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MCL coexpression mm9:479: Difference between revisions

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{{MCL_coexpression_mm9
{{MCL_coexpression_mm9|coexpression_dpi_cluster_scores_mean=-0.0161628306625238,0.0527129870701925,0.0311010926576085,0.0747331258868463,0.0382255180155191,0.0409904816607278,0.083621443179098,-0.0190290498402391,-0.0285085358365608,-0.0173909203061673,-0.0165067634663853,-0.0222963875848545,-0.0134052620722647,-0.0217652534791346,-0.0118597480239005,-0.0231701256676863,-0.0285085358365608,-0.0163294655030772,-0.0148127466173421,-0.0285085358365608,0.351310899032454,-0.0188253807569424,-0.0163399588382653,0.0766595566466602,0.061839841307084,0.0583594156179149,0.0178451089593581,0.0337668090216521,0.156643224131674,0.0895916643022236,0.0322199121985575,-0.00477269624487499,0.00743203921488947,0.0532616432973772,0.091629274448765,0.0425178821302059,0.07708423811535,-0.0285085358365608,-0.0285085358365608,-0.0285085358365608,-0.0285085358365608,-0.0285085358365608,-0.0285085358365608,-0.00929633715703431,-0.00229134820344472,0.00274845542529896,0.00495853942705707,-0.0123201415727337,-0.00646391128660363,0.00516718997966791,-0.00935311881238648,-0.00271192294793825,-0.0156400624672614,-0.0285085358365608,-0.00832023147396494,-0.0164902232134671,-0.0212137972367404,0.047512868229161,0.00889414355520628,-0.0285085358365608,0.0165467273377472,-0.00507909431171633,0.0154045378308495,-0.00992649062850241,-0.0285085358365608,0.00454107367254707,-0.00570141565581386,0.00310339772797479,-0.0184630494157101,-0.0179214747641227,-0.0183427310340475,-0.00331360333573479,0.00458841582028823,-0.0184719778598942,-0.0207810054762729,0.00169675396820529,-0.00701127726754927,-0.0121605983816036,-0.00636629631458921,-0.00659031358077147,-0.0141783134302128,0.0125230981329325,-0.00376376204590012,0.0130493826922115,-0.0105818110586909,-0.0210321897008987,-0.0101458562955101,-0.0027883540985236,-0.0225813514230255,-0.0204830109815691,0.965814306970128,0.187751092976764,0.0245468924417332,0.105288643957137,0.140452756954373,0.136721865991968,0.232018368260367,0.00949019066507552,0.0260092487350533,-0.0197480837237688,-0.018304434952987,0.0561153561247889,0.0081574658166406,0.110925416839707,0.0930190323024986,0.104111340282059,0.101528223794171,0.353846246833125,0.00530225185279293,-0.0110062442557349,0.0116648170739689,0.0413708516192673,0.0687636833970137,-0.00868601004301927,0.0542822763892486,-0.0158189594482389,0.209426578422681,0.0192960873896835,0.0273561409965515,0.0533888212277653,0.0363918936401862,0.0372416322335515,0.1056861520498,-0.00606290478818248,-0.0108888602166276,0.102128919692083,-0.0149172689947452,-0.0285085358365608,-0.0250451373352854,0.00372393466446853,0.00972161359516067,-0.0185905678117984,-0.00176092023433732,-0.00995656641938273,0.00748390451044139,0.0025919184549756,0.313875061460599,0.253412799042369,0.401373184585165,0.0378119788791032,-0.0147283340127098,0.0145635572117003,0.0200986696955587,0.0224369527112015,0.0250659647342503,0.000440458514851627,0.0204898228942185,0.0848874780660046,-0.0115526846026358,0.0269396633756965,0.0332225893533712,0.0276434905489037,0.0266972427120877,0.0359911960507256,0.0304259684161779,0.208889860360368,-0.0285085358365608,-0.0285085358365608,-0.0212671810682442,0.0456047364953258,0.0262530294466209,0.0345560359679651,0.0746072334563843,0.0486717903898871,0.0564144464386501,0.0471203689018817,0.0735813984095227,0.063292973424709,0.0559385624802071,0.0624154805833392,0.0410261336564413,0.0537791336431248,0.0556315831410278,0.0685950075369732,0.000646933900115034,-0.010093379736975,0.0705412638460005,0.0683004408834914,0.0940515078040892,0.123734201549285,0.133744359200863,0.144923857475656,0.0663909744435616,0.133292584815945,0.0730805975797337,0.096956220536766,0.112024866929785,0.145113682520128,0.17070562376825,0.130914532988071,0.105548396757315,0.10800292127642,0.302081929301386,0.471527415909634,0.606272676220019,0.689782221584958,0.719166388369036,0.737271840616304,0.979806345321249,0.994134990070408,1.05990750305834,0.94976002002842,0.200863316219301,0.0394387281768561,0.0663571988669757,0.06401373443508,0.0809019690733768,0.0989510978871997,0.139743363214661,0.136718971328091,0.135802546638052,0.135246187311403,0.352009967863727,0.219540225754751,0.332187549011416,0.275766271655966,0.234153899442985,0.151488840046148,0.133915140561641,0.06289078670966,0.10523995951562,0.0964539717344765,0.153171382793476,0.126055405200882,0.11447754148939,0.123913398793347,0.185510149989231,0.170894654939783,0.122203534301732,0.111323876413452,0.105940115495431,0.129313594314436,-0.00188770658017031,-0.00719578531080587,0.0272492366945419,0.0195482287638772,0.00331028961547021,-4.95566988892529e-05,0.00342385394637473,0.0620901263272643,0.0351846294228413,0.0252826595942305,-0.00370225248545527,-0.00665473668588373,-0.00683496110292655,-0.0155195889169045,0.0202403368128552,-0.0151821721901631,0.00858994555060774,-0.0060717670628372,0.059017841443513,0.100307108386309,0.0975558904714487,0.144734136331605,0.3782046688591,0.330677823399403,0.261380690722514,0.354178248871453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synthase activity;0.0259232866376788;21391!GO:0048731;system development;0.0259232866376788;110596,21410,231532,241035!GO:0048856;anatomical structure development;0.0259232866376788;110596,21410,231532,241035!GO:0001826;inner cell mass cell differentiation;0.0259232866376788;21410!GO:0007275;multicellular organismal development;0.0259232866376788;110596,21410,231532,241035!GO:0048646;anatomical structure formation;0.0259232866376788;21410,231532!GO:0009746;response to hexose stimulus;0.0259232866376788;21410!GO:0009743;response to carbohydrate stimulus;0.0259232866376788;21410!GO:0009749;response to glucose stimulus;0.0259232866376788;21410!GO:0001825;blastocyst formation;0.0291605017960454;21410!GO:0007417;central nervous system development;0.0294311949806488;110596,21410!GO:0009653;anatomical structure morphogenesis;0.0294311949806488;110596,21410,231532!GO:0046457;prostanoid biosynthetic process;0.0294311949806488;21391!GO:0001516;prostaglandin biosynthetic process;0.0294311949806488;21391!GO:0032502;developmental process;0.0294311949806488;110596,21410,231532,241035!GO:0021955;central nervous system neuron axonogenesis;0.0294311949806488;110596!GO:0060052;neurofilament cytoskeleton organization and biogenesis;0.0294311949806488;110596!GO:0030695;GTPase regulator activity;0.0294311949806488;110596,231532!GO:0048513;organ development;0.0360718416571888;21410,231532,241035!GO:0006693;prostaglandin metabolic process;0.0360718416571888;21391!GO:0006692;prostanoid metabolic process;0.0360718416571888;21391!GO:0045104;intermediate filament cytoskeleton organization and biogenesis;0.04305018068093;110596!GO:0007492;endoderm development;0.04305018068093;21410!GO:0051271;negative regulation of cell motility;0.043678484892207;241035!GO:0040013;negative regulation of locomotion;0.0442560147190313;241035!GO:0045103;intermediate filament-based process;0.0447062043621739;110596!GO:0021954;central nervous system neuron development;0.0447062043621739;110596!GO:0030073;insulin secretion;0.0447062043621739;21410!GO:0046456;icosanoid biosynthetic process;0.0447062043621739;21391!GO:0021953;central nervous system neuron differentiation;0.0447062043621739;110596!GO:0048869;cellular developmental process;0.0447062043621739;110596,21410,231532!GO:0030154;cell differentiation;0.0447062043621739;110596,21410,231532!GO:0030072;peptide hormone secretion;0.0474422975110747;21410!GO:0002790;peptide secretion;0.0474422975110747;21410!GO:0010033;response to organic substance;0.0474422975110747;21410!GO:0006690;icosanoid metabolic process;0.0474422975110747;21391!GO:0050673;epithelial cell proliferation;0.0474422975110747;21410!GO:0001824;blastocyst development;0.0474422975110747;21410!GO:0032501;multicellular organismal 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|coexpression_dpi_cluster_scores_median=0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.202843190349958,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.931278659592412,0,0,0,0,0,0.152695919012311,0,0,0,0,0,0,0,0,0,0,0.353343460740044,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.207105294575038,0.210060181764701,0.245060439302742,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.145528461145601,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0906941294286938,0.0526429550379996,0.0797901069290224,0,0.0756292965920817,0,0,0,0.0788034163803455,0.0773548534010084,0,0,0,0.139670008859883,0.353480302513185,0.641596258002333,0.537039931131814,0.613126898020799,0.580404056653903,0.813018825934344,0.899693420157211,0.914974381383991,0.824533862091472,0.112756652096095,0,0,0,0,0.093833775061694,0.0253288140122851,0.0366279750010614,0.0652566657696677,0,0.386977062110387,0.137398724818722,0.210606173730573,0.177582020809476,0.133153884834288,0,0,0,0,0,0,0.0672592169170953,0,0.0699128886591125,0.0635717028550276,0.086880916817156,0,0,0,0.0341009293634831,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0711694759496908,0.0655375003561515,0.0663147875126409,0.36688061805648,0.237629660753576,0.114718896326828,0.2441336485308,0.201562011772837,0.283822395835769,0.360241417805924,0.389898434712572,0.384888919274974,0.289613536706145,0.312639783153065,0.307785919889371,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.111087966368681,0,0,0,0,0,0,0,0,0,0,0,0,0.0803809427109337,0.0445418537893845,0.0824580172145032,0.0857765460992942,0.103710933695783,0.066440322267935,0,0.0529304404135566,0,0,0,0,0,0,0,0,0.0531569878936061,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0767094571656325,0.120786737690969,0.0730404042754446,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.081359932135904,0,0.0978461107777356,0,0.139013627015232,0.0388749848471105,0.0763037466917402,0.0690411384905589,0,0.0905291472420136,0.0766073954291401,0,0.112067779638927,0,0.0709519923534245,0.092873634605593,0,0.0390607415003592,0.0352754493378881,0.0729583017401753,0,0.0553034373508932,0.193442483447008,0.0486884105045233,0.0408018333703219,0,0.0625582350728301,0.0766064454112358,0,0.091291089277545,0.0845301845292944,0,0,0
|gostat_on_MCL_coexpression=GO:0004796;thromboxane-A synthase activity;0.0259232866376788;21391!GO:0048731;system development;0.0259232866376788;110596,21410,231532,241035!GO:0048856;anatomical structure development;0.0259232866376788;110596,21410,231532,241035!GO:0001826;inner cell mass cell differentiation;0.0259232866376788;21410!GO:0007275;multicellular organismal development;0.0259232866376788;110596,21410,231532,241035!GO:0048646;anatomical structure formation;0.0259232866376788;21410,231532!GO:0009746;response to hexose stimulus;0.0259232866376788;21410!GO:0009743;response to carbohydrate stimulus;0.0259232866376788;21410!GO:0009749;response to glucose stimulus;0.0259232866376788;21410!GO:0001825;blastocyst formation;0.0291605017960454;21410!GO:0007417;central nervous system development;0.0294311949806488;110596,21410!GO:0009653;anatomical structure morphogenesis;0.0294311949806488;110596,21410,231532!GO:0046457;prostanoid biosynthetic process;0.0294311949806488;21391!GO:0001516;prostaglandin biosynthetic process;0.0294311949806488;21391!GO:0032502;developmental process;0.0294311949806488;110596,21410,231532,241035!GO:0021955;central nervous system neuron axonogenesis;0.0294311949806488;110596!GO:0060052;neurofilament cytoskeleton organization and biogenesis;0.0294311949806488;110596!GO:0030695;GTPase regulator activity;0.0294311949806488;110596,231532!GO:0048513;organ development;0.0360718416571888;21410,231532,241035!GO:0006693;prostaglandin metabolic process;0.0360718416571888;21391!GO:0006692;prostanoid metabolic process;0.0360718416571888;21391!GO:0045104;intermediate filament cytoskeleton organization and biogenesis;0.04305018068093;110596!GO:0007492;endoderm development;0.04305018068093;21410!GO:0051271;negative regulation of cell motility;0.043678484892207;241035!GO:0040013;negative regulation of locomotion;0.0442560147190313;241035!GO:0045103;intermediate filament-based process;0.0447062043621739;110596!GO:0021954;central nervous system neuron development;0.0447062043621739;110596!GO:0030073;insulin secretion;0.0447062043621739;21410!GO:0046456;icosanoid biosynthetic process;0.0447062043621739;21391!GO:0021953;central nervous system neuron differentiation;0.0447062043621739;110596!GO:0048869;cellular developmental process;0.0447062043621739;110596,21410,231532!GO:0030154;cell differentiation;0.0447062043621739;110596,21410,231532!GO:0030072;peptide hormone secretion;0.0474422975110747;21410!GO:0002790;peptide secretion;0.0474422975110747;21410!GO:0010033;response to organic substance;0.0474422975110747;21410!GO:0006690;icosanoid metabolic process;0.0474422975110747;21391!GO:0050673;epithelial cell proliferation;0.0474422975110747;21410!GO:0001824;blastocyst development;0.0474422975110747;21410!GO:0032501;multicellular organismal process;0.0497068242388782;110596,21410,231532,241035!
}}

Latest revision as of 15:22, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr10:24562097..24562114,+p@chr10:24562097..24562114
+
Mm9::chr11:83664365..83664383,+p1@Hnf1b
Mm9::chr11:83666422..83666446,+p4@Hnf1b
Mm9::chr12:25367561..25367565,+p@chr12:25367561..25367565
+
Mm9::chr13:73484734..73484745,-p3@D630045M09Rik
Mm9::chr13:98786218..98786238,-p7@Rgnef
Mm9::chr1:20157166..20157171,-p@chr1:20157166..20157171
-
Mm9::chr1:20501784..20501787,-p@chr1:20501784..20501787
-
Mm9::chr1:20576990..20576994,-p@chr1:20576990..20576994
-
Mm9::chr1:20608054..20608071,-p2@Pkhd1
Mm9::chr1:20608073..20608170,-p1@Pkhd1
Mm9::chr1:20608173..20608178,-p3@Pkhd1
Mm9::chr4:155458412..155458438,-p@chr4:155458412..155458438
-
Mm9::chr5:103197888..103197908,+p2@Arhgap24
Mm9::chr6:38933302..38933316,+p3@Tbxas1


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:0004796thromboxane-A synthase activity0.0259232866376788
GO:0048731system development0.0259232866376788
GO:0048856anatomical structure development0.0259232866376788
GO:0001826inner cell mass cell differentiation0.0259232866376788
GO:0007275multicellular organismal development0.0259232866376788
GO:0048646anatomical structure formation0.0259232866376788
GO:0009746response to hexose stimulus0.0259232866376788
GO:0009743response to carbohydrate stimulus0.0259232866376788
GO:0009749response to glucose stimulus0.0259232866376788
GO:0001825blastocyst formation0.0291605017960454
GO:0007417central nervous system development0.0294311949806488
GO:0009653anatomical structure morphogenesis0.0294311949806488
GO:0046457prostanoid biosynthetic process0.0294311949806488
GO:0001516prostaglandin biosynthetic process0.0294311949806488
GO:0032502developmental process0.0294311949806488
GO:0021955central nervous system neuron axonogenesis0.0294311949806488
GO:0060052neurofilament cytoskeleton organization and biogenesis0.0294311949806488
GO:0030695GTPase regulator activity0.0294311949806488
GO:0048513organ development0.0360718416571888
GO:0006693prostaglandin metabolic process0.0360718416571888
GO:0006692prostanoid metabolic process0.0360718416571888
GO:0045104intermediate filament cytoskeleton organization and biogenesis0.04305018068093
GO:0007492endoderm development0.04305018068093
GO:0051271negative regulation of cell motility0.043678484892207
GO:0040013negative regulation of locomotion0.0442560147190313
GO:0045103intermediate filament-based process0.0447062043621739
GO:0021954central nervous system neuron development0.0447062043621739
GO:0030073insulin secretion0.0447062043621739
GO:0046456icosanoid biosynthetic process0.0447062043621739
GO:0021953central nervous system neuron differentiation0.0447062043621739
GO:0048869cellular developmental process0.0447062043621739
GO:0030154cell differentiation0.0447062043621739
GO:0030072peptide hormone secretion0.0474422975110747
GO:0002790peptide secretion0.0474422975110747
GO:0010033response to organic substance0.0474422975110747
GO:0006690icosanoid metabolic process0.0474422975110747
GO:0050673epithelial cell proliferation0.0474422975110747
GO:0001824blastocyst development0.0474422975110747
GO:0032501multicellular organismal process0.0497068242388782



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
trunk region element2.77e-1679
kidney7.48e-1514
kidney mesenchyme7.48e-1514
upper urinary tract7.48e-1514
kidney rudiment7.48e-1514
kidney field7.48e-1514
pancreas3.31e-1412
trunk1.11e-1290
urinary system structure4.21e-1218
renal system3.24e-1119
cavitated compound organ1.04e-0921
immaterial anatomical entity7.16e-0979
viscus8.02e-0919
abdomen element2.23e-0849
abdominal segment element2.23e-0849
abdominal segment of trunk2.23e-0849
abdomen2.23e-0849
body cavity precursor1.12e-0738
anatomical cavity2.48e-0739
subdivision of trunk2.83e-0766
body cavity5.45e-0737
body cavity or lining5.45e-0737


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)
MA0003.10.0397115
MA0004.10.239244
MA0006.10.118059
MA0007.10.227553
MA0009.10.623671
MA0014.10.0171266
MA0017.10.832511
MA0019.10.456268
MA0024.10.582844
MA0025.10.845702
MA0027.12.24512
MA0028.10.12472
MA0029.12.36679
MA0030.11.39542
MA0031.10.535959
MA0038.10.358622
MA0040.10.635404
MA0041.10.18185
MA0042.10.172351
MA0043.10.71494
MA0046.16.57701
MA0048.10.0239691
MA0050.10.270164
MA0051.10.366328
MA0052.10.642973
MA0055.10.119754
MA0056.10
MA0057.10.0903541
MA0058.10.167504
MA0059.10.522737
MA0060.10.071412
MA0061.10.0877629
MA0063.10
MA0066.10.349199
MA0067.10.953264
MA0068.10.0945752
MA0069.10.643292
MA0070.10.634186
MA0071.10.269487
MA0072.10.626238
MA0073.10.000384675
MA0074.10.318792
MA0076.10.148159
MA0077.10.605975
MA0078.10.395048
MA0081.10.193203
MA0083.10.714187
MA0084.11.27474
MA0087.10.673355
MA0088.10.143884
MA0089.10
MA0090.10.610307
MA0091.10.696557
MA0092.10.213012
MA0093.10.130107
MA0095.10
MA0098.10
MA0100.10.309116
MA0101.10.538493
MA0103.10.14251
MA0105.10.147614
MA0106.10.401864
MA0107.10.428571
MA0108.20.476838
MA0109.10
MA0111.10.223614
MA0113.10.377232
MA0114.10.609093
MA0115.10.717599
MA0116.10.117928
MA0117.10.686999
MA0119.10.183219
MA0122.11.68206
MA0124.10.901619
MA0125.10.830088
MA0130.10
MA0131.10.452196
MA0132.10
MA0133.10
MA0135.10.749615
MA0136.10.891604
MA0139.10.0558308
MA0140.10.30902
MA0141.10.155997
MA0142.10.522654
MA0143.10.391481
MA0144.10.0881858
MA0145.10.0124347
MA0146.10.0253534
MA0147.10.0952713
MA0148.10.252062
MA0149.10.18682
MA0062.20.154316
MA0035.20.312946
MA0039.20.00174261
MA0138.20.445088
MA0002.20.458095
MA0137.20.153989
MA0104.20.0641853
MA0047.20.357963
MA0112.20.0599393
MA0065.20.321967
MA0150.10.227466
MA0151.10
MA0152.10.358055
MA0153.13.01496
MA0154.10.465695
MA0155.10.0729675
MA0156.10.885026
MA0157.10.493416
MA0158.10
MA0159.10.679844
MA0160.10.707761
MA0161.10
MA0162.10.00143236
MA0163.10.0738452
MA0164.10.335886
MA0080.20.848376
MA0018.20.344133
MA0099.20.439458
MA0079.20.00035791
MA0102.21.32652
MA0258.10.0789466
MA0259.10.0890842
MA0442.10
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