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MCL coexpression mm9:321: Difference between revisions

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{{MCL_coexpression_mm9|gostat_on_MCL_coexpression=GO:0043283;biopolymer metabolic process;0.00794587097948635;22751,27223,59026,76580,242466,15441,54169,232906,101739,22693,224170,30944,52206!GO:0003677;DNA binding;0.00794587097948635;22751,27223,59026,15441,54169,232906,101739,22693,30944!GO:0043170;macromolecule metabolic process;0.0113426159567994;22751,27223,59026,76580,242466,15441,226432,54169,232906,101739,22693,224170,30944,52206!GO:0005634;nucleus;0.0113426159567994;22751,27223,59026,242466,15441,228876,226432,54169,232906,101739,22693,30944!GO:0003676;nucleic acid binding;0.0113426159567994;22751,27223,59026,15441,54169,232906,101739,224170,22693,30944!GO:0006355;regulation of transcription, DNA-dependent;0.0116253998330533;22751,27223,242466,54169,232906,101739,22693,30944!GO:0006351;transcription, DNA-dependent;0.0116253998330533;22751,27223,242466,54169,232906,101739,22693,30944!GO:0032774;RNA biosynthetic process;0.0116253998330533;22751,27223,242466,54169,232906,101739,22693,30944!GO:0008270;zinc ion binding;0.0116253998330533;22751,235315,76580,228876,54169,224170,22693,30944!GO:0045449;regulation of transcription;0.0121275033569461;22751,27223,242466,54169,232906,101739,22693,30944!GO:0019219;regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process;0.0125967280283161;22751,27223,242466,54169,232906,101739,22693,30944!GO:0006350;transcription;0.0126131748376515;22751,27223,242466,54169,232906,101739,22693,30944!GO:0010468;regulation of gene expression;0.0145568400482656;22751,27223,242466,54169,232906,101739,22693,30944!GO:0031323;regulation of cellular metabolic process;0.0176996880778582;22751,27223,242466,54169,232906,101739,22693,30944!GO:0006512;ubiquitin cycle;0.0189891975018616;76580,224170,59026,52206!GO:0019222;regulation of metabolic process;0.0196114607507608;22751,27223,242466,54169,232906,101739,22693,30944!GO:0044238;primary metabolic process;0.0196114607507608;22751,27223,59026,76580,242466,15441,226432,54169,232906,101739,22693,224170,30944,52206!GO:0044237;cellular metabolic process;0.0196114607507608;22751,27223,59026,76580,242466,15441,226432,54169,232906,101739,22693,224170,30944,52206!GO:0016070;RNA metabolic process;0.0197265385463275;22751,27223,242466,54169,232906,101739,22693,30944!GO:0046914;transition metal ion binding;0.0222689625102905;22751,235315,76580,228876,54169,224170,22693,30944!GO:0006139;nucleobase, nucleoside, nucleotide and nucleic acid metabolic process;0.0234264727644384;22751,27223,15441,242466,54169,232906,101739,22693,30944!GO:0051100;negative regulation of binding;0.0234264727644384;242466!GO:0043392;negative regulation of DNA binding;0.0234264727644384;242466!GO:0004406;H3/H4 histone acetyltransferase activity;0.0323117080144102;54169!GO:0044427;chromosomal part;0.0385349237162417;27223,15441,54169!GO:0065003;macromolecular complex assembly;0.0407551671595038;15441,54169,226432!GO:0006334;nucleosome assembly;0.0407551671595038;15441,54169!GO:0010467;gene expression;0.0407551671595038;22751,27223,242466,54169,232906,101739,22693,30944!GO:0016874;ligase activity;0.0407551671595038;76580,224170,59026!GO:0004842;ubiquitin-protein ligase activity;0.0407551671595038;76580,59026!GO:0000786;nucleosome;0.0407551671595038;15441,54169!GO:0006610;ribosomal protein import into nucleus;0.0407551671595038;226432!GO:0008639;small protein conjugating enzyme activity;0.0413391853083521;76580,59026!GO:0031497;chromatin assembly;0.0416704877530539;15441,54169!GO:0005694;chromosome;0.0437425671811541;27223,15441,54169!GO:0043231;intracellular membrane-bound organelle;0.0437425671811541;22751,27223,59026,76580,242466,228876,15441,226432,54169,232906,101739,22693,30944!GO:0019787;small conjugating protein ligase activity;0.0437425671811541;76580,59026!GO:0043227;membrane-bound organelle;0.0437425671811541;22751,27223,59026,76580,242466,228876,15441,226432,54169,232906,101739,22693,30944!GO:0022607;cellular component assembly;0.0437425671811541;15441,54169,226432!GO:0033036;macromolecule localization;0.0437425671811541;226432,20844,99683,59026!GO:0065004;protein-DNA complex assembly;0.0437425671811541;15441,54169!GO:0008536;Ran GTPase binding;0.0437425671811541;226432!GO:0016881;acid-amino acid ligase activity;0.0467068866387382;76580,59026!GO:0050821;protein stabilization;0.0467068866387382;226432!GO:0042393;histone binding;0.0467068866387382;226432!GO:0006333;chromatin assembly or disassembly;0.0467102769164932;15441,54169!GO:0043687;post-translational protein modification;0.0483164904506294;76580,54169,224170,59026,52206!GO:0031647;regulation of protein stability;0.0483164904506294;226432!GO:0016573;histone acetylation;0.0483164904506294;54169!}}
{{MCL_coexpression_mm9
|coexpression_dpi_cluster_scores_mean=0.203810100501028,-0.552102389529675,-0.495243495146797,-0.544174374067569,-0.589667760854877,-0.362269849556238,-0.411109373091112,-0.291979659095553,-0.428500731028361,-0.395665887748717,-0.459371820558574,-0.461146755928185,-0.330063173893671,-0.331169543933575,-0.338427111088365,-0.365102343333282,-0.424384980978408,-0.330806468454985,-0.318237375119139,-0.4098332932301,-0.0480251450430084,-0.224586406063324,-0.248000583590228,-0.453583197497872,-0.45755387523052,-0.498256386383681,-0.526892116025507,-0.474562817981223,-0.524413738846744,-0.453223326202271,-0.465842305184959,-0.44917182979497,-0.493019782585864,-0.721477767538629,-0.36665699493532,-0.397822293315648,-0.36012025389503,-0.459307925960012,-0.451815054675849,-0.44763950711289,-0.475052729189904,-0.528012259703127,-0.494858747758195,-0.0344748532165553,-0.0618773161006327,-0.0302981369872693,-0.159451475242696,-0.139904644948463,-0.207709048361505,-0.122371038093235,-0.156849612616214,-0.297271593767742,-0.357188153015803,-0.344827273588455,-0.30064643481749,-0.186055547745116,-0.0855844846121474,-0.154235059337448,0.393979021171501,0.305877520980363,0.355952091336639,-0.229638181284283,-0.203337670068703,-0.474481076564315,-0.513705451962062,-0.515386388934236,-0.253094572102152,-0.19887805503391,0.442023742240761,0.370360891418631,0.374205351364094,0.221298444942099,0.179646611423697,0.400184256342276,0.411907442683085,0.330863820731245,0.154193952119972,0.200875308649005,0.195581120310175,0.388604605285583,0.410597161189901,0.454961903675804,0.0397128734089568,0.146623999550049,0.213114764090586,0.36033425377791,0.372891100952775,0.418722721892129,-0.174979599347805,-0.0798373683702459,-0.0536873030674632,-0.347272770003596,-0.506076562715109,-0.444327494738802,-0.387357465489179,-0.430874491329458,-0.268836360256605,-0.139763294479447,-0.213485420134852,-0.239090626591185,0.119364874381029,-0.0776357290811728,-0.0178542094040837,-0.0674215283768771,-0.341449116166059,-0.363986602431752,-0.399207694421705,-0.296808154465505,-0.178432199132006,-0.0091330908149917,0.105194241235195,0.0126490465031933,0.014847020137695,0.0131796090245436,0.0961153966747999,-0.0803887341382237,-0.224088391109854,-0.17495489748303,-0.365220900679177,0.0353557347866323,-0.143510971887359,-0.176721665810818,-0.451080675883222,0.164595685570092,0.224047823200204,-0.384393275408925,-0.26905307570309,-0.324925783536625,-0.304747824555529,0.242740539621089,0.199321071788604,0.448418320234817,0.180030470571972,0.196377213736693,0.179545404105525,0.20728433450767,0.260127556495813,-0.0954976330581817,-0.215273709599495,-0.0456692249062936,0.300484962878994,0.265873401888955,0.291876116980416,0.310410708807507,0.389755151580323,0.341728043442786,0.363254555845958,0.123501770883013,0.276134546674561,0.39881104704077,0.369170145371537,0.197018507297318,0.249443913798346,0.121979491544978,0.0899377807434213,0.286584757502034,-0.406972200569214,-0.337631027145203,-0.343661757593987,0.105522902239228,0.147895047128203,0.110913160918886,0.156041264207819,0.121858160517373,0.0966081813471991,0.0413574671134171,0.0104422255236245,0.0511407027206647,0.0398876808970369,-0.0102653874978024,-0.0548976080842863,-0.113122710608129,-0.112550694886664,-0.0891655391807862,0.202736680701245,0.447420245869584,-0.490122760621689,-0.430811659384021,0.293771424654379,0.302314039227141,0.136075092499302,0.0346668449461638,-0.0265291940811551,-0.119850636599459,-0.287977178206281,-0.179752849535238,-0.15888781930162,-0.115319110756269,-0.10111553256367,-0.272065964760666,-0.338903587950287,-0.300520365887873,0.0907912929205043,0.221176030672944,0.153397654305682,0.168630641785166,0.161035416834814,0.17273047787325,0.111047862688742,-0.0952071182495054,-0.122374436796297,-0.165541085088657,-0.367056380752889,-0.143323225155014,-0.169294690361655,-0.288363523130268,-0.273751215223718,-0.266643374155512,-0.255259322706001,-0.265360567835745,-0.265888946646888,-0.287312816555883,-0.222129560308734,-0.191882267433099,-0.203440653602622,-0.305522328453826,-0.32666395560457,-0.338598167872722,-0.117994369433299,0.210368445742612,0.251380176566294,0.206707635848306,0.183285769792061,0.122510775450584,0.0700800477880559,0.0322433078381707,0.126358241476486,0.110306510355503,0.123674663314811,-0.0669471626065148,-0.0665460502064513,-0.0682238167914245,-0.439249814944129,-0.388886405899344,-0.333530075419564,-0.241306659497771,0.124557851358471,0.165268313172883,-0.0246636889322677,-0.16817140329127,0.210966806364401,0.158468482288092,0.257740809647205,0.198621915001535,0.22868471689468,0.288343224958223,0.247321557730405,0.226847644218796,0.219369919343272,0.302578035964715,0.0778568639315274,0.193178978500912,0.275581978725529,0.10975864374864,-0.472282470548125,0.0880629475461007,0.0147799293983593,-0.0922775000931214,-0.154192277639002,-0.0388323988388746,-0.0569538414304655,-0.0225940422483291,-0.0218928502190454,-0.183247243161607,-0.302382062848771,-0.3694305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|gostat_on_MCL_coexpression=GO:0043283;biopolymer metabolic process;0.00794587097948635;22751,27223,59026,76580,242466,15441,54169,232906,101739,22693,224170,30944,52206!GO:0003677;DNA binding;0.00794587097948635;22751,27223,59026,15441,54169,232906,101739,22693,30944!GO:0043170;macromolecule metabolic process;0.0113426159567994;22751,27223,59026,76580,242466,15441,226432,54169,232906,101739,22693,224170,30944,52206!GO:0005634;nucleus;0.0113426159567994;22751,27223,59026,242466,15441,228876,226432,54169,232906,101739,22693,30944!GO:0003676;nucleic acid binding;0.0113426159567994;22751,27223,59026,15441,54169,232906,101739,224170,22693,30944!GO:0006355;regulation of transcription, DNA-dependent;0.0116253998330533;22751,27223,242466,54169,232906,101739,22693,30944!GO:0006351;transcription, DNA-dependent;0.0116253998330533;22751,27223,242466,54169,232906,101739,22693,30944!GO:0032774;RNA biosynthetic process;0.0116253998330533;22751,27223,242466,54169,232906,101739,22693,30944!GO:0008270;zinc ion binding;0.0116253998330533;22751,235315,76580,228876,54169,224170,22693,30944!GO:0045449;regulation of transcription;0.0121275033569461;22751,27223,242466,54169,232906,101739,22693,30944!GO:0019219;regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process;0.0125967280283161;22751,27223,242466,54169,232906,101739,22693,30944!GO:0006350;transcription;0.0126131748376515;22751,27223,242466,54169,232906,101739,22693,30944!GO:0010468;regulation of gene expression;0.0145568400482656;22751,27223,242466,54169,232906,101739,22693,30944!GO:0031323;regulation of cellular metabolic process;0.0176996880778582;22751,27223,242466,54169,232906,101739,22693,30944!GO:0006512;ubiquitin cycle;0.0189891975018616;76580,224170,59026,52206!GO:0019222;regulation of metabolic process;0.0196114607507608;22751,27223,242466,54169,232906,101739,22693,30944!GO:0044238;primary metabolic process;0.0196114607507608;22751,27223,59026,76580,242466,15441,226432,54169,232906,101739,22693,224170,30944,52206!GO:0044237;cellular metabolic process;0.0196114607507608;22751,27223,59026,76580,242466,15441,226432,54169,232906,101739,22693,224170,30944,52206!GO:0016070;RNA metabolic process;0.0197265385463275;22751,27223,242466,54169,232906,101739,22693,30944!GO:0046914;transition metal ion binding;0.0222689625102905;22751,235315,76580,228876,54169,224170,22693,30944!GO:0006139;nucleobase, nucleoside, nucleotide and nucleic acid metabolic process;0.0234264727644384;22751,27223,15441,242466,54169,232906,101739,22693,30944!GO:0051100;negative regulation of binding;0.0234264727644384;242466!GO:0043392;negative regulation of DNA binding;0.0234264727644384;242466!GO:0004406;H3/H4 histone acetyltransferase activity;0.0323117080144102;54169!GO:0044427;chromosomal part;0.0385349237162417;27223,15441,54169!GO:0065003;macromolecular complex assembly;0.0407551671595038;15441,54169,226432!GO:0006334;nucleosome assembly;0.0407551671595038;15441,54169!GO:0010467;gene expression;0.0407551671595038;22751,27223,242466,54169,232906,101739,22693,30944!GO:0016874;ligase activity;0.0407551671595038;76580,224170,59026!GO:0004842;ubiquitin-protein ligase activity;0.0407551671595038;76580,59026!GO:0000786;nucleosome;0.0407551671595038;15441,54169!GO:0006610;ribosomal protein import into nucleus;0.0407551671595038;226432!GO:0008639;small protein conjugating enzyme activity;0.0413391853083521;76580,59026!GO:0031497;chromatin assembly;0.0416704877530539;15441,54169!GO:0005694;chromosome;0.0437425671811541;27223,15441,54169!GO:0043231;intracellular membrane-bound organelle;0.0437425671811541;22751,27223,59026,76580,242466,228876,15441,226432,54169,232906,101739,22693,30944!GO:0019787;small conjugating protein ligase activity;0.0437425671811541;76580,59026!GO:0043227;membrane-bound organelle;0.0437425671811541;22751,27223,59026,76580,242466,228876,15441,226432,54169,232906,101739,22693,30944!GO:0022607;cellular component assembly;0.0437425671811541;15441,54169,226432!GO:0033036;macromolecule localization;0.0437425671811541;226432,20844,99683,59026!GO:0065004;protein-DNA complex assembly;0.0437425671811541;15441,54169!GO:0008536;Ran GTPase binding;0.0437425671811541;226432!GO:0016881;acid-amino acid ligase activity;0.0467068866387382;76580,59026!GO:0050821;protein stabilization;0.0467068866387382;226432!GO:0042393;histone binding;0.0467068866387382;226432!GO:0006333;chromatin assembly or disassembly;0.0467102769164932;15441,54169!GO:0043687;post-translational protein modification;0.0483164904506294;76580,54169,224170,59026,52206!GO:0031647;regulation of protein stability;0.0483164904506294;226432!GO:0016573;histone acetylation;0.0483164904506294;54169!
}}

Revision as of 11:06, 11 October 2012


Phase1 CAGE Peaks

 Short description
Mm9::chr10:62486608..62486619,-p2@Hnrnph3
Mm9::chr11:50641183..50641244,-p1@Zfp354c
Mm9::chr14:22319053..22319105,+p2@Myst4
Mm9::chr16:48994044..48994062,-p1@Dzip3
Mm9::chr18:65740410..65740452,+p@chr18:65740410..65740452
+
Mm9::chr1:137327004..137327065,-p1@Ipo9
Mm9::chr2:121097091..121097133,-p1@Trp53bp1
Mm9::chr2:13995774..13995818,+p2@Stam
Mm9::chr2:165213745..165213815,-p1@Zfp334
Mm9::chr3:129763728..129763744,-p4@Sec24b
Mm9::chr4:137772539..137772565,+p1@Hp1bp3
Mm9::chr4:155043228..155043272,-p2@Mib2
Mm9::chr4:54960870..54960926,+p1@Zfp462
Mm9::chr4:83132361..83132382,-p2@Psip1
Mm9::chr5:111308807..111308861,+p1@Ttc28
Mm9::chr5:31754831..31754876,+p1@Zfp512
Mm9::chr5:53225284..53225351,+p2@Anapc4
Mm9::chr7:17199897..17199955,-p1@Grlf1
Mm9::chr7:30568977..30569047,+p1@Zfp30
Mm9::chr8:108939219..108939296,+p1@Zfp90
Mm9::chr8:86707764..86707815,-p@chr8:86707764..86707815
-
Mm9::chr9:45714452..45714520,-p1@Rnf214
Mm9::chrX:143988594..143988630,-p1@Lrch2
Mm9::chrX:148235416..148235455,+p2@Huwe1
Mm9::chrX:148235556..148235626,+p5@Huwe1


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:0043283biopolymer metabolic process0.00794587097948635
GO:0003677DNA binding0.00794587097948635
GO:0043170macromolecule metabolic process0.0113426159567994
GO:0005634nucleus0.0113426159567994
GO:0003676nucleic acid binding0.0113426159567994
GO:0006355regulation of transcription, DNA-dependent0.0116253998330533
GO:0006351transcription, DNA-dependent0.0116253998330533
GO:0032774RNA biosynthetic process0.0116253998330533
GO:0008270zinc ion binding0.0116253998330533
GO:0045449regulation of transcription0.0121275033569461
GO:0019219regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process0.0125967280283161
GO:0006350transcription0.0126131748376515
GO:0010468regulation of gene expression0.0145568400482656
GO:0031323regulation of cellular metabolic process0.0176996880778582
GO:0006512ubiquitin cycle0.0189891975018616
GO:0019222regulation of metabolic process0.0196114607507608
GO:0044238primary metabolic process0.0196114607507608
GO:0044237cellular metabolic process0.0196114607507608
GO:0016070RNA metabolic process0.0197265385463275
GO:0046914transition metal ion binding0.0222689625102905
GO:0006139nucleobase, nucleoside, nucleotide and nucleic acid metabolic process0.0234264727644384
GO:0051100negative regulation of binding0.0234264727644384
GO:0043392negative regulation of DNA binding0.0234264727644384
GO:0004406H3/H4 histone acetyltransferase activity0.0323117080144102
GO:0044427chromosomal part0.0385349237162417
GO:0065003macromolecular complex assembly0.0407551671595038
GO:0006334nucleosome assembly0.0407551671595038
GO:0010467gene expression0.0407551671595038
GO:0016874ligase activity0.0407551671595038
GO:0004842ubiquitin-protein ligase activity0.0407551671595038
GO:0000786nucleosome0.0407551671595038
GO:0006610ribosomal protein import into nucleus0.0407551671595038
GO:0008639small protein conjugating enzyme activity0.0413391853083521
GO:0031497chromatin assembly0.0416704877530539
GO:0005694chromosome0.0437425671811541
GO:0043231intracellular membrane-bound organelle0.0437425671811541
GO:0019787small conjugating protein ligase activity0.0437425671811541
GO:0043227membrane-bound organelle0.0437425671811541
GO:0022607cellular component assembly0.0437425671811541
GO:0033036macromolecule localization0.0437425671811541
GO:0065004protein-DNA complex assembly0.0437425671811541
GO:0008536Ran GTPase binding0.0437425671811541
GO:0016881acid-amino acid ligase activity0.0467068866387382
GO:0050821protein stabilization0.0467068866387382
GO:0042393histone binding0.0467068866387382
GO:0006333chromatin assembly or disassembly0.0467102769164932
GO:0043687post-translational protein modification0.0483164904506294
GO:0031647regulation of protein stability0.0483164904506294
GO:0016573histone acetylation0.0483164904506294



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


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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}}}

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