Mm9::chr19:5826671..5826746,-p@chr19:5826671..5826746
-
Mm9::chr1:129627925..129627959,+p@chr1:129627925..129627959
+
Mm9::chr1:142278108..142278111,+p@chr1:142278108..142278111
+
Mm9::chr1:152980073..152980094,+p@chr1:152980073..152980094
+
Mm9::chr1:152980097..152980108,+p@chr1:152980097..152980108
+
Mm9::chr1:152980110..152980124,+p@chr1:152980110..152980124
+
Mm9::chr1:152980130..152980141,+p@chr1:152980130..152980141
+
Mm9::chr1:40220289..40220292,-p@chr1:40220289..40220292
-
Mm9::chr1:89470480..89470509,-p3@Ngef
Mm9::chr2:118133412..118133420,-p@chr2:118133412..118133420
-
Mm9::chr2:126378471..126378483,+p4@Slc27a2
Mm9::chr2:126378493..126378504,+p5@Slc27a2
Mm9::chr2:132515856..132515898,+p4@1110034G24Rik
Mm9::chr2:132524238..132524262,-p1@ENSMUST00000147868
Mm9::chr2:169425295..169425296,+p@chr2:169425295..169425296
+
Mm9::chr2:4914307..4914346,-p5@Mcm10
Mm9::chr2:4915515..4915520,+p@chr2:4915515..4915520
+
Mm9::chr2:4922613..4922630,-p4@Mcm10
Mm9::chr2:67808715..67808722,+p@chr2:67808715..67808722
+
Mm9::chr2:67809304..67809319,+p@chr2:67809304..67809319
+
Mm9::chr2:71994483..71994498,-p@chr2:71994483..71994498
-
Mm9::chr2:72011296..72011299,+p@chr2:72011296..72011299
+
Mm9::chr2:72012294..72012308,+p@chr2:72012294..72012308
+
Mm9::chr2:72018109..72018123,+p5@Rapgef4
Mm9::chr3:81799618..81799631,+p@chr3:81799618..81799631
+
Mm9::chr3:86816166..86816175,-p@chr3:86816166..86816175
-
Mm9::chr4:107897933..107897941,-p@chr4:107897933..107897941
-
Mm9::chr4:107897984..107897993,-p@chr4:107897984..107897993
-
Mm9::chr4:150228479..150228494,+p@chr4:150228479..150228494
+
Mm9::chr4:98704584..98704588,+p@chr4:98704584..98704588
+
Mm9::chr5:66475935..66475939,-p@chr5:66475935..66475939
-
Mm9::chr5:87808974..87808979,-p@chr5:87808974..87808979
-
Mm9::chr6:149138217..149138221,+p@chr6:149138217..149138221
+
Mm9::chr7:104106630..104106658,+p@chr7:104106630..104106658
+
Mm9::chr7:15078366..15078390,-p1@ENSMUST00000118150
Mm9::chr7:20277295..20277305,-p@chr7:20277295..20277305
-
Mm9::chr7:56133347..56133350,+p2@ENSMUST00000129551
Mm9::chr8:107628743..107628746,+p@chr8:107628743..107628746
+
Mm9::chr8:116614660..116614666,-p@chr8:116614660..116614666
-
Mm9::chr8:131003594..131003606,+p@chr8:131003594..131003606
+
Mm9::chr8:13201413..13201428,-p@chr8:13201413..13201428
-
Mm9::chr8:25686748..25686755,-p3@Ido2
Mm9::chr8:47922918..47922931,+p@chr8:47922918..47922931
+
Mm9::chr9:106173293..106173301,+p@chr9:106173293..106173301
+
Mm9::chr9:74376459..74376475,-p@chr9:74376459..74376475
-
Mm9::chr9:74713442..74713460,+p@chr9:74713442..74713460
+
Mm9::chr9:74714303..74714318,+p2@Onecut1


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:0006629lipid metabolic process0.0277682095850798
GO:0031529ruffle organization and biogenesis0.0277682095850798
GO:0030948negative regulation of vascular endothelial growth factor receptor signaling pathway0.0277682095850798
GO:0009966regulation of signal transduction0.0277682095850798
GO:0032868response to insulin stimulus0.0277682095850798
GO:0043434response to peptide hormone stimulus0.0277682095850798
GO:0032870cellular response to hormone stimulus0.0277682095850798
GO:0032869cellular response to insulin stimulus0.0277682095850798
GO:0042579microbody0.0277682095850798
GO:0005777peroxisome0.0277682095850798
GO:0031532actin cytoskeleton reorganization0.0371242313547847
GO:0005085guanyl-nucleotide exchange factor activity0.039670377237159
GO:0003997acyl-CoA oxidase activity0.039670377237159
GO:0051056regulation of small GTPase mediated signal transduction0.039670377237159
GO:0044255cellular lipid metabolic process0.0425148821081574
GO:0030947regulation of vascular endothelial growth factor receptor signaling pathway0.0425148821081574
GO:0008195phosphatidate phosphatase activity0.048003657065088



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
metabolising cell2.48e-245
endopolyploid cell2.48e-245
parenchymal cell2.48e-245
polyploid cell2.48e-245
hepatocyte2.48e-245
fibroblast7.41e-091
hepatic stellate cell7.41e-091

Uber Anatomy
Ontology termp-valuen
liver1.33e-3222
epithelial sac1.33e-3222
digestive gland1.33e-3222
epithelium of foregut-midgut junction1.33e-3222
anatomical boundary1.33e-3222
hepatobiliary system1.33e-3222
foregut-midgut junction1.33e-3222
hepatic diverticulum1.33e-3222
liver primordium1.33e-3222
septum transversum1.33e-3222
liver bud1.33e-3222
digestive tract diverticulum3.71e-3123
sac3.71e-3123
exocrine gland1.30e-2825
exocrine system1.30e-2825
trunk mesenchyme1.44e-1545
epithelial tube7.19e-1547
abdomen element3.14e-1449
abdominal segment element3.14e-1449
abdominal segment of trunk3.14e-1449
abdomen3.14e-1449
gut epithelium1.39e-1255
endocrine gland1.83e-1160
mesenchyme2.92e-1161
entire embryonic mesenchyme2.92e-1161
gland1.64e-1065
unilaminar epithelium2.44e-1066
subdivision of trunk2.44e-1066
endo-epithelium7.53e-1069
endocrine system2.12e-0972
immaterial anatomical entity1.75e-0879
trunk region element1.75e-0879
foregut2.30e-0880
trunk2.52e-0790


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)
MA0003.11.38858e-12
MA0004.11.025
MA0006.10.0545783
MA0007.10.245853
MA0009.10.46576
MA0014.16.60087e-08
MA0017.11.41868
MA0019.10.519556
MA0024.10.12989
MA0025.12.26713
MA0027.11.59941
MA0028.10.000883268
MA0029.10.118998
MA0030.10.775333
MA0031.11.15283
MA0038.10.925152
MA0040.10.483091
MA0041.10.459147
MA0042.10.254235
MA0043.11.13973
MA0046.10.992857
MA0048.10.122836
MA0050.10.580263
MA0051.10.956711
MA0052.10.494368
MA0055.10.0220108
MA0056.10
MA0057.10.000945085
MA0058.10.398282
MA0059.10.0620265
MA0060.10.641135
MA0061.10.456037
MA0063.10
MA0066.10.560747
MA0067.10.387388
MA0068.10.102868
MA0069.10.164922
MA0070.10.934729
MA0071.10.868643
MA0072.10.469536
MA0073.10.0142121
MA0074.10.474988
MA0076.10.00170201
MA0077.10.142892
MA0078.10.174236
MA0081.10.17383
MA0083.10.210065
MA0084.10.664822
MA0087.10.183562
MA0088.10.0733481
MA0089.10
MA0090.11.53357
MA0091.10.146366
MA0092.10.380367
MA0093.11.06324
MA0095.10
MA0098.10
MA0100.10.236549
MA0101.10.463214
MA0103.10.463373
MA0105.10.17048
MA0106.10.717683
MA0107.10.0808299
MA0108.20.266897
MA0109.10
MA0111.10.112742
MA0113.10.358538
MA0114.12.25916
MA0115.11.14661
MA0116.10.00530013
MA0117.10.192271
MA0119.10.286362
MA0122.10.204518
MA0124.10.346379
MA0125.10.793271
MA0130.10
MA0131.10.237396
MA0132.10
MA0133.10
MA0135.11.23006
MA0136.10.521849
MA0139.10.0184675
MA0140.11.06816
MA0141.11.67225
MA0142.10.667303
MA0143.10.68599
MA0144.11.95706
MA0145.10.0100079
MA0146.15.69442e-05
MA0147.10.230754
MA0148.11.8881
MA0149.10.0039909
MA0062.20.000564861
MA0035.22.44148
MA0039.26.99506e-09
MA0138.20.0641537
MA0002.20.229976
MA0137.22.01645
MA0104.20.107492
MA0047.21.7827
MA0112.20.010006
MA0065.20.741795
MA0150.10.245658
MA0151.10
MA0152.10.922839
MA0153.10.68621
MA0154.10.0101745
MA0155.10.00842769
MA0156.10.038486
MA0157.11.50123
MA0158.10
MA0159.10.564224
MA0160.10.153045
MA0161.10
MA0162.12.26037e-05
MA0163.13.42301e-05
MA0164.10.282353
MA0080.20.0816674
MA0018.20.124921
MA0099.20.48382
MA0079.20
MA0102.20.712096
MA0258.10.0451601
MA0259.10.0605653
MA0442.10
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