Personal tools

MCL coexpression mm9:635: Difference between revisions

From FANTOM5_SSTAR

Jump to: navigation, search
(Created page with "{{MCL_coexpression_mm9|gostat_on_MCL_coexpression=GO:0006096;glycolysis;0.000719686101583094;17448,18293!GO:0006007;glucose catabolic process;0.000719686101583094;17448,18293!...")
 
No edit summary
Line 1: Line 1:
{{MCL_coexpression_mm9|gostat_on_MCL_coexpression=GO:0006096;glycolysis;0.000719686101583094;17448,18293!GO:0006007;glucose catabolic process;0.000719686101583094;17448,18293!GO:0046365;monosaccharide catabolic process;0.000719686101583094;17448,18293!GO:0019320;hexose catabolic process;0.000719686101583094;17448,18293!GO:0046164;alcohol catabolic process;0.000719686101583094;17448,18293!GO:0044275;cellular carbohydrate catabolic process;0.000835044202329801;17448,18293!GO:0016052;carbohydrate catabolic process;0.000852708932219754;17448,18293!GO:0006006;glucose metabolic process;0.00135788563649404;17448,18293!GO:0005739;mitochondrion;0.0017805292280721;17448,18747,18293!GO:0019318;hexose metabolic process;0.0017805292280721;17448,18293!GO:0005996;monosaccharide metabolic process;0.0017805292280721;17448,18293!GO:0050164;oxoglutarate dehydrogenase (NADP+) activity;0.0017805292280721;18293!GO:0004591;oxoglutarate dehydrogenase (succinyl-transferring) activity;0.00305216858660128;18293!GO:0004691;cAMP-dependent protein kinase activity;0.00305216858660128;18747!GO:0044265;cellular macromolecule catabolic process;0.00377011932676117;17448,18293!GO:0030976;thiamin pyrophosphate binding;0.00377011932676117;18293!GO:0030060;L-malate dehydrogenase activity;0.00377011932676117;17448!GO:0044262;cellular carbohydrate metabolic process;0.0039228738921035;17448,18293!GO:0006066;alcohol metabolic process;0.0039228738921035;17448,18293!GO:0004690;cyclic nucleotide-dependent protein kinase activity;0.0042725677946356;18747!GO:0009057;macromolecule catabolic process;0.00468653004588212;17448,18293!GO:0006108;malate metabolic process;0.00485492465245523;17448!GO:0005975;carbohydrate metabolic process;0.00603378529492736;17448,18293!GO:0016624;oxidoreductase activity, acting on the aldehyde or oxo group of donors, disulfide as acceptor;0.00622980388168085;18293!GO:0016615;malate dehydrogenase activity;0.00683461031047704;17448!GO:0044248;cellular catabolic process;0.00711899562963582;17448,18293!GO:0043648;dicarboxylic acid metabolic process;0.00711899562963582;17448!GO:0031594;neuromuscular junction;0.00991357063876156;18747!GO:0009056;catabolic process;0.0106749828994384;17448,18293!GO:0006100;tricarboxylic acid cycle intermediate metabolic process;0.0106749828994384;17448!GO:0051969;regulation of transmission of nerve impulse;0.0133400725415185;18747!GO:0050804;regulation of synaptic transmission;0.0133400725415185;18747!GO:0006099;tricarboxylic acid cycle;0.0145990669148224;17448!GO:0046356;acetyl-CoA catabolic process;0.0145990669148224;17448!GO:0001707;mesoderm formation;0.0145990669148224;18747!GO:0048332;mesoderm morphogenesis;0.0145990669148224;18747!GO:0031644;regulation of neurological process;0.0145990669148224;18747!GO:0009060;aerobic respiration;0.0145990669148224;17448!GO:0001704;formation of primary germ layer;0.0147303354289522;18747!GO:0044444;cytoplasmic part;0.0147303354289522;17448,18747,18293!GO:0009109;coenzyme catabolic process;0.0147303354289522;17448!GO:0016620;oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor;0.0147303354289522;18293!GO:0045333;cellular respiration;0.0148060594833286;17448!GO:0016491;oxidoreductase activity;0.0148060594833286;17448,18293!GO:0051187;cofactor catabolic process;0.0151680576498623;17448!GO:0006084;acetyl-CoA metabolic process;0.0157639835889618;17448!GO:0016903;oxidoreductase activity, acting on the aldehyde or oxo group of donors;0.0172399256059361;18293!GO:0007498;mesoderm development;0.0217541713803542;18747!GO:0007369;gastrulation;0.0269447198396174;18747!GO:0015980;energy derivation by oxidation of organic compounds;0.0281032602653716;17448!GO:0048729;tissue morphogenesis;0.0312938817120633;18747!GO:0019842;vitamin binding;0.0428982228502034;18293!GO:0016616;oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor;0.0440809510405541;17448!GO:0050662;coenzyme binding;0.0456094997535444;18293!GO:0016614;oxidoreductase activity, acting on CH-OH group of donors;0.0459307794156284;17448!}}
{{MCL_coexpression_mm9
|coexpression_dpi_cluster_scores_mean=-0.0959183857982524,0.720835542712653,0.704465792784776,0.832785705659773,0.777317781409097,0.289422898618858,0.323810819779195,-0.216517361990078,-0.107212787775519,-0.104377671844224,-0.222144429223647,-0.221944099856474,-0.216919566777085,-0.217135228320113,-0.102541400365299,-0.125800687376887,-0.112539000088369,-0.277453422541986,-0.254374135168902,-0.242038837237772,0.036072038474689,-0.101692185687918,-0.068236629061184,0.66389153575835,0.60802699350466,0.711459410014734,0.668927114870788,0.59795416047189,0.633123149341475,0.598721892726377,0.394880822049068,-0.0426969850130565,-0.0743555518339443,-0.299979616701059,0.0830246299370188,0.15646777294057,0.123877942552394,-0.0125832998797067,-0.0311498320730635,-0.0814372971177936,-0.0499946265835504,-0.0329301450718827,-0.0659109920412506,-0.133968049096322,-0.125082722875364,-0.0881149911552142,-0.104173861368699,0.146255214011342,0.107834212033433,0.091794307573462,0.0327769539701767,0.139621189886877,-0.309000185366197,-0.124961110047687,-0.152396087257154,-0.0610391940004224,-0.0995859020863694,-0.0209449013885907,-0.0477531313378492,-0.0147078281305229,-0.0573278586821632,-0.0181394402567134,0.00651092669473039,-0.168016508034931,-0.172278686033805,-0.183685254768719,-0.0117182871311352,0.0407159218591585,-0.186888978402639,-0.158811781260209,-0.189201413997073,0.131789156869246,0.124601728289065,-0.171254393399589,-0.17829176276913,-0.188672550370548,0.193886772003694,0.123351250402472,0.13509765286955,-0.086640055837761,-0.0699337387537273,-0.0947557197528039,0.177373008552849,0.0897991028900915,0.0967274668484701,0.08003377563131,0.103160776366711,-0.0160715673599014,-0.0969615815719633,-0.0478794348721848,-0.132778114660469,0.0582281912447856,0.166763589421397,0.16429934155182,0.249012106229509,0.288916058999977,0.454678047747649,-0.110738560119514,-0.11542556991689,-0.102849810872167,-0.0431412025796448,-0.139984365716154,-0.299597225261581,-0.35026643130783,-0.0425986413971172,-0.0410697048781335,-0.0632762507134696,0.390891344163227,-0.308393470298242,-0.00584796895108088,-0.0418177310206283,0.0550155977953421,0.045878681805782,0.0362290067171707,-0.00737752505806585,0.274620983651708,-0.0176716868308296,0.623589790360454,0.0818535942720621,0.220900278293665,0.386893737129054,0.205600535729931,0.381183053872811,0.000226835388560863,-0.0124608328567662,0.693079108190276,-0.16332164202404,-0.0812189387805724,-0.162021553038633,0.0434392620613957,0.0583744479668228,-0.0934578349082521,0.0208649528589533,0.00875652867086304,0.0875540326796928,0.0478216770114723,-0.17483328881861,0.135522752461828,-0.0348175053036492,0.110103948863227,-0.121208245304505,-0.161618939831779,-0.137820753270854,-0.144701018092182,-0.199088201626483,-0.102134496059305,-0.118065873966773,0.067990805228815,-0.0770077720877238,-0.171288156266855,-0.182494523502625,-0.13331407094806,-0.163333220758759,-0.032243648675946,-0.115430124653617,-0.190739919388712,-0.0693600842222327,-0.036889394464916,-0.0581416553111313,0.245028419822017,0.255507116662974,0.270799193546279,0.285767184910446,0.378569458544678,0.389106886713452,0.478307215067555,0.49735423106161,0.49722219438022,0.561274378838888,0.793230698143756,0.862378236925455,0.92374641276706,0.878016608384261,0.810373872799122,0.0180234859352923,-0.131580649709104,0.988312278393251,0.689438070826772,-0.102164201890026,-0.0981732433719918,-0.02531864352321,0.144864310627009,0.177025038295932,0.229195526739575,0.616018209369581,0.338102541427001,0.285838915792509,0.237942595496144,0.246418994327385,0.582423648043272,0.614884348349467,0.666443826649839,-0.056633372778993,-0.0934759918759242,-0.0820978785293692,0.00652073848720705,0.0179994928042434,0.0345043155998074,0.0759425490874869,0.243512264192632,0.302746065167221,0.294875797867377,0.175220723964922,-0.0603047813550426,-0.00625901014698214,-0.0327005482139311,-0.0238725839765367,-0.0164565146525061,0.00446827184384217,-0.0264485140956528,-0.0529065474506096,0.0378364677029917,-0.0698025805295769,0.0273816076787268,0.0407494791099244,0.079736838177554,0.180851616806441,0.254483452208373,-0.1151749156372,-0.0551650204336925,-0.0914388674952102,-0.116831541656378,-0.169684873800962,-0.0975658265176032,-0.0823230358592016,-0.0967854982384488,-0.124068839371751,-0.127080534273597,-0.11651125729619,-0.0291513978533874,-0.0204483736379633,-0.117254359393697,-0.22979392269538,-0.14749000335147,0.0942813340259168,0.0344864068757092,0.193332456499287,0.143125995622857,-0.0787358293034856,0.714311764141989,-0.0690722480107158,-0.0676001771023154,-0.0450679304698655,-0.102628241351423,-0.118144162622331,-0.126046627823694,-0.0519408105550607,-0.0553682188981329,-0.0698725454375105,0.00724270067145826,-0.0210638530728606,-0.108539744740529,-0.130671944990398,-0.0964344673706938,-0.162756809459951,-0.11555501809142,-0.0562157111048611,0.00981058027407817,0.0258856888262036,-0.0157583337985714,0.0826912696497431,-0.191057765391022,-0.0637580020265866,-0.0979957405558209,-0.102467254452497,-0.0830307471763992,-0.151895570677466,-0.138788860213114,-0.0955952004099759,-0.0977606544369869,-0.0782752439128798,-0.129066914079051,-0.0875793812580803,-0.0359914123693361,0.0226355731566512,-0.00662993443364341,-0.0827305174770427,0.0818221189420706,-0.0109158807401988,0.0506171092266367,0.00360165616932146,-0.0600878247771409,0.556395081283781,0.173929175321903,-0.145083594660595,-0.140071576885411,-0.134914172769926,-0.134116370727744,-0.137603986545034,-0.158410405864042,-0.222112547157645,-0.174919168941892,-0.198263789097889,0.338072838602638,-0.158041763389441,-0.098556703425903,-0.0314833963329819,0.00842038755798387,0.0608231844901435,0.0863466578204485,0.057208824383778,0.294476107931569,0.211162303315384,0.0629367562865183,-0.154183841789647,-0.11579906479649,-0.0964349296100309,-0.101732404584577,-0.0611721940666156,-0.104714303575593,-0.126526470458622,-0.112444054217912,-0.0868388691110555,-0.279236075134308,0.0517754509976068,-0.101388346841948,-0.039545659061556,-0.047426772795642,-0.075064328694655,-0.100428334623835,-0.089081996873108,-0.12835680535012,-0.110007170580264,-0.0693617202186673,-0.135322098380727,-0.116161267996312,-0.156524663866011,-0.180972329365585,-0.187340114403218,0.584760085227494,-0.0128590270056056,0.0564003060825085,0.00780432129092916,-0.0604866772256848,-0.0863406361162533,-0.0850416437893568,-0.0482609428369521,-0.126480548041063,0.0644389817052651,0.0985553887769662,0.111593060137866,0.0972849304741621,0.0110778206693804,-0.013438226313476,0.0420289106762828,0.0281647355205304,0.0196082191286838,0.0278683622992845,-0.112421300138307,-0.127047365306853,-0.100508055097995,-0.0701062083327978,-0.0635101887040452,0.112208482506623,0.21692766085212,0.218358367695414,0.216689698979885,0.19781113963241,0.244733097205175,0.218005159424727,0.206282069673322,0.178946373825387,0.209376097871684,0.158051243949403,0.175243133566432,0.180302290709007,0.191826404941551,0.253977755222613,0.235779012309049,0.215954013064333,0.265359405318094,0.218868793039719,0.213479668625818,0.183421555846971,0.196697766905804,0.223143840342138,0.174870762560834,0.22142324915649,0.174037543542148,0.178390499899143,0.20773782039677,0.194667970341978,0.105808553590006,0.0710945421761745,0.186803663561242,0.263158806209921,0.284582569225731,0.345822467863808,0.481922458724753
|gostat_on_MCL_coexpression=GO:0006096;glycolysis;0.000719686101583094;17448,18293!GO:0006007;glucose catabolic process;0.000719686101583094;17448,18293!GO:0046365;monosaccharide catabolic process;0.000719686101583094;17448,18293!GO:0019320;hexose catabolic process;0.000719686101583094;17448,18293!GO:0046164;alcohol catabolic process;0.000719686101583094;17448,18293!GO:0044275;cellular carbohydrate catabolic process;0.000835044202329801;17448,18293!GO:0016052;carbohydrate catabolic process;0.000852708932219754;17448,18293!GO:0006006;glucose metabolic process;0.00135788563649404;17448,18293!GO:0005739;mitochondrion;0.0017805292280721;17448,18747,18293!GO:0019318;hexose metabolic process;0.0017805292280721;17448,18293!GO:0005996;monosaccharide metabolic process;0.0017805292280721;17448,18293!GO:0050164;oxoglutarate dehydrogenase (NADP+) activity;0.0017805292280721;18293!GO:0004591;oxoglutarate dehydrogenase (succinyl-transferring) activity;0.00305216858660128;18293!GO:0004691;cAMP-dependent protein kinase activity;0.00305216858660128;18747!GO:0044265;cellular macromolecule catabolic process;0.00377011932676117;17448,18293!GO:0030976;thiamin pyrophosphate binding;0.00377011932676117;18293!GO:0030060;L-malate dehydrogenase activity;0.00377011932676117;17448!GO:0044262;cellular carbohydrate metabolic process;0.0039228738921035;17448,18293!GO:0006066;alcohol metabolic process;0.0039228738921035;17448,18293!GO:0004690;cyclic nucleotide-dependent protein kinase activity;0.0042725677946356;18747!GO:0009057;macromolecule catabolic process;0.00468653004588212;17448,18293!GO:0006108;malate metabolic process;0.00485492465245523;17448!GO:0005975;carbohydrate metabolic process;0.00603378529492736;17448,18293!GO:0016624;oxidoreductase activity, acting on the aldehyde or oxo group of donors, disulfide as acceptor;0.00622980388168085;18293!GO:0016615;malate dehydrogenase activity;0.00683461031047704;17448!GO:0044248;cellular catabolic process;0.00711899562963582;17448,18293!GO:0043648;dicarboxylic acid metabolic process;0.00711899562963582;17448!GO:0031594;neuromuscular junction;0.00991357063876156;18747!GO:0009056;catabolic process;0.0106749828994384;17448,18293!GO:0006100;tricarboxylic acid cycle intermediate metabolic process;0.0106749828994384;17448!GO:0051969;regulation of transmission of nerve impulse;0.0133400725415185;18747!GO:0050804;regulation of synaptic transmission;0.0133400725415185;18747!GO:0006099;tricarboxylic acid cycle;0.0145990669148224;17448!GO:0046356;acetyl-CoA catabolic process;0.0145990669148224;17448!GO:0001707;mesoderm formation;0.0145990669148224;18747!GO:0048332;mesoderm morphogenesis;0.0145990669148224;18747!GO:0031644;regulation of neurological process;0.0145990669148224;18747!GO:0009060;aerobic respiration;0.0145990669148224;17448!GO:0001704;formation of primary germ layer;0.0147303354289522;18747!GO:0044444;cytoplasmic part;0.0147303354289522;17448,18747,18293!GO:0009109;coenzyme catabolic process;0.0147303354289522;17448!GO:0016620;oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor;0.0147303354289522;18293!GO:0045333;cellular respiration;0.0148060594833286;17448!GO:0016491;oxidoreductase activity;0.0148060594833286;17448,18293!GO:0051187;cofactor catabolic process;0.0151680576498623;17448!GO:0006084;acetyl-CoA metabolic process;0.0157639835889618;17448!GO:0016903;oxidoreductase activity, acting on the aldehyde or oxo group of donors;0.0172399256059361;18293!GO:0007498;mesoderm development;0.0217541713803542;18747!GO:0007369;gastrulation;0.0269447198396174;18747!GO:0015980;energy derivation by oxidation of organic compounds;0.0281032602653716;17448!GO:0048729;tissue morphogenesis;0.0312938817120633;18747!GO:0019842;vitamin binding;0.0428982228502034;18293!GO:0016616;oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor;0.0440809510405541;17448!GO:0050662;coenzyme binding;0.0456094997535444;18293!GO:0016614;oxidoreductase activity, acting on CH-OH group of donors;0.0459307794156284;17448!
}}

Revision as of 11:12, 11 October 2012


Phase1 CAGE Peaks

 Short description
Mm9::chr10:127774817..127774874,+p1@Cs
Mm9::chr11:6191663..6191690,+p2@Ogdh
Mm9::chr4:116230385..116230404,+p5@Gpbp1l1
Mm9::chr5:136254498..136254515,+p3@Mdh2
Mm9::chr5:136254517..136254533,+p1@Mdh2
Mm9::chr5:136254544..136254559,+p2@Mdh2
Mm9::chr5:136254570..136254582,+p4@Mdh2
Mm9::chr7:104727938..104728011,-p1@1810020D17Rik
Mm9::chr8:42101937..42101968,-p5@Mtus1
Mm9::chr9:108839183..108839195,-p@chr9:108839183..108839195
-
Mm9::chr9:108839202..108839231,-p@chr9:108839202..108839231
-


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:0006096glycolysis0.000719686101583094
GO:0006007glucose catabolic process0.000719686101583094
GO:0046365monosaccharide catabolic process0.000719686101583094
GO:0019320hexose catabolic process0.000719686101583094
GO:0046164alcohol catabolic process0.000719686101583094
GO:0044275cellular carbohydrate catabolic process0.000835044202329801
GO:0016052carbohydrate catabolic process0.000852708932219754
GO:0006006glucose metabolic process0.00135788563649404
GO:0005739mitochondrion0.0017805292280721
GO:0019318hexose metabolic process0.0017805292280721
GO:0005996monosaccharide metabolic process0.0017805292280721
GO:0050164oxoglutarate dehydrogenase (NADP+) activity0.0017805292280721
GO:0004591oxoglutarate dehydrogenase (succinyl-transferring) activity0.00305216858660128
GO:0004691cAMP-dependent protein kinase activity0.00305216858660128
GO:0044265cellular macromolecule catabolic process0.00377011932676117
GO:0030976thiamin pyrophosphate binding0.00377011932676117
GO:0030060L-malate dehydrogenase activity0.00377011932676117
GO:0044262cellular carbohydrate metabolic process0.0039228738921035
GO:0006066alcohol metabolic process0.0039228738921035
GO:0004690cyclic nucleotide-dependent protein kinase activity0.0042725677946356
GO:0009057macromolecule catabolic process0.00468653004588212
GO:0006108malate metabolic process0.00485492465245523
GO:0005975carbohydrate metabolic process0.00603378529492736
GO:0016624oxidoreductase activity, acting on the aldehyde or oxo group of donors, disulfide as acceptor0.00622980388168085
GO:0016615malate dehydrogenase activity0.00683461031047704
GO:0044248cellular catabolic process0.00711899562963582
GO:0043648dicarboxylic acid metabolic process0.00711899562963582
GO:0031594neuromuscular junction0.00991357063876156
GO:0009056catabolic process0.0106749828994384
GO:0006100tricarboxylic acid cycle intermediate metabolic process0.0106749828994384
GO:0051969regulation of transmission of nerve impulse0.0133400725415185
GO:0050804regulation of synaptic transmission0.0133400725415185
GO:0006099tricarboxylic acid cycle0.0145990669148224
GO:0046356acetyl-CoA catabolic process0.0145990669148224
GO:0001707mesoderm formation0.0145990669148224
GO:0048332mesoderm morphogenesis0.0145990669148224
GO:0031644regulation of neurological process0.0145990669148224
GO:0009060aerobic respiration0.0145990669148224
GO:0001704formation of primary germ layer0.0147303354289522
GO:0044444cytoplasmic part0.0147303354289522
GO:0009109coenzyme catabolic process0.0147303354289522
GO:0016620oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor0.0147303354289522
GO:0045333cellular respiration0.0148060594833286
GO:0016491oxidoreductase activity0.0148060594833286
GO:0051187cofactor catabolic process0.0151680576498623
GO:0006084acetyl-CoA metabolic process0.0157639835889618
GO:0016903oxidoreductase activity, acting on the aldehyde or oxo group of donors0.0172399256059361
GO:0007498mesoderm development0.0217541713803542
GO:0007369gastrulation0.0269447198396174
GO:0015980energy derivation by oxidation of organic compounds0.0281032602653716
GO:0048729tissue morphogenesis0.0312938817120633
GO:0019842vitamin binding0.0428982228502034
GO:0016616oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor0.0440809510405541
GO:0050662coenzyme binding0.0456094997535444
GO:0016614oxidoreductase activity, acting on CH-OH group of donors0.0459307794156284



Relative expression of the co-expression cluster over median <br>Analyst:



"{{{coexpression_dpi_cluster_scores_median}}}" is not a number.

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>disease_data<br>


Cell Type
Ontology termp-valuen

Uber Anatomy
Ontology termp-valuen

Disease
Ontology termp-valuen


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)

{{{tfbs_overrepresentation_jaspar}}}