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MCL coexpression mm9:1728: Difference between revisions

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{{MCL_coexpression_mm9
{{MCL_coexpression_mm9|coexpression_dpi_cluster_scores_mean=-0.0289332800188934,0.0767163121053041,0.0849779579109191,0.0348643720976065,0.00774773682237466,0.00904405090228974,0.0186773100391853,0.207887021348617,0.946729688599334,0.914779992298101,0.411954884804246,0.430246324898053,0.246361382996135,0.316088221625976,0.2187639393764,0.225936230922122,0.0202012151402586,0.237718430274451,0.29177898539433,0.369051899480621,0.0154376503745073,0.057442447064403,0.117010405540099,0.0020760617241818,-0.00325472622261602,-0.00550796401556632,-0.0179598497068306,0.0462249391541411,-0.0139214393259857,-0.0524106212734703,-0.0226574811828293,0.0934791968847177,0.0730109254022859,-0.0719335773089009,-0.0323285138544748,-0.0276539338529012,-0.0200780134166843,0.0290864480299686,-0.0217844402925209,-0.00970799377743734,0.0956133304152941,0.0249017947582279,-0.0129953399739288,0.130269209724477,0.0995737544727338,0.244573062100223,0.165012809058564,0.162427799562538,0.290212956281965,0.197369049722512,0.161231337595828,0.0731274691077533,0.353867106846179,0.350558165592433,0.404316731337258,0.124519815160552,0.0587231050366823,0.0618652273648126,-0.0204331004371239,0.0267849066696225,0.0133493184032809,0.142795683219727,0.0385863140303746,0.105508539406444,0.107471204754303,0.150636388190455,0.0749455909303954,0.0612561888045915,-0.0194662922620652,-0.0203961525277922,-0.0294441226607081,0.0453053115451051,0.0186926862520242,-0.00247116609521398,-0.0273425343648258,0.0186822921053975,0.0548303084290261,0.0171132222018865,0.0234004363310799,-0.0351347661274953,-0.0197577210984229,-0.00992979984400326,-0.00680040240071822,0.0139615758896173,0.0230953555520499,-0.0169226648001535,0.00496279761241904,0.00059292555271056,1.03224693333061,0.680926125703522,0.275434369503972,0.0150072709615161,0.288044678510089,-0.0344461753048957,-0.0719335773089009,-0.00762292692643914,0.070682654510191,0.352477684424766,0.385944344054032,0.315319216917528,0.0298985144120425,-0.000222322012011178,-0.0719335773089009,-0.0719335773089009,0.238871595230092,0.3616172486647,0.191211815770734,0.0100401574957013,0.311754667241829,-0.0253096844605934,0.0388041289804709,0.0315132319929266,0.0694743829580502,0.0119324982047142,0.0040044044412916,-0.0231276818872366,0.0577313062750932,-0.0381389050811674,0.129087656040541,0.024673148070364,0.0859435688264368,0.0212866607214011,-0.0719335773089009,-0.0719335773089009,-0.0554162300445195,-0.0521732049871125,0.161503745255199,0.0751709818555189,0.0828568911785604,-0.00351519298415402,-0.0154997669637489,-0.0295881991314645,-0.017606065999575,0.0838733191428179,-0.0134522427315392,-0.0128884584046659,0.0550813735126324,0.030078173901401,-0.0719335773089009,0.0806851923233704,0.0158599674896452,0.0434432754742051,0.0060756298599491,0.0494976020202784,-0.0231064457939409,0.00444282950331728,-0.00648547263280862,-0.0220395999251303,0.0340743881742124,0.0122302201402175,0.0192275248324885,0.0362390708442293,-0.0293148133390611,0.0416107202349841,0.0652914222569448,0.0353672110167652,0.0265245963970591,0.0175425435865101,0.0157373269359381,0.0329047021413618,0.0307425962976283,0.0405071355508582,-0.0382641699203613,-0.0431104085458271,-0.0236540312123797,0.0261369445684389,-0.00860979489523236,-0.0223996591390057,-0.0472207583011831,-0.023947478619379,-0.0339965906121975,-0.0403455683936237,0.0316729501330172,-0.0512814515404125,-0.0387778067107278,-0.0334825215471661,-0.0223382302420446,0.0521645665573923,0.00188704206645514,0.159434840606199,-0.0130967738263932,-0.0265413008886043,0.0270416609573016,0.0924005036274672,0.0784545410717218,0.0558335991112982,0.0317200993600866,0.0423031187926515,0.0470224938267226,-0.0162368448727616,0.0303832562657545,-0.00527091563390898,0.00145090256403294,0.03441099783297,-0.00637692041999388,-0.0397332975977055,0.065684430385779,0.0172313963079309,0.00552280270148302,0.00371141764569458,-0.0146923632586591,0.0347266447525717,0.0572732365783366,0.0884711674892907,0.100869077054566,0.105880389139854,0.0930227996007727,0.0774300846392625,0.0380205010798831,0.0371399055958757,0.0133530485560415,0.0698936269639305,0.0457289257347971,0.00386950227141648,0.0558176474499297,-0.0364171731470057,0.0316429331703537,0.0209295717300102,0.0328909431525741,0.00820617810831146,0.0196024809625661,0.0467943891408172,0.0132317347249386,0.00194276792780777,-0.00657758863427968,0.0236053623687828,0.029596398779142,-0.0276823454050834,0.0060278447791892,0.0601916623725454,0.00135432978942247,0.0692557346264074,0.00792891046027046,0.0936670790548723,0.0067917390766144,-0.00843609026953494,0.0127538477915882,-0.0457616876445231,0.172175878435296,-0.036429633176384,0.0612939365375295,0.00977394042352526,-0.00844138574377968,0.0134591167981987,0.0337999043522852,0.0420819426198964,0.0117015746649579,0.00629860215910336,-0.0213350470267938,0.0142836587856466,0.0498666597083668,0.0565482637459072,0.0133344721106912,0.0832470833199817,-0.0719335773089009,0.0058880433024959,-0.0260460187781695,0.01146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metabolic process;0.00468416150769736;74167!GO:0046031;ADP metabolic process;0.00468416150769736;74167!GO:0046032;ADP catabolic process;0.00468416150769736;74167!GO:0046709;IDP catabolic process;0.00468416150769736;74167!GO:0009137;purine nucleoside diphosphate catabolic process;0.00749342659366859;74167!GO:0009181;purine ribonucleoside diphosphate catabolic process;0.00749342659366859;74167!GO:0047631;ADP-ribose diphosphatase activity;0.00749342659366859;74167!GO:0043154;negative regulation of caspase activity;0.00749342659366859;12633!GO:0009179;purine ribonucleoside diphosphate metabolic process;0.00749342659366859;74167!GO:0009135;purine nucleoside diphosphate metabolic process;0.00749342659366859;74167!GO:0009154;purine ribonucleotide catabolic process;0.00780522501817802;74167!GO:0009191;ribonucleoside diphosphate catabolic process;0.00780522501817802;74167!GO:0009185;ribonucleoside diphosphate metabolic process;0.00802779156024886;74167!GO:0009134;nucleoside diphosphate catabolic process;0.00802779156024886;74167!GO:0006195;purine nucleotide catabolic process;0.00819458818282635;74167!GO:0009261;ribonucleotide catabolic process;0.00819458818282635;74167!GO:0017110;nucleoside-diphosphatase activity;0.0110161225902179;74167!GO:0009132;nucleoside diphosphate metabolic process;0.0135231271277465;74167!GO:0030693;caspase activity;0.0137961185645107;12633!GO:0009166;nucleotide catabolic process;0.02058660592066;74167!GO:0007259;JAK-STAT cascade;0.0240556729352763;56708!GO:0043281;regulation of caspase activity;0.0263582653766011;12633!GO:0030183;B cell differentiation;0.0284592064882177;56708!GO:0009150;purine ribonucleotide metabolic 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|gostat_on_MCL_coexpression=GO:0046707;IDP metabolic process;0.00468416150769736;74167!GO:0046031;ADP metabolic process;0.00468416150769736;74167!GO:0046032;ADP catabolic process;0.00468416150769736;74167!GO:0046709;IDP catabolic process;0.00468416150769736;74167!GO:0009137;purine nucleoside diphosphate catabolic process;0.00749342659366859;74167!GO:0009181;purine ribonucleoside diphosphate catabolic process;0.00749342659366859;74167!GO:0047631;ADP-ribose diphosphatase activity;0.00749342659366859;74167!GO:0043154;negative regulation of caspase activity;0.00749342659366859;12633!GO:0009179;purine ribonucleoside diphosphate metabolic process;0.00749342659366859;74167!GO:0009135;purine nucleoside diphosphate metabolic process;0.00749342659366859;74167!GO:0009154;purine ribonucleotide catabolic process;0.00780522501817802;74167!GO:0009191;ribonucleoside diphosphate catabolic process;0.00780522501817802;74167!GO:0009185;ribonucleoside diphosphate metabolic process;0.00802779156024886;74167!GO:0009134;nucleoside diphosphate catabolic process;0.00802779156024886;74167!GO:0006195;purine nucleotide catabolic process;0.00819458818282635;74167!GO:0009261;ribonucleotide catabolic process;0.00819458818282635;74167!GO:0017110;nucleoside-diphosphatase activity;0.0110161225902179;74167!GO:0009132;nucleoside diphosphate metabolic process;0.0135231271277465;74167!GO:0030693;caspase activity;0.0137961185645107;12633!GO:0009166;nucleotide catabolic process;0.02058660592066;74167!GO:0007259;JAK-STAT cascade;0.0240556729352763;56708!GO:0043281;regulation of caspase activity;0.0263582653766011;12633!GO:0030183;B cell differentiation;0.0284592064882177;56708!GO:0009150;purine ribonucleotide metabolic process;0.0497921237927268;74167!
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|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0002384!3.85e-11!46
|tfbs_overrepresentation_for_novel_motifs=1.37236,0.293744,0.529553,0.603273,1.04755,0.618805,0.715644,0.300268,1.51246,1.22306,0.668936,0.702872,0.300533,0.728641,0.424775,0,0.930881,0.397593,0.775038,0.185796,0.489529,0.44579,0.727684,0.404661,0.537749,0.757752,0.274609,0.641282,0.456327,0.645258,0.626183,1.03545,0.395107,0.253145,0.425309,0.791367,0.384813,0.699032,0.360612,0.328675,0.401916,0.631725,0.134724,0.426986,0.84962,0.591277,0.847828,0.658142,0.115788,1.16276,0.912738,1.84811,0.627649,1.18062,1.19842,0.73621,0.469329,0.689304,0.731291,0.734051,1.01481,0.796017,0.865544,0.901018,0.747985,0.943088,1.33705,1.68977,1.00999,1.54147,0.509047,0.827208,0.152094,1.23259,0.257421,0.245132,0.70455,0.835925,0.997094,1.23692,0.830212,0.948899,0.794502,1.44895,1.1148,0.0793594,0.0882907,1.20595,0.852952,1.85284,1.40768,1.11989,1.04863,0.412897,0.937248,0.3366,0.806207,1.05152,0.848095,0.20438,0.384901,1.03517,1.16282,0.913356,0.91226,0.631253,2.23351,0.653843,0.499439,0.491483,0.550229,1.16464,0.495367,0.674448,1.41481,0.399936,0.0998646,0.607321,0.932233,0.380707,1.23809,0.879184,0.759676,0.834976,1.46955,1.00091,0.724289,1.04166,1.33551,0.416189,1.14546,0.595426,1.3055,0.750642,1.43666,0.143464,0.566955,0.633235,1.3869,2.2222,1.82084,1.34183,0.772375,1.04623,0.905521,0.632211,0.851091,2.18247,0.569503,0.408309,0.230371,0.826123,1.18223,0.343194,0.749664,1.26545,0.787153,0.438007,0.555203,0.566652,1.39653,1.11392,1.00137,0.547782,0.90208,2.94037,1.76812,0.701187,2.71086
|tfbs_overrepresentation_jaspar=MA0003.1;0.406907,MA0004.1;2.50003,MA0006.1;0.419915,MA0007.1;0.587678,MA0009.1;1.06266,MA0014.1;0.736185,MA0017.1;0.449113,MA0019.1;0.874061,MA0024.1;1.01759,MA0025.1;1.30092,MA0027.1;2.72141,MA0028.1;0.43138,MA0029.1;0.995171,MA0030.1;1.00195,MA0031.1;0.965177,MA0038.1;0.757669,MA0040.1;1.07552,MA0041.1;0.522007,MA0042.1;0.507715,MA0043.1;1.1618,MA0046.1;1.09955,MA0048.1;0.205696,MA0050.1;1.55615,MA0051.1;0.767098,MA0052.1;1.08379,MA0055.1;0.0851423,MA0056.1;0,MA0057.1;1.06992,MA0058.1;5.52096,MA0059.1;1.27866,MA0060.1;0.330907,MA0061.1;0.364227,MA0063.1;0,MA0066.1;0.746072,MA0067.1;1.41352,MA0068.1;1.08757,MA0069.1;1.08414,MA0070.1;1.07418,MA0071.1;0.644448,MA0072.1;1.06547,MA0073.1;3.29146,MA0074.1;0.708108,MA0076.1;0.470037,MA0077.1;1.04318,MA0078.1;0.801834,MA0081.1;0.53877,MA0083.1;1.16099,MA0084.1;1.74401,MA0087.1;1.11687,MA0088.1;2.0536,MA0089.1;0,MA0090.1;0.566938,MA0091.1;0.617887,MA0092.1;0.567278,MA0093.1;3.97297,MA0095.1;0,MA0098.1;0,MA0100.1;0.695835,MA0101.1;0.523409,MA0103.1;0.460936,MA0105.1;0.248108,MA0106.1;0.809991,MA0107.1;0.454197,MA0108.2;0.897859,MA0109.1;0,MA0111.1;1.4237,MA0113.1;0.780358,MA0114.1;0.361633,MA0115.1;1.16466,MA0116.1;0.419688,MA0117.1;1.13165,MA0119.1;0.524046,MA0122.1;1.15196,MA0124.1;1.35963,MA0125.1;1.28445,MA0130.1;0,MA0131.1;0.869325,MA0132.1;0,MA0133.1;0,MA0135.1;1.19898,MA0136.1;0.729175,MA0139.1;0.8026,MA0140.1;0.695713,MA0141.1;0.482463,MA0142.1;0.950155,MA0143.1;0.797553,MA0144.1;0.365053,MA0145.1;0.157686,MA0146.1;1.74263,MA0147.1;0.986917,MA0148.1;0.621195,MA0149.1;2.25784,MA0062.2;0.254018,MA0035.2;0.700704,MA0039.2;0.140205,MA0138.2;2.00218,MA0002.2;0.809945,MA0137.2;0.479301,MA0104.2;0.845917,MA0047.2;0.75686,MA0112.2;0.927461,MA0065.2;2.13004,MA0150.1;0.587557,MA0151.1;0,MA0152.1;0.756973,MA0153.1;1.21594,MA0154.1;0.203217,MA0155.1;0.99229,MA0156.1;0.469089,MA0157.1;0.91689,MA0158.1;0,MA0159.1;1.01146,MA0160.1;0.624415,MA0161.1;0,MA0162.1;0.245828,MA0163.1;7.58347,MA0164.1;0.729558,MA0080.2;0.455167,MA0018.2;0.739807,MA0099.2;0.854449,MA0079.2;10.2544,MA0102.2;1.79669,MA0258.1;0.346619,MA0259.1;0.366802,MA0442.1;0
}}

Latest revision as of 17:24, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr19:4214351..4214363,+p4@Clcf1
Mm9::chr19:4214367..4214375,+p5@Clcf1
Mm9::chr19:4214383..4214397,+p2@Clcf1
Mm9::chr1:58782908..58782919,+p@chr1:58782908..58782919
+
Mm9::chr5:104475807..104475829,+p4@Nudt9


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:0046707IDP metabolic process0.00468416150769736
GO:0046031ADP metabolic process0.00468416150769736
GO:0046032ADP catabolic process0.00468416150769736
GO:0046709IDP catabolic process0.00468416150769736
GO:0009137purine nucleoside diphosphate catabolic process0.00749342659366859
GO:0009181purine ribonucleoside diphosphate catabolic process0.00749342659366859
GO:0047631ADP-ribose diphosphatase activity0.00749342659366859
GO:0043154negative regulation of caspase activity0.00749342659366859
GO:0009179purine ribonucleoside diphosphate metabolic process0.00749342659366859
GO:0009135purine nucleoside diphosphate metabolic process0.00749342659366859
GO:0009154purine ribonucleotide catabolic process0.00780522501817802
GO:0009191ribonucleoside diphosphate catabolic process0.00780522501817802
GO:0009185ribonucleoside diphosphate metabolic process0.00802779156024886
GO:0009134nucleoside diphosphate catabolic process0.00802779156024886
GO:0006195purine nucleotide catabolic process0.00819458818282635
GO:0009261ribonucleotide catabolic process0.00819458818282635
GO:0017110nucleoside-diphosphatase activity0.0110161225902179
GO:0009132nucleoside diphosphate metabolic process0.0135231271277465
GO:0030693caspase activity0.0137961185645107
GO:0009166nucleotide catabolic process0.02058660592066
GO:0007259JAK-STAT cascade0.0240556729352763
GO:0043281regulation of caspase activity0.0263582653766011
GO:0030183B cell differentiation0.0284592064882177
GO:0009150purine ribonucleotide metabolic process0.0497921237927268



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
motile cell3.21e-1454
lymphoid lineage restricted progenitor cell6.76e-1212
connective tissue cell3.85e-1146
mesenchymal cell3.85e-1146
T cell6.14e-1111
pro-T cell6.14e-1111
lymphocyte1.20e-1013
common lymphoid progenitor1.20e-1013
mature alpha-beta T cell1.59e-109
alpha-beta T cell1.59e-109
immature T cell1.59e-109
mature T cell1.59e-109
immature alpha-beta T cell1.59e-109
hematopoietic lineage restricted progenitor cell6.59e-1025
CD4-positive, alpha-beta T cell1.61e-098
hematopoietic cell1.78e-0832
hematopoietic oligopotent progenitor cell1.78e-0832
hematopoietic stem cell1.78e-0832
angioblastic mesenchymal cell1.78e-0832
hematopoietic multipotent progenitor cell1.78e-0832
leukocyte3.34e-0817
nongranular leukocyte3.34e-0817
nucleate cell7.08e-0816
thymocyte9.92e-086
double negative thymocyte9.92e-086
naive T cell9.92e-086
double-positive, alpha-beta thymocyte9.92e-086
CD4-positive, alpha-beta thymocyte9.92e-086
naive thymus-derived CD4-positive, alpha-beta T cell9.92e-086
DN4 thymocyte9.92e-086
DN1 thymic pro-T cell9.92e-086
DN2 thymocyte9.92e-086
DN3 thymocyte9.92e-086
immature single positive thymocyte9.92e-086
early T lineage precursor9.92e-086
mature CD4 single-positive thymocyte9.92e-086
resting double-positive thymocyte9.92e-086
double-positive blast9.92e-086
CD69-positive double-positive thymocyte9.92e-086
CD69-positive, CD4-positive single-positive thymocyte9.92e-086
CD4-positive, CD8-intermediate double-positive thymocyte9.92e-086
CD24-positive, CD4 single-positive thymocyte9.92e-086

Uber Anatomy
Ontology termp-valuen
connective tissue3.85e-1146


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)
MA0003.10.406907
MA0004.12.50003
MA0006.10.419915
MA0007.10.587678
MA0009.11.06266
MA0014.10.736185
MA0017.10.449113
MA0019.10.874061
MA0024.11.01759
MA0025.11.30092
MA0027.12.72141
MA0028.10.43138
MA0029.10.995171
MA0030.11.00195
MA0031.10.965177
MA0038.10.757669
MA0040.11.07552
MA0041.10.522007
MA0042.10.507715
MA0043.11.1618
MA0046.11.09955
MA0048.10.205696
MA0050.11.55615
MA0051.10.767098
MA0052.11.08379
MA0055.10.0851423
MA0056.10
MA0057.11.06992
MA0058.15.52096
MA0059.11.27866
MA0060.10.330907
MA0061.10.364227
MA0063.10
MA0066.10.746072
MA0067.11.41352
MA0068.11.08757
MA0069.11.08414
MA0070.11.07418
MA0071.10.644448
MA0072.11.06547
MA0073.13.29146
MA0074.10.708108
MA0076.10.470037
MA0077.11.04318
MA0078.10.801834
MA0081.10.53877
MA0083.11.16099
MA0084.11.74401
MA0087.11.11687
MA0088.12.0536
MA0089.10
MA0090.10.566938
MA0091.10.617887
MA0092.10.567278
MA0093.13.97297
MA0095.10
MA0098.10
MA0100.10.695835
MA0101.10.523409
MA0103.10.460936
MA0105.10.248108
MA0106.10.809991
MA0107.10.454197
MA0108.20.897859
MA0109.10
MA0111.11.4237
MA0113.10.780358
MA0114.10.361633
MA0115.11.16466
MA0116.10.419688
MA0117.11.13165
MA0119.10.524046
MA0122.11.15196
MA0124.11.35963
MA0125.11.28445
MA0130.10
MA0131.10.869325
MA0132.10
MA0133.10
MA0135.11.19898
MA0136.10.729175
MA0139.10.8026
MA0140.10.695713
MA0141.10.482463
MA0142.10.950155
MA0143.10.797553
MA0144.10.365053
MA0145.10.157686
MA0146.11.74263
MA0147.10.986917
MA0148.10.621195
MA0149.12.25784
MA0062.20.254018
MA0035.20.700704
MA0039.20.140205
MA0138.22.00218
MA0002.20.809945
MA0137.20.479301
MA0104.20.845917
MA0047.20.75686
MA0112.20.927461
MA0065.22.13004
MA0150.10.587557
MA0151.10
MA0152.10.756973
MA0153.11.21594
MA0154.10.203217
MA0155.10.99229
MA0156.10.469089
MA0157.10.91689
MA0158.10
MA0159.11.01146
MA0160.10.624415
MA0161.10
MA0162.10.245828
MA0163.17.58347
MA0164.10.729558
MA0080.20.455167
MA0018.20.739807
MA0099.20.854449
MA0079.210.2544
MA0102.21.79669
MA0258.10.346619
MA0259.10.366802
MA0442.10
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