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MCL coexpression mm9:1418: Difference between revisions

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{{MCL_coexpression_mm9
{{MCL_coexpression_mm9|coexpression_dpi_cluster_scores_mean=-0.0428016497940224,0.0810804366503217,0.0719311233395402,0.135387597242664,0.0925060106561082,0.158104913097007,0.105727385325774,-0.092364296664532,-0.157555894374685,-0.16709009755628,-0.155650476474834,-0.16709009755628,-0.137088139661156,-0.115164854222088,-0.146279112790454,-0.109532658608748,-0.16709009755628,-0.0122786457458259,-0.0405580926819225,-0.0754600784331285,0.201354385150853,-0.0128103312044963,-0.0522811721281055,0.0845859596539827,0.0842585650482307,0.0847724602639985,-0.00462466915303308,0.0685189630437338,-0.00835213858296766,0.0411256934776806,-0.0667011895173377,-0.16709009755628,-0.077238659927654,-0.16709009755628,0.478501420039885,0.355947106632711,0.524834201330129,-0.141783593516989,-0.12529915004263,-0.136615226381287,-0.100118830214497,-0.16709009755628,-0.117974899777136,-0.045621614196383,-0.0577455086791836,-0.0557029246674457,-0.0989150019399427,-0.0244203742489584,-0.0653913888202267,-0.0365429045599192,-0.0920531104469497,-0.102598565334723,-0.116636002563697,-0.127610053474014,-0.16709009755628,-0.150519280257904,-0.0691948251459473,0.0163332459232327,-0.0203946109605373,-0.0329314748299559,-0.0535048409478692,-0.0742294919254328,-0.16709009755628,-0.140197933562195,-0.16709009755628,-0.0893840876584076,-0.0596101259780862,-0.0241595156514511,-0.0559715603740532,-0.0581229422417537,-0.057906361915327,0.0366630831669466,0.0286366554747928,-0.0585648785706168,-0.0719676826030778,-0.0240831730212832,-0.0315400457291439,0.0524931243637036,0.0728560494325225,-0.0212139671986027,-0.0281246834447603,-0.0255533519289276,0.130362846484709,0.0280110781043583,0.0569160252582352,0.0112905637779268,0.0221848105123141,0.0463599981098086,-0.161806473625872,-0.137425918817849,0.00961636700138692,-0.0497040732174367,-0.104939855502472,0.0170956629186852,0.127576300185374,0.150505972449926,0.159345666186108,-0.0950808665234257,-0.133657837785114,-0.128398117119284,-0.0398169403056626,-0.107330718142205,-0.16709009755628,-0.16709009755628,-0.0737692070369218,-0.137418018302088,-0.107860827058953,0.223535121623966,-0.0019129746933775,0.133705926824303,0.0620400508492173,0.0696493411455647,0.117054386448189,0.128000601259772,0.115306946694737,0.176351266515358,-0.0721242919216799,0.701407627169979,-0.0732986752080502,0.0190092516354613,0.0101424730500829,0.0999209514093065,0.200094816347752,0.169503200325022,0.21992996398738,0.209395789239105,-0.122636177204783,-0.16709009755628,-0.0976559490031437,0.122634798507367,0.0418977598110182,-0.00119726966634003,0.113454781419854,0.11479250524119,0.187988872012553,0.0995169351827047,-0.0127637849487278,0.0701801427438672,0.146910054838033,0.356246518417329,0.01755232227944,-0.0180703569217546,-0.000429518378007806,0.0118677125781231,-0.0100221373356452,0.0257624804367451,0.0056862813626738,0.228787871308369,0.0205493730028779,0.0842156554305744,0.0415877005253574,-0.0294155778944519,-0.0018240945088324,-0.0210999247173882,-0.01684875463189,0.165414595939462,-0.16709009755628,-0.10910178152392,-0.12246409937805,0.291889805863743,0.392924549525088,0.407232967032858,0.409154267894962,0.531734587301042,0.54863772419273,0.611051567864172,0.648035356021347,0.487212182353826,0.564904261680023,0.567469715652229,0.529300576129211,0.599236343785164,0.582027575331723,0.550829477750712,0.0670366687373828,-0.0366779453988463,0.195056369612103,0.0944754995072703,0.0240916697671736,-0.00175769651950167,0.0537554085396913,0.11135763612397,0.070169334702056,0.0338827643754207,0.211747749956061,-0.00975383619214908,0.0702070694662811,0.0757884471021865,0.0795174707970158,0.180473285412299,0.221788911239897,0.256201542881607,0.0618648498361393,0.270246173702023,0.413602105340874,0.456111952042799,0.536210491176087,0.564170495515698,0.871826632317772,0.982125608371872,1.00307731198852,0.89041051883481,0.0908561642985148,-0.0285257118231966,-0.0221805154877238,-0.0552743568100682,-0.0039209344749249,-0.00378505317018025,0.0332476743268646,0.0384591514636834,0.0493075715552417,-0.00937460011475484,0.158006428220013,0.117256001033282,0.133117826278319,0.234485435546184,0.207133397848801,0.165836332849111,0.0245082298210348,0.0195553181046763,0.0641956670905749,0.000698595471738582,0.0602129544380278,0.0928425913543167,0.0483260780606281,-0.00236273458903442,0.0785763472535773,0.0362393487665397,0.126463518616966,0.0508055136409898,0.0818453405803892,0.0809724598637393,-0.16709009755628,-0.16709009755628,0.150510764417151,-0.0320008839247984,0.175086351941292,0.180139692293443,-0.0568657183475674,0.189904734670399,-0.0406978635809081,-0.0412983129759924,0.00638462444456067,-0.0172103645964488,-0.0308295678250785,-0.0362566623143061,0.0388029312748946,-0.0377810553619564,-0.0164506164095663,0.377091917293368,0.159477584397213,0.0433446849046639,0.0371791806366688,0.00943004245900386,-0.0508509984998257,0.0598668167770193,0.141565478447124,0.188345060905582,0.0472578462260297,0.0881074958208339,0.063648892797807,0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domain binding;0.00437322249490112;26381!GO:0045893;positive regulation of transcription, DNA-dependent;0.00437322249490112;18046,26381!GO:0045941;positive regulation of transcription;0.00437322249490112;18046,26381!GO:0045935;positive regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process;0.00437322249490112;18046,26381!GO:0031325;positive regulation of cellular metabolic process;0.00479707233637392;18046,26381!GO:0009893;positive regulation of metabolic process;0.00479707233637392;18046,26381!GO:0043565;sequence-specific DNA binding;0.00556400150565914;18046,26381!GO:0016439;tRNA-pseudouridine synthase activity;0.012219825711145;26381!GO:0048522;positive regulation of cellular process;0.012219825711145;18046,26381!GO:0003700;transcription factor activity;0.012219825711145;18046,26381!GO:0009982;pseudouridine synthase activity;0.012219825711145;26381!GO:0048518;positive regulation of biological process;0.012219825711145;18046,26381!GO:0016866;intramolecular transferase activity;0.0173410538729427;26381!GO:0005496;steroid binding;0.0260841264964928;26381!GO:0019904;protein domain specific binding;0.0274485626190369;26381!GO:0006355;regulation of transcription, DNA-dependent;0.035536894862443;18046,26381!GO:0006351;transcription, DNA-dependent;0.035536894862443;18046,26381!GO:0032774;RNA biosynthetic process;0.035536894862443;18046,26381!GO:0003677;DNA binding;0.035536894862443;18046,26381!GO:0045449;regulation of transcription;0.035536894862443;18046,26381!GO:0019219;regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process;0.035536894862443;18046,26381!GO:0006350;transcription;0.035536894862443;18046,26381!GO:0005516;calmodulin binding;0.035536894862443;26381!GO:0010468;regulation of gene expression;0.035536894862443;18046,26381!GO:0031323;regulation of cellular metabolic process;0.0369695037747075;18046,26381!GO:0019222;regulation of metabolic process;0.0382249283767296;18046,26381!GO:0016070;RNA metabolic process;0.0387779922786696;18046,26381!GO:0016853;isomerase activity;0.0420571120835355;26381!GO:0016563;transcription activator activity;0.047518768087866;26381!GO:0010467;gene 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|gostat_on_MCL_coexpression=GO:0050682;AF-2 domain binding;0.00437322249490112;26381!GO:0045893;positive regulation of transcription, DNA-dependent;0.00437322249490112;18046,26381!GO:0045941;positive regulation of transcription;0.00437322249490112;18046,26381!GO:0045935;positive regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process;0.00437322249490112;18046,26381!GO:0031325;positive regulation of cellular metabolic process;0.00479707233637392;18046,26381!GO:0009893;positive regulation of metabolic process;0.00479707233637392;18046,26381!GO:0043565;sequence-specific DNA binding;0.00556400150565914;18046,26381!GO:0016439;tRNA-pseudouridine synthase activity;0.012219825711145;26381!GO:0048522;positive regulation of cellular process;0.012219825711145;18046,26381!GO:0003700;transcription factor activity;0.012219825711145;18046,26381!GO:0009982;pseudouridine synthase activity;0.012219825711145;26381!GO:0048518;positive regulation of biological process;0.012219825711145;18046,26381!GO:0016866;intramolecular transferase activity;0.0173410538729427;26381!GO:0005496;steroid binding;0.0260841264964928;26381!GO:0019904;protein domain specific binding;0.0274485626190369;26381!GO:0006355;regulation of transcription, DNA-dependent;0.035536894862443;18046,26381!GO:0006351;transcription, DNA-dependent;0.035536894862443;18046,26381!GO:0032774;RNA biosynthetic process;0.035536894862443;18046,26381!GO:0003677;DNA binding;0.035536894862443;18046,26381!GO:0045449;regulation of transcription;0.035536894862443;18046,26381!GO:0019219;regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process;0.035536894862443;18046,26381!GO:0006350;transcription;0.035536894862443;18046,26381!GO:0005516;calmodulin binding;0.035536894862443;26381!GO:0010468;regulation of gene expression;0.035536894862443;18046,26381!GO:0031323;regulation of cellular metabolic process;0.0369695037747075;18046,26381!GO:0019222;regulation of metabolic process;0.0382249283767296;18046,26381!GO:0016070;RNA metabolic process;0.0387779922786696;18046,26381!GO:0016853;isomerase activity;0.0420571120835355;26381!GO:0016563;transcription activator activity;0.047518768087866;26381!GO:0010467;gene expression;0.049980793853034;18046,26381!
|ontology_enrichment_celltype=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0003103!2.05e-09!43;UBERON:0007100!1.15e-08!18;UBERON:0000948!1.15e-08!18;UBERON:0005498!1.15e-08!18;UBERON:0004140!1.15e-08!18;UBERON:0009881!1.15e-08!18;UBERON:0004141!1.15e-08!18;UBERON:0003084!1.15e-08!18;UBERON:0007005!1.15e-08!18;UBERON:0004139!1.15e-08!18;UBERON:0004291!1.15e-08!18
}}

Latest revision as of 16:54, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr19:34953822..34953888,-p3@Pank1
Mm9::chr1:166829711..166829727,-p@chr1:166829711..166829727
-
Mm9::chr1:189432857..189432870,+p7@Esrrg
Mm9::chr1:189432881..189432903,+p2@Esrrg
Mm9::chr1:189432907..189432926,+p3@Esrrg
Mm9::chr4:120488308..120488366,-p1@Nfyc


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:0050682AF-2 domain binding0.00437322249490112
GO:0045893positive regulation of transcription, DNA-dependent0.00437322249490112
GO:0045941positive regulation of transcription0.00437322249490112
GO:0045935positive regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process0.00437322249490112
GO:0031325positive regulation of cellular metabolic process0.00479707233637392
GO:0009893positive regulation of metabolic process0.00479707233637392
GO:0043565sequence-specific DNA binding0.00556400150565914
GO:0016439tRNA-pseudouridine synthase activity0.012219825711145
GO:0048522positive regulation of cellular process0.012219825711145
GO:0003700transcription factor activity0.012219825711145
GO:0009982pseudouridine synthase activity0.012219825711145
GO:0048518positive regulation of biological process0.012219825711145
GO:0016866intramolecular transferase activity0.0173410538729427
GO:0005496steroid binding0.0260841264964928
GO:0019904protein domain specific binding0.0274485626190369
GO:0006355regulation of transcription, DNA-dependent0.035536894862443
GO:0006351transcription, DNA-dependent0.035536894862443
GO:0032774RNA biosynthetic process0.035536894862443
GO:0003677DNA binding0.035536894862443
GO:0045449regulation of transcription0.035536894862443
GO:0019219regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process0.035536894862443
GO:0006350transcription0.035536894862443
GO:0005516calmodulin binding0.035536894862443
GO:0010468regulation of gene expression0.035536894862443
GO:0031323regulation of cellular metabolic process0.0369695037747075
GO:0019222regulation of metabolic process0.0382249283767296
GO:0016070RNA metabolic process0.0387779922786696
GO:0016853isomerase activity0.0420571120835355
GO:0016563transcription activator activity0.047518768087866
GO:0010467gene expression0.049980793853034



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
compound organ2.05e-0943
primary circulatory organ1.15e-0818
heart1.15e-0818
primitive heart tube1.15e-0818
primary heart field1.15e-0818
anterior lateral plate mesoderm1.15e-0818
heart tube1.15e-0818
heart primordium1.15e-0818
cardiac mesoderm1.15e-0818
cardiogenic plate1.15e-0818
heart rudiment1.15e-0818


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)
MA0003.10.135108
MA0004.10.536396
MA0006.10.359699
MA0007.10.52077
MA0009.10.987341
MA0014.10.0315641
MA0017.10.387481
MA0019.10.800946
MA0024.10.942716
MA0025.11.22395
MA0027.12.64231
MA0028.10.370592
MA0029.10.920529
MA0030.10.927235
MA0031.10.890871
MA0038.10.686534
MA0040.11.00009
MA0041.10.457338
MA0042.10.443591
MA0043.11.08567
MA0046.11.02391
MA0048.10.486223
MA0050.10.57678
MA0051.10.695779
MA0052.15.36027
MA0055.10.0585191
MA0056.10
MA0057.10.457693
MA0058.10.436487
MA0059.11.14076
MA0060.10.757042
MA0061.10.307097
MA0063.10
MA0066.10.675169
MA0067.11.33603
MA0068.12.09737
MA0069.11.00864
MA0070.10.998765
MA0071.11.41046
MA0072.10.990133
MA0073.15.00847
MA0074.11.54084
MA0076.10.407465
MA0077.10.968053
MA0078.10.729877
MA0081.12.07288
MA0083.11.08487
MA0084.11.66561
MA0087.11.04109
MA0088.10.358337
MA0089.10
MA0090.12.16326
MA0091.11.3559
MA0092.10.501022
MA0093.10.379257
MA0095.10
MA0098.10
MA0100.10.626021
MA0101.10.458688
MA0103.10.398766
MA0105.10.199622
MA0106.10.737893
MA0107.10.392331
MA0108.21.92698
MA0109.10
MA0111.10.515457
MA0113.10.708789
MA0114.10.304661
MA0115.11.08851
MA0116.10.359483
MA0117.11.05576
MA0119.10.459301
MA0122.11.07591
MA0124.11.28237
MA0125.11.20757
MA0130.10
MA0131.10.796279
MA0132.10
MA0133.10
MA0135.11.1226
MA0136.10.658622
MA0139.10.243463
MA0140.10.625902
MA0141.11.07584
MA0142.10.876028
MA0143.10.725672
MA0144.10.829535
MA0145.10.379391
MA0146.10.153598
MA0147.10.320675
MA0148.10.553294
MA0149.10.464445
MA0062.20.204999
MA0035.20.630778
MA0039.20.769467
MA0138.20.788113
MA0002.20.246463
MA0137.20.416331
MA0104.20.261255
MA0047.20.685741
MA0112.20.119197
MA0065.21.24784
MA0150.10.520653
MA0151.10
MA0152.10.685852
MA0153.11.13945
MA0154.10.480757
MA0155.11.33283
MA0156.10.406559
MA0157.10.843181
MA0158.10
MA0159.10.331229
MA0160.10.556423
MA0161.10
MA0162.11.08528
MA0163.10.372305
MA0164.10.658997
MA0080.20.393257
MA0018.20.669032
MA0099.21.83891
MA0079.20.730639
MA0102.21.7182
MA0258.10.290587
MA0259.10.309517
MA0442.10
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