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MCL coexpression mm9:2280: Difference between revisions

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{{MCL_coexpression_mm9
{{MCL_coexpression_mm9|coexpression_dpi_cluster_scores_mean=0.0799914364975128,0.0574812764589593,0.0702582553383563,0.151382701653063,0,0,0,0,0.0143013047723918,0.071740812188197,0.0171594316221685,0.00833303134164643,0,0,0,0,0,0,0,0,0.0177235328243841,0.0102781632737099,0.0251959723664523,0.0586775493251232,0.0224241218442176,0.1322991981956,0.0388918489795202,0.0600917141989733,0.0826105722672728,0,0.0217438549458489,0,0,0,0.0495063293180325,0.0333929694362378,0.0201718927682114,0,0,0,0,0,0.0429689207243575,0.0610928426262865,0.0515891722798365,0.0476277636466625,0.0627507661192835,0,0,0,0.0380689714314527,0,0,0,0,0,0,0,0,0,0,0.0316825373104117,0,0.0403382459911265,0,0,0,0.0618973743015742,0,0,0,0.0490649136668427,0.039721517195473,0.0518718332243645,0.0352355210309327,0,0,0.013047176027362,0.0601154485400567,0,0.0182439180372271,0,0.0801995090849708,0,0.0308766538450896,0.0783348429345972,0.038614745952892,0,0,0.00790982755944537,0.0276360215863565,0.453097667741144,0.528230683249322,0.646398417459324,0.467904406579588,0.523506363836705,0.369623671010743,0.0669191335382363,0.0454303212931485,0.03285169542297,0.0143065104486891,0,0,0,0.0212772287166846,0,0,0.534185288102761,0,0,0,0,0,0,0.0350028366341689,0.0128524442124787,0.047967174931957,0.0146633743922599,0.0688054046018268,0.0541778428339997,0.0551920171310475,0,0,0,0.0206466840804766,0,0,0,0,0.0284508616161765,0.0409021857635518,0.0442121040040478,0,0.0448470752474052,0.0409953631877679,0.0163240725348775,0,0.0749996435717022,0.0489274836994468,0.0381396339431775,0,0,0,0.0664621217290201,0.00714652363876167,0,0,0.0249808488038572,0,0.0188051499407343,0,0,0.0266367274811498,0.379994156062301,0.322536548910715,0,0,0,0,0,0.0228750655043173,0.0179762120471446,0.0420867592356743,0,0.0155765805041843,0,0,0.0227874893168061,0,0,0.00846333437061438,0.0148150998392991,0.0215499128982231,0,0,0.0106344882395355,0,0.331484680179801,0,0,0,0.0367928187931153,0,0,0,0.0165534214268825,0.0243434161187066,0.0560708856667609,0,0.0696209155451742,0,0.050855039016624,0,0.0117455157566797,0,0,0,0,0,0,0,0,0.745911051437687,0,0,0.0220218002973959,0.0200537817225039,0,0,0.0768005261313842,0.193615286669752,0.293845643510312,0.193488531055194,0.0604041682707162,0.140607898038311,0.530577236094103,0.538550700997151,0.576736282879441,0,0,0.0163916589557577,0,0.0228895045139265,0,0,0.0193541184301787,0,0,0,0.0472526612643332,0.0322104318863553,0.0146680888560183,0,0,0.603429180337189,0.402723979250026,0.0161660191737831,0.0240677349949528,0.064998440822553,0.0443799301656463,0,0,0,0,0,0,0,0.027837127384974,0,0.0302521103423715,0,0,0,0.0331573937563205,0,0,0,0.0187593954939335,0,0,0,0,0.03310473969135,0.0298170049079623,0,0,0.0318118128455325,0,0,0.0210848100991354,0,0,0,0,0,0.020860610454652,0.0216369721519619,1.05838999289939,0.764282159392542,0.676121828777492,0.819435553078958,0.851442309030538,0,0.0184685481726609,0,0,0,0,0,0,0,0.0142215890540973,0.0140546428192639,0.0727683962091365,0.0159428900178226,0,0,0,0,0.0643596040335585,0.199056888272972,0.025243839658108,0,0.0876917610084215,0,0,0.0166242025215361,0,0,0.0485564603906336,0.0228916350926443,0.0132892469734015,0.0108267482772483,0.0234940373908708,0,0,0,0,0,0.0178809096388747,0,0.0357130938052069,0,0.0104435211997064,0.007973933622322,0.010429687873019,0.0294312877958821,0.0290812705809588,0.0480053095083702,0.0406008283755465,0,0.0093281183360862,0.0168499844629979,0.10274744259923,0,0.0338867752296645,0.0387380545716563,0,0,0,0,0,0,0.0610936460506332,0,0,0,0,0,0,0,0.0472542065752338,0,0.0549707227941157,0.0217897208111099,0,0,0.0489230553888678,0.024529291590377,0.0375226752578547,0.061422286708655,0.0492297632530981,0.0528559647337815,0,0.0226322868105034,0.0620936782073268,0,0.0397109494193258,0.0566975517146915,0.0507189446071579,0.0655541507762442,0.042439940000731,0.0382544720468534,0.0245608612488475,0.0182395754350438,0.0253568302075752,0.0700898634865993,0,0.0352882264933707,0,0.037245550361761,0.0156395587682075,0.127892621645578,0.233659466239029,0.250268870346876,0.259841294879365,0.117487960283442,0.217850604058755,0.0866477220954863|coexpression_dpi_cluster_scores_median=0.032256856393288,0,0,0.102727834147052,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0177235328243841,0,0,0.0322275761868389,0,0.098534363157864,0,0.0423723422916016,0,0,0,0,0,0,0,0.0333929694362378,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0620577069359474,0,0,0,0.106932678779961,0,0.0308766538450896,0.0560725960174655,0,0,0,0,0,0.494370751908922,0.539375230045527,0.646872623997464,0.512958928019751,0.538686469444597,0.29294630269212,0,0,0,0,0,0,0,0,0,0,0.427166677805585,0,0,0,0,0,0,0.02414100236309,0,0.047967174931957,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0409953631877679,0,0,0,0.0489274836994468,0,0,0,0,0.0304819657131131,0,0,0,0,0,0,0,0,0,0.400265812092489,0.258032988669288,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.207652748325792,0,0,0,0,0,0,0,0,0,0.0394017081901728,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0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dioxygenase activity;0.00423663040837316;170442!GO:0006991;response to sterol depletion;0.00423663040837316;72999!GO:0045329;carnitine biosynthetic process;0.00423663040837316;170442!GO:0009437;carnitine metabolic process;0.00635459742497994;170442!GO:0042401;biogenic amine biosynthetic process;0.0254016766960898;170442!GO:0016706;oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, 2-oxoglutarate as one donor, and incorporation of one atom each of oxygen into both donors;0.0254016766960898;170442!GO:0042398;amino acid derivative biosynthetic process;0.0254016766960898;170442!GO:0006767;water-soluble vitamin metabolic process;0.0283527507694216;170442!GO:0009309;amine biosynthetic process;0.0283527507694216;170442!GO:0016702;oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen;0.0283527507694216;170442!GO:0051213;dioxygenase 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|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0002365!6.31e-12!25;UBERON:0002330!6.31e-12!25;UBERON:0002107!2.02e-10!22;UBERON:0007499!2.02e-10!22;UBERON:0006925!2.02e-10!22;UBERON:0009497!2.02e-10!22;UBERON:0000015!2.02e-10!22;UBERON:0002423!2.02e-10!22;UBERON:0006235!2.02e-10!22;UBERON:0008835!2.02e-10!22;UBERON:0003894!2.02e-10!22;UBERON:0004161!2.02e-10!22;UBERON:0008836!2.02e-10!22;UBERON:0009854!8.71e-10!23;UBERON:0009856!8.71e-10!23;UBERON:0000014!1.29e-08!5;UBERON:0001003!1.29e-08!5;UBERON:0002097!1.29e-08!5;UBERON:0002199!1.29e-08!5;UBERON:0007029!1.29e-08!5;UBERON:0007376!1.29e-08!5;UBERON:0002416!1.29e-08!5;UBERON:0007383!1.29e-08!5
|tfbs_overrepresentation_for_novel_motifs=0.641384,0.128156,0.612053,0.688265,1.21364,0.704257,0.803568,0.370124,0.381467,0.489964,0.755749,0.790506,0.37041,0.81685,0.502646,0,1.02248,0.473993,0.352304,0.24402,1.39891,0.197567,0.815872,0.481455,0.620553,0.846564,0.906602,0.727368,0.535752,0.790816,0.711848,1.12823,0.471365,0.318879,0.503207,0.30022,0.460474,0.786577,1.10929,0.40068,0.478558,0.717547,0.544696,0.504971,2.22741,1.61988,0.938241,0.744678,0.49007,0.539131,1.0041,0.875451,0.771943,1.2746,1.29252,0.82458,0.549352,0.776619,0.331485,0.822375,1.10737,0.885556,0.39557,0.992216,0.8366,1.03484,1.43193,1.78579,1.1025,1.63712,0.590754,0.377213,0.205546,1.32691,0.864765,0.310084,0.318792,0.926147,1.08947,0.575233,0.37865,1.04072,0.884013,0.362446,1.20828,0.758875,0.808001,0.290918,0.943446,1.94914,1.50286,1.21342,1.14153,0.490141,0.430015,0.409166,0.961641,1.14445,0.938512,0.264911,0.460566,1.12793,1.25667,1.00472,1.00361,0.717061,1.06633,0.740267,0.580757,0.57247,0.633483,1.25851,0.576517,0.7614,1.51002,0.476467,0.442329,0.692434,1.02384,0.456123,1.33244,2.22508,0.848526,0.925183,1.56496,1.09333,0.812403,1.13449,1.43038,0.493609,1.23918,0.680176,1.40022,0.839311,1.53196,0.195549,2.65107,0.719099,1.482,2.31884,1.91709,1.43673,0.861473,1.1391,0.996781,0.718046,0.941555,2.27909,0.653418,2.11223,0.79777,0.184289,1.27621,0.416214,0.838313,1.35996,0.87653,0.516549,0.63863,0.650472,1.49167,1.20739,1.09379,0.630949,0.993294,0.830321,0.459159,0.788782,0.0824127
|tfbs_overrepresentation_jaspar=MA0003.1;0.600426,MA0004.1;0.6888,MA0006.1;0.497533,MA0007.1;0.672186,MA0009.1;1.15569,MA0014.1;0.0809287,MA0017.1;0.528196,MA0019.1;0.964875,MA0024.1;1.11019,MA0025.1;1.39562,MA0027.1;2.81824,MA0028.1;0.509589,MA0029.1;1.08753,MA0030.1;1.09438,MA0031.1;1.05719,MA0038.1;1.97232,MA0040.1;4.2615,MA0041.1;0.604221,MA0042.1;0.589368,MA0043.1;1.25564,MA0046.1;1.1929,MA0048.1;1.35097,MA0050.1;0.731539,MA0051.1;0.856094,MA0052.1;1.17701,MA0055.1;1.28762,MA0056.1;0,MA0057.1;0.251896,MA0058.1;0.581673,MA0059.1;0.59559,MA0060.1;0.403071,MA0061.1;0.438628,MA0063.1;0,MA0066.1;0.834648,MA0067.1;1.50873,MA0068.1;0.256913,MA0069.1;1.17737,MA0070.1;1.16732,MA0071.1;0.73062,MA0072.1;1.15853,MA0073.1;0.0471131,MA0074.1;0.795862,MA0076.1;1.35592,MA0077.1;1.13603,MA0078.1;0.891476,MA0081.1;0.621611,MA0083.1;1.25482,MA0084.1;1.84013,MA0087.1;1.21037,MA0088.1;0.582815,MA0089.1;0,MA0090.1;0.650768,MA0091.1;0.703314,MA0092.1;0.651119,MA0093.1;0.519148,MA0095.1;0,MA0098.1;0,MA0100.1;0.783305,MA0101.1;0.605676,MA0103.1;2.29453,MA0105.1;0.313353,MA0106.1;0.899777,MA0107.1;0.533522,MA0108.2;0.989014,MA0109.1;0,MA0111.1;0.666525,MA0113.1;0.869608,MA0114.1;1.11164,MA0115.1;1.25852,MA0116.1;0.497293,MA0117.1;1.22527,MA0119.1;0.606338,MA0122.1;1.24573,MA0124.1;1.45461,MA0125.1;1.37907,MA0130.1;0,MA0131.1;0.960068,MA0132.1;0,MA0133.1;0,MA0135.1;1.29308,MA0136.1;0.817395,MA0139.1;0.365453,MA0140.1;0.78318,MA0141.1;0.563066,MA0142.1;1.04199,MA0143.1;0.887119,MA0144.1;0.439506,MA0145.1;0.21199,MA0146.1;0.0944145,MA0147.1;0.453952,MA0148.1;0.706718,MA0149.1;0.611881,MA0062.2;0.856416,MA0035.2;0.788288,MA0039.2;0.0959929,MA0138.2;0.951653,MA0002.2;0.368961,MA0137.2;0.559766,MA0104.2;0.386166,MA0047.2;0.845655,MA0112.2;0.211985,MA0065.2;0.609584,MA0150.1;0.67206,MA0151.1;0,MA0152.1;0.84577,MA0153.1;1.31015,MA0154.1;0.263609,MA0155.1;0.230016,MA0156.1;0.549102,MA0157.1;1.0083,MA0158.1;0,MA0159.1;2.0472,MA0160.1;0.71003,MA0161.1;0,MA0162.1;0.346529,MA0163.1;0.0996272,MA0164.1;0.817786,MA0080.2;0.534538,MA0018.2;0.828253,MA0099.2;0.944966,MA0079.2;0.0553806,MA0102.2;1.8929,MA0258.1;0.419871,MA0259.1;0.441366,MA0442.1;0
}}

Latest revision as of 18:17, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr1:123224249..123224267,-p9@Insig2
Mm9::chr2:110154372..110154384,-p7@Bbox1
Mm9::chr2:110154391..110154403,-p9@Bbox1
Mm9::chr2:110154423..110154449,-p6@Bbox1


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:0008336gamma-butyrobetaine dioxygenase activity0.00423663040837316
GO:0006991response to sterol depletion0.00423663040837316
GO:0045329carnitine biosynthetic process0.00423663040837316
GO:0009437carnitine metabolic process0.00635459742497994
GO:0042401biogenic amine biosynthetic process0.0254016766960898
GO:0016706oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, 2-oxoglutarate as one donor, and incorporation of one atom each of oxygen into both donors0.0254016766960898
GO:0042398amino acid derivative biosynthetic process0.0254016766960898
GO:0006767water-soluble vitamin metabolic process0.0283527507694216
GO:0009309amine biosynthetic process0.0283527507694216
GO:0016702oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen0.0283527507694216
GO:0051213dioxygenase activity0.0283527507694216
GO:0016701oxidoreductase activity, acting on single donors with incorporation of molecular oxygen0.0283527507694216
GO:0006766vitamin metabolic process0.0283527507694216
GO:0008203cholesterol metabolic process0.0283527507694216
GO:0016125sterol metabolic process0.0283527507694216
GO:0006576biogenic amine metabolic process0.0283527507694216
GO:0044271nitrogen compound biosynthetic process0.0283527507694216
GO:0006575amino acid derivative metabolic process0.03064404692869
GO:0016705oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen0.0416679741868591
GO:0008202steroid metabolic process0.044316444686879



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
exocrine gland6.31e-1225
exocrine system6.31e-1225
liver2.02e-1022
epithelial sac2.02e-1022
digestive gland2.02e-1022
epithelium of foregut-midgut junction2.02e-1022
anatomical boundary2.02e-1022
hepatobiliary system2.02e-1022
foregut-midgut junction2.02e-1022
hepatic diverticulum2.02e-1022
liver primordium2.02e-1022
septum transversum2.02e-1022
liver bud2.02e-1022
digestive tract diverticulum8.71e-1023
sac8.71e-1023
zone of skin1.29e-085
skin epidermis1.29e-085
skin of body1.29e-085
integument1.29e-085
surface1.29e-085
outer epithelium1.29e-085
integumental system1.29e-085
enveloping layer of ectoderm1.29e-085


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)
MA0003.10.600426
MA0004.10.6888
MA0006.10.497533
MA0007.10.672186
MA0009.11.15569
MA0014.10.0809287
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
MA0038.11.97232
MA0040.14.2615
MA0041.10.604221
MA0042.10.589368
MA0043.11.25564
MA0046.11.1929
MA0048.11.35097
MA0050.10.731539
MA0051.10.856094
MA0052.11.17701
MA0055.11.28762
MA0056.10
MA0057.10.251896
MA0058.10.581673
MA0059.10.59559
MA0060.10.403071
MA0061.10.438628
MA0063.10
MA0066.10.834648
MA0067.11.50873
MA0068.10.256913
MA0069.11.17737
MA0070.11.16732
MA0071.10.73062
MA0072.11.15853
MA0073.10.0471131
MA0074.10.795862
MA0076.11.35592
MA0077.11.13603
MA0078.10.891476
MA0081.10.621611
MA0083.11.25482
MA0084.11.84013
MA0087.11.21037
MA0088.10.582815
MA0089.10
MA0090.10.650768
MA0091.10.703314
MA0092.10.651119
MA0093.10.519148
MA0095.10
MA0098.10
MA0100.10.783305
MA0101.10.605676
MA0103.12.29453
MA0105.10.313353
MA0106.10.899777
MA0107.10.533522
MA0108.20.989014
MA0109.10
MA0111.10.666525
MA0113.10.869608
MA0114.11.11164
MA0115.11.25852
MA0116.10.497293
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
MA0142.11.04199
MA0143.10.887119
MA0144.10.439506
MA0145.10.21199
MA0146.10.0944145
MA0147.10.453952
MA0148.10.706718
MA0149.10.611881
MA0062.20.856416
MA0035.20.788288
MA0039.20.0959929
MA0138.20.951653
MA0002.20.368961
MA0137.20.559766
MA0104.20.386166
MA0047.20.845655
MA0112.20.211985
MA0065.20.609584
MA0150.10.67206
MA0151.10
MA0152.10.84577
MA0153.11.31015
MA0154.10.263609
MA0155.10.230016
MA0156.10.549102
MA0157.11.0083
MA0158.10
MA0159.12.0472
MA0160.10.71003
MA0161.10
MA0162.10.346529
MA0163.10.0996272
MA0164.10.817786
MA0080.20.534538
MA0018.20.828253
MA0099.20.944966
MA0079.20.0553806
MA0102.21.8929
MA0258.10.419871
MA0259.10.441366
MA0442.10
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