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MCL coexpression mm9:886: Difference between revisions

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{{MCL_coexpression_mm9|gostat_on_MCL_coexpression=GO:0030125;clathrin vesicle coat;0.0152668967658284;108800!GO:0030665;clathrin coated vesicle membrane;0.0152668967658284;108800!GO:0030119;AP-type membrane coat adaptor complex;0.0152668967658284;108800!GO:0030120;vesicle coat;0.0152668967658284;108800!GO:0030131;clathrin adaptor complex;0.0152668967658284;108800!GO:0030662;coated vesicle membrane;0.0152668967658284;108800!GO:0030100;regulation of endocytosis;0.0152668967658284;108800!GO:0030118;clathrin coat;0.0152668967658284;108800!GO:0030659;cytoplasmic vesicle membrane;0.0152668967658284;108800!GO:0044433;cytoplasmic vesicle part;0.0155759432590639;108800!GO:0030117;membrane coat;0.0155759432590639;108800!GO:0048475;coated membrane;0.0155759432590639;108800!GO:0012506;vesicle membrane;0.0155759432590639;108800!GO:0030136;clathrin-coated vesicle;0.0191123181316574;108800!GO:0051049;regulation of transport;0.0196611515915192;108800!GO:0030135;coated vesicle;0.0196611515915192;108800!GO:0006461;protein complex assembly;0.0265870880209861;108800!GO:0008565;protein transporter activity;0.0287258715462298;108800!GO:0010324;membrane invagination;0.0303730893551745;108800!GO:0006897;endocytosis;0.0303730893551745;108800!GO:0016023;cytoplasmic membrane-bound vesicle;0.031885169561168;108800!GO:0031988;membrane-bound vesicle;0.031885169561168;108800!GO:0016044;membrane organization and biogenesis;0.0366300715308264;108800!GO:0031410;cytoplasmic vesicle;0.0413040638209104;108800!GO:0012505;endomembrane system;0.0413040638209104;108800!GO:0031982;vesicle;0.0413040638209104;108800!GO:0065003;macromolecular complex assembly;0.0421848463266313;108800!GO:0022607;cellular component assembly;0.0479099326138169;108800!GO:0006886;intracellular protein transport;0.0480034458199597;108800!GO:0016192;vesicle-mediated transport;0.0483317810770832;108800!}}
{{MCL_coexpression_mm9|coexpression_dpi_cluster_scores_mean=0,0.0548153617754631,0.0203578457864595,0.0143457248414071,0,0,0.0113973513578923,0.00659267229832749,0,0,0,0,0.00857891679764385,0.0228917267533174,0.106442109419049,0.180793470617195,0.165470271839224,0.0265542264670491,0.0307129409770493,0,0.0129581330137118,0.0707435987661491,0.0564425752413978,0.00805689404670971,0.0112120609221088,0.0543748920178452,0.0194459244897601,0.046520142868582,0.00944443853967459,0,0,0,0.0260237435676099,0,0,0,0.0100859463841057,0,0,0,0.0251142252531686,0,0,0,0,0,0,0.0107070322567694,0,0,0,0,0,0,0,0,0,0,0.0200046982636228,0,0.0444473096318332,0,0,0,0,0,0,0,0.00535586938535935,0,0,0,0,0,0.00952045478925366,0,0,0,0,0,0.00475235294475781,0,0,0,0,0.0140181490043664,0,0,0.0430887913287838,0.061699745289912,0,0,0,0,0,0,0.0360112936889123,0.0159229555289355,0,0,0,0,0,0,0,0,0,0.0321618063662676,0,0,0.203432012548729,0.0804924995294277,0.0623410118559872,0.0371672358628904,0.0181057517723175,0,0.0737340649191361,0.0137899829462035,0.12618318100297,0.0683214605986442,0.0783259763835422,0.175468395805454,0,0,0,0.0123502327011177,0.00614329111119324,0,0.017532491023663,0.0201474803183595,0,0,0,0,0.010248840796942,0,0,0.0495877510932755,0,0.0103679915937455,0.0797588469170892,0.0317706445093952,0.0166973233622761,0.0484720437210666,0.00357326181938084,0.0224603034804841,0.0134480981339266,0,0.0376743488778794,0.0535442623708037,0.0406075275491468,0.0304938164005514,0.0133183637405749,0.0286943716518449,0.0187125822102766,0.0499834920917195,0,0.0124319329043004,0,0.227925420298291,0.294731033522585,0.0989754859088973,0.0441133972157518,0.0612135939648056,0.0545275094227754,0.0400793405830667,0.0129016105497064,0.0208060351799793,0.00827022662807776,0.0274044962722774,0.0227044995071741,0.0148150998392991,0.0323248693473347,0.0312750532235995,0,0,0.0275408949313843,0.0127377319240807,0.0850132961845066,0.180751204014501,0.0501238706583387,0.0099737633661278,0,0,0,0.0165534214268825,0.0464513832102554,0.0197008540950864,0.0312981189977739,0,0,0,0.00942821797736692,0.0953481072443474,0,0,0,0.00367986264120577,0,0.00747429749119195,0,0,0,1.12146821338778,1.03095917099067,0.961545240972315,0.839164928003356,0.706308144497429,0.523256106455489,0.318573773301544,0.155086855999481,0.162223518603577,0.12191119716611,0.0407003050398465,0.0147432881633845,0,0.00895752137663766,0,0.060221253841191,0.120839175636936,0.0405501701081432,0.024378845086214,0.0228895045139265,0.0221024883427851,0.0347759826678655,0.0467503633958933,0.0440840408558475,0.0307657491166978,0.0487258888050562,0.0574295990795115,0.0472478221265617,0.0417361119222694,0,0,0,0,0,0,0,0,0,0,0.0105909490697472,0,0,0,0,0.013918563692487,0,0,0.0291150024894532,0.00889618449371135,0.00819218754451894,0,0,0.0998285416116977,0.0256724424178741,0.00937969774696677,0,0.0260172057681976,0,0,0,0,0,0,0,0.112604848932194,0.0836466479565098,0,0.00886274819537199,0.00891015519222358,0.0237143490532845,0,0.0289341806350854,0.15495861372669,0,0.0154721686650217,0,0.00618257953313911,0,0.00825069344543005,0.0138859957960851,0,0.137375237118478,0.0530457916302808,0.167820999001423,0.255526813332494,0.193731337331946,0.107602143183793,0,0.00711079452704863,0.00702732140963195,0,0.107746659852591,0.0544222789370482,0.0314215605464595,0.0103072521518129,0.0214441365248236,0.0253118079971607,0.0163362824581821,0,0,0,0,0.0907430164379938,0.0853390813678214,0,0.00659442714518033,0,0.00602400585703865,0,0,0,0,0.0149074448990132,0.108001425382058,0.0894697994392932,0.0687992904891944,0.0778637796832866,0.0253806096736109,0.0330062048087427,0.0398217428339337,0.0284007271476574,0.0485838810048723,0.0251595557975324,0.0229187524029732,0.0308753767249303,0.0180019910656388,0,0,0,0,0.00958868214570406,0.00933754354957456,0,0,0.0220682739294146,0,0,0,0,0,0,0,0,0,0,0.0517172642876114,0.484791209109154,0.390865043944151,0.281230143927694,0.236288550162564,0.0274853613970579,0.0604180694594271,0.110895340556769,0.0722448977454519,0.0244615276944339,0.056705579771456,0.0593184836650496,0.0553122992859234,0.0480883160290967,0.0650592182132531,0,0.0534695076322884,0.034364326734461,0.0326332172545389,0.074476106508932,0.060357208337301,0.0687108620515648,0.0655541507762442,0.0769491578846102,0.0693914713842403,0.0575834704777717,0.0707990597425629,0.0672103298245438,0.0562289247486714,0,0.0745356928138908,0.0628575379823414,0.0186227751808805,0.0564741460857633,0.130632020817978,0,0.0530827830728866,0.0442403351038093,0.0175861527944552,0.0216425781243506,0.0413656641795425|coexpression_dpi_cluster_scores_median=0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.073830516978053,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.205436104810215,0.0577162951573975,0.0450611899487389,0.03048532897689,0,0,0,0,0,0.0325594900422539,0,0.0858449846883365,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0265623655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vesicle coat;0.0152668967658284;108800!GO:0030665;clathrin coated vesicle membrane;0.0152668967658284;108800!GO:0030119;AP-type membrane coat adaptor complex;0.0152668967658284;108800!GO:0030120;vesicle coat;0.0152668967658284;108800!GO:0030131;clathrin adaptor complex;0.0152668967658284;108800!GO:0030662;coated vesicle membrane;0.0152668967658284;108800!GO:0030100;regulation of endocytosis;0.0152668967658284;108800!GO:0030118;clathrin coat;0.0152668967658284;108800!GO:0030659;cytoplasmic vesicle membrane;0.0152668967658284;108800!GO:0044433;cytoplasmic vesicle part;0.0155759432590639;108800!GO:0030117;membrane coat;0.0155759432590639;108800!GO:0048475;coated membrane;0.0155759432590639;108800!GO:0012506;vesicle membrane;0.0155759432590639;108800!GO:0030136;clathrin-coated vesicle;0.0191123181316574;108800!GO:0051049;regulation of transport;0.0196611515915192;108800!GO:0030135;coated vesicle;0.0196611515915192;108800!GO:0006461;protein complex assembly;0.0265870880209861;108800!GO:0008565;protein transporter activity;0.0287258715462298;108800!GO:0010324;membrane invagination;0.0303730893551745;108800!GO:0006897;endocytosis;0.0303730893551745;108800!GO:0016023;cytoplasmic membrane-bound vesicle;0.031885169561168;108800!GO:0031988;membrane-bound vesicle;0.031885169561168;108800!GO:0016044;membrane organization and biogenesis;0.0366300715308264;108800!GO:0031410;cytoplasmic vesicle;0.0413040638209104;108800!GO:0012505;endomembrane system;0.0413040638209104;108800!GO:0031982;vesicle;0.0413040638209104;108800!GO:0065003;macromolecular complex assembly;0.0421848463266313;108800!GO:0022607;cellular component assembly;0.0479099326138169;108800!GO:0006886;intracellular protein transport;0.0480034458199597;108800!GO:0016192;vesicle-mediated transport;0.0483317810770832;108800!|ontology_enrichment_celltype=|ontology_enrichment_disease=|ontology_enrichment_uberon=UBERON:0005172!1.20e-07!49;UBERON:0005173!1.20e-07!49;UBERON:0002417!1.20e-07!49;UBERON:0000916!1.20e-07!49|tfbs_overrepresentation_for_novel_motifs=0.393008,0.0293268,0.367606,0.434198,0.720982,0.448401,0.538088,0.515265,0.535519,0.170907,0.494602,0.526159,0.173454,0.550255,0.275867,0,0.742571,1.30041,0.483643,0.29826,0.332107,0.223663,0.549359,0.717658,0.374936,0.577606,2.09255,0.469052,0.303071,0.376624,0.455168,0.843667,0.250677,0.136998,0.276324,0.0153121,0.242032,0.522578,0.221921,0.195877,0.712303,0.460258,1.19668,0.27776,0.0824666,0.423266,0.662995,0.484612,1.06276,0.305876,0.725127,0.604356,0.362495,0.985264,1.00271,0.557354,0.314394,0.513517,0.145699,0.555328,0.823643,0.613749,0.192045,0.713876,0.568415,0.754324,1.139,1.48833,0.818971,1.34113,0.349355,0.527912,0.0665967,1.03623,0.433216,0.131016,0.42492,0.651651,0.806481,0.892913,0.179489,0.759925,0.612313,0.501608,0.920903,0.025519,0.0299392,0.376919,0.667883,1.65055,1.20871,0.925879,0.856465,0.733735,0.218233,0.585369,0.1711,0.859272,0.663249,0.101559,0.242106,0.843387,0.967837,0.725721,0.724668,0.459825,0.784351,0.480639,0.340849,0.333829,0.386136,0.96962,0.337254,0.499714,1.21576,0.708441,0.0359654,1.11602,0.743872,0.238599,1.04163,0.692953,0.579418,0.650748,1.26989,0.810177,0.546178,0.849691,1.13749,0.740166,0.950857,0.427043,1.10792,0.570914,1.23736,0.220515,0.401212,0.461647,1.18819,2.01886,1.6187,1.14372,0.591394,0.854131,0.718197,2.03014,0.666107,1.9792,1.04134,0.261837,0.120154,0.0553085,0.986833,0.207643,1.39798,1.06851,0.605358,0.782826,0.39061,0.400939,1.1977,0.920047,0.810622,0.998505,0.714896,0.562634,0.676555,1.30183,0.331912|tfbs_overrepresentation_jaspar=MA0003.1;0.00271136,MA0004.1;0.434673,MA0006.1;0.271714,MA0007.1;0.419994,MA0009.1;0.870101,MA0014.1;0.012738,MA0017.1;0.296816,MA0019.1;0.688051,MA0024.1;0.826339,MA0025.1;1.10341,MA0027.1;2.51754,MA0028.1;0.281528,MA0029.1;3.13779,MA0030.1;0.811181,MA0031.1;0.775627,MA0038.1;0.577528,MA0040.1;0.882616,MA0041.1;0.360875,MA0042.1;0.348174,MA0043.1;0.966833,MA0046.1;0.906029,MA0048.1;0.335404,MA0050.1;0.472794,MA0051.1;0.586414,MA0052.1;0.890676,MA0055.1;0.523649,MA0056.1;0,MA0057.1;0.31126,MA0058.1;0.90507,MA0059.1;0.931383,MA0060.1;0.574356,MA0061.1;0.224905,MA0063.1;0,MA0066.1;1.39085,MA0067.1;1.21448,MA0068.1;0.657844,MA0069.1;0.891016,MA0070.1;0.881319,MA0071.1;0.471969,MA0072.1;0.872842,MA0073.1;0.577203,MA0074.1;1.31555,MA0076.1;0.315013,MA0077.1;0.851175,MA0078.1;0.61926,MA0081.1;0.375851,MA0083.1;0.96604,MA0084.1;1.54225,MA0087.1;0.922929,MA0088.1;0.064239,MA0089.1;0,MA0090.1;0.401197,MA0091.1;0.447561,MA0092.1;0.401504,MA0093.1;0.289361,MA0095.1;0,MA0098.1;0,MA0100.1;0.519598,MA0101.1;0.362124,MA0103.1;0.307078,MA0105.1;0.133231,MA0106.1;0.626997,MA0107.1;0.301222,MA0108.2;0.710846,MA0109.1;0,MA0111.1;1.06639,MA0113.1;0.598933,MA0114.1;0.633896,MA0115.1;0.969632,MA0116.1;0.27152,MA0117.1;0.937363,MA0119.1;3.50866,MA0122.1;0.957212,MA0124.1;1.16127,MA0125.1;1.0872,MA0130.1;0,MA0131.1;0.683521,MA0132.1;0,MA0133.1;0,MA0135.1;1.00325,MA0136.1;0.550755,MA0139.1;0.506952,MA0140.1;1.29098,MA0141.1;0.325895,MA0142.1;0.761136,MA0143.1;0.615203,MA0144.1;1.19766,MA0145.1;0.246409,MA0146.1;0.385068,MA0147.1;0.666991,MA0148.1;0.450593,MA0149.1;0.367458,MA0062.2;0.137653,MA0035.2;1.30087,MA0039.2;0.402847,MA0138.2;0.675599,MA0002.2;1.56981,MA0137.2;0.863775,MA0104.2;0.54394,MA0047.2;0.576767,MA0112.2;0.527225,MA0065.2;0.247168,MA0150.1;0.419883,MA0151.1;0,MA0152.1;0.576873,MA0153.1;1.01988,MA0154.1;0.330759,MA0155.1;0.0804339,MA0156.1;0.843735,MA0157.1;0.729116,MA0158.1;0,MA0159.1;0.688775,MA0160.1;0.453546,MA0161.1;0,MA0162.1;0.0211019,MA0163.1;0.0836563,MA0164.1;1.35808,MA0080.2;0.302064,MA0018.2;0.560731,MA0099.2;0.669311,MA0079.2;0.000949666,MA0102.2;1.59466,MA0258.1;1.13923,MA0259.1;0.227035,MA0442.1;0}}

Latest revision as of 16:03, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr11:105018259..105018270,+p@chr11:105018259..105018270
+
Mm9::chr11:75263386..75263400,-p5@Wdr81
Mm9::chr12:92984460..92984529,-p4@Ston2
Mm9::chr16:12704492..12704509,+p@chr16:12704492..12704509
+
Mm9::chr16:93365564..93365588,-p@chr16:93365564..93365588
-
Mm9::chr19:40844025..40844047,-p@chr19:40844025..40844047
-
Mm9::chr1:158143264..158143294,+p@chr1:158143264..158143294
+
Mm9::chr1:88209180..88209184,+p@chr1:88209180..88209184
+


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:0030125clathrin vesicle coat0.0152668967658284
GO:0030665clathrin coated vesicle membrane0.0152668967658284
GO:0030119AP-type membrane coat adaptor complex0.0152668967658284
GO:0030120vesicle coat0.0152668967658284
GO:0030131clathrin adaptor complex0.0152668967658284
GO:0030662coated vesicle membrane0.0152668967658284
GO:0030100regulation of endocytosis0.0152668967658284
GO:0030118clathrin coat0.0152668967658284
GO:0030659cytoplasmic vesicle membrane0.0152668967658284
GO:0044433cytoplasmic vesicle part0.0155759432590639
GO:0030117membrane coat0.0155759432590639
GO:0048475coated membrane0.0155759432590639
GO:0012506vesicle membrane0.0155759432590639
GO:0030136clathrin-coated vesicle0.0191123181316574
GO:0051049regulation of transport0.0196611515915192
GO:0030135coated vesicle0.0196611515915192
GO:0006461protein complex assembly0.0265870880209861
GO:0008565protein transporter activity0.0287258715462298
GO:0010324membrane invagination0.0303730893551745
GO:0006897endocytosis0.0303730893551745
GO:0016023cytoplasmic membrane-bound vesicle0.031885169561168
GO:0031988membrane-bound vesicle0.031885169561168
GO:0016044membrane organization and biogenesis0.0366300715308264
GO:0031410cytoplasmic vesicle0.0413040638209104
GO:0012505endomembrane system0.0413040638209104
GO:0031982vesicle0.0413040638209104
GO:0065003macromolecular complex assembly0.0421848463266313
GO:0022607cellular component assembly0.0479099326138169
GO:0006886intracellular protein transport0.0480034458199597
GO:0016192vesicle-mediated transport0.0483317810770832



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
abdomen element1.20e-0749
abdominal segment element1.20e-0749
abdominal segment of trunk1.20e-0749
abdomen1.20e-0749


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)
MA0003.10.00271136
MA0004.10.434673
MA0006.10.271714
MA0007.10.419994
MA0009.10.870101
MA0014.10.012738
MA0017.10.296816
MA0019.10.688051
MA0024.10.826339
MA0025.11.10341
MA0027.12.51754
MA0028.10.281528
MA0029.13.13779
MA0030.10.811181
MA0031.10.775627
MA0038.10.577528
MA0040.10.882616
MA0041.10.360875
MA0042.10.348174
MA0043.10.966833
MA0046.10.906029
MA0048.10.335404
MA0050.10.472794
MA0051.10.586414
MA0052.10.890676
MA0055.10.523649
MA0056.10
MA0057.10.31126
MA0058.10.90507
MA0059.10.931383
MA0060.10.574356
MA0061.10.224905
MA0063.10
MA0066.11.39085
MA0067.11.21448
MA0068.10.657844
MA0069.10.891016
MA0070.10.881319
MA0071.10.471969
MA0072.10.872842
MA0073.10.577203
MA0074.11.31555
MA0076.10.315013
MA0077.10.851175
MA0078.10.61926
MA0081.10.375851
MA0083.10.96604
MA0084.11.54225
MA0087.10.922929
MA0088.10.064239
MA0089.10
MA0090.10.401197
MA0091.10.447561
MA0092.10.401504
MA0093.10.289361
MA0095.10
MA0098.10
MA0100.10.519598
MA0101.10.362124
MA0103.10.307078
MA0105.10.133231
MA0106.10.626997
MA0107.10.301222
MA0108.20.710846
MA0109.10
MA0111.11.06639
MA0113.10.598933
MA0114.10.633896
MA0115.10.969632
MA0116.10.27152
MA0117.10.937363
MA0119.13.50866
MA0122.10.957212
MA0124.11.16127
MA0125.11.0872
MA0130.10
MA0131.10.683521
MA0132.10
MA0133.10
MA0135.11.00325
MA0136.10.550755
MA0139.10.506952
MA0140.11.29098
MA0141.10.325895
MA0142.10.761136
MA0143.10.615203
MA0144.11.19766
MA0145.10.246409
MA0146.10.385068
MA0147.10.666991
MA0148.10.450593
MA0149.10.367458
MA0062.20.137653
MA0035.21.30087
MA0039.20.402847
MA0138.20.675599
MA0002.21.56981
MA0137.20.863775
MA0104.20.54394
MA0047.20.576767
MA0112.20.527225
MA0065.20.247168
MA0150.10.419883
MA0151.10
MA0152.10.576873
MA0153.11.01988
MA0154.10.330759
MA0155.10.0804339
MA0156.10.843735
MA0157.10.729116
MA0158.10
MA0159.10.688775
MA0160.10.453546
MA0161.10
MA0162.10.0211019
MA0163.10.0836563
MA0164.11.35808
MA0080.20.302064
MA0018.20.560731
MA0099.20.669311
MA0079.20.000949666
MA0102.21.59466
MA0258.11.13923
MA0259.10.227035
MA0442.10
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