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MCL coexpression mm9:225: Difference between revisions

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{{MCL_coexpression_mm9
{{MCL_coexpression_mm9
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|coexpression_dpi_cluster_scores_median=0.1455322972644,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0578074284787346,0,0,0,0,0,0,0,0,0,0.152695919012311,0,0,0,0.107781924973909,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.137610809203654,1.1711142240395,0.856339875679642,1.11799610576829,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.686333774245849,0,0,0,0,0,0.0633819931896364,0.0405277496980155,0.0523528812100954,0.0388988969149198,0,0.0847792561696249,0.289038021474128,0.480317123592907,0.765095035157837,0.73402368375046,1.00210225010966,0.861870465366058,0,0,0,0,0,0,0,0,0,0.0623063220167371,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0376806553706894,0,0,0,0,0.0927359537809747,0.0602552389750834,0.0635717028550276,0,0,0.0659019793256198,0,0,0,0,0,0,0,0,0,0.354560683876484,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.187572405034986,0.0241428626497415,0.15493316250826,0.0709019855629759,0.132495872273197,0.0661577744756082,0.057716207064756,0,0,0,0,0.0126678477086623,0.195114606084109,0.132937195692582,0.0660055475634404,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0424616899933645,0,0.0715236385554987,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.145825435924841,0.418397287662917,0.708510619337853,0.332503048492315,0.341049960246911,0.0871588832444397,0.149856261570464,0.120876255993453,0.137748206855213,0.138109243799297,0.139013627015232,0.180213252801698,0.129922896128301,0.0997261746927171,0.169172763866184,0.0905291472420136,0.141706336142815,0,0.158843797677303,0.226790206858766,0.158651849966934,0.201842612947909,0.199037798091534,0.138756502969784,0.126604887871452,0.135404897539632,0.101427320830301,0.104353329269123,0.193442483447008,0.18546004356206,0.112441925220423,0.148982201447044,0.141505433941488,0.792775438043027,0.698706676659676,0.593552050314649,0.670168115417827,1.27607741439365,1.09343286920712,1.03560964418252
|gostat_on_MCL_coexpression=GO:0005578;proteinaceous extracellular matrix;9.94805947125308e-09;12824,11595,17180,12950,12839,12815,17182!GO:0005201;extracellular matrix structural constituent;9.94805947125308e-09;12824,17180,12839,12815,17182!GO:0022610;biological adhesion;4.72297215510633e-07;213119,12824,12845,11595,12950,12839,12815!GO:0007155;cell adhesion;4.72297215510633e-07;213119,12824,12845,11595,12950,12839,12815!GO:0030198;extracellular matrix organization and biogenesis;6.55853841387458e-07;12824,11595,17180,17182!GO:0044420;extracellular matrix part;3.81878223203534e-06;12824,11595,12839,12815!GO:0043062;extracellular structure organization and biogenesis;4.39897247315514e-06;12824,11595,17180,17182!GO:0030020;extracellular matrix structural constituent conferring tensile strength;7.75836238883046e-06;12824,12839,12815!GO:0005581;collagen;1.23252054246797e-05;12824,12839,12815!GO:0005518;collagen binding;6.5611849078916e-05;17180,17182!GO:0044421;extracellular region part;6.68622318005401e-05;12824,12845,11595,17180,12950,12839,12815,17182!GO:0006817;phosphate transport;6.68622318005401e-05;12824,12839,12815!GO:0001502;cartilage condensation;0.000108032930554557;12824,11595!GO:0030199;collagen fibril organization;0.000233644177338014;12824,11595!GO:0005540;hyaluronic acid binding;0.000249129426871181;11595,12950!GO:0006029;proteoglycan metabolic process;0.000332456786598914;12824,11595!GO:0015698;inorganic anion transport;0.000429192999854446;12824,12839,12815!GO:0006820;anion transport;0.000671512432102679;12824,12839,12815!GO:0051216;cartilage development;0.00182731708572627;12824,11595!GO:0030246;carbohydrate binding;0.00238614933504166;11595,12950,403395!GO:0005615;extracellular space;0.00306266264442543;12824,12845,17180,12950,12839,12815!GO:0005539;glycosaminoglycan binding;0.00374314072995;11595,12950!GO:0030247;polysaccharide binding;0.0042839181942941;11595,12950!GO:0001871;pattern binding;0.00451696322521827;11595,12950!GO:0001501;skeletal development;0.0189008761426242;12824,11595!GO:0005529;sugar binding;0.0193667460790394;11595,403395!GO:0016337;cell-cell adhesion;0.0231487892777975;12824,11595!GO:0006811;ion transport;0.0260616293747252;12824,12839,12815!GO:0030166;proteoglycan biosynthetic process;0.0285255231838653;11595!GO:0044262;cellular carbohydrate metabolic process;0.0292110437925668;12824,11595!GO:0009888;tissue development;0.0345915528954376;12824,11595!GO:0005921;gap junction;0.039418383839295;208098!GO:0005975;carbohydrate metabolic process;0.0473343727651521;12824,11595!
|gostat_on_MCL_coexpression=GO:0005578;proteinaceous extracellular matrix;9.94805947125308e-09;12824,11595,17180,12950,12839,12815,17182!GO:0005201;extracellular matrix structural constituent;9.94805947125308e-09;12824,17180,12839,12815,17182!GO:0022610;biological adhesion;4.72297215510633e-07;213119,12824,12845,11595,12950,12839,12815!GO:0007155;cell adhesion;4.72297215510633e-07;213119,12824,12845,11595,12950,12839,12815!GO:0030198;extracellular matrix organization and biogenesis;6.55853841387458e-07;12824,11595,17180,17182!GO:0044420;extracellular matrix part;3.81878223203534e-06;12824,11595,12839,12815!GO:0043062;extracellular structure organization and biogenesis;4.39897247315514e-06;12824,11595,17180,17182!GO:0030020;extracellular matrix structural constituent conferring tensile strength;7.75836238883046e-06;12824,12839,12815!GO:0005581;collagen;1.23252054246797e-05;12824,12839,12815!GO:0005518;collagen binding;6.5611849078916e-05;17180,17182!GO:0044421;extracellular region part;6.68622318005401e-05;12824,12845,11595,17180,12950,12839,12815,17182!GO:0006817;phosphate transport;6.68622318005401e-05;12824,12839,12815!GO:0001502;cartilage condensation;0.000108032930554557;12824,11595!GO:0030199;collagen fibril organization;0.000233644177338014;12824,11595!GO:0005540;hyaluronic acid binding;0.000249129426871181;11595,12950!GO:0006029;proteoglycan metabolic process;0.000332456786598914;12824,11595!GO:0015698;inorganic anion transport;0.000429192999854446;12824,12839,12815!GO:0006820;anion transport;0.000671512432102679;12824,12839,12815!GO:0051216;cartilage development;0.00182731708572627;12824,11595!GO:0030246;carbohydrate binding;0.00238614933504166;11595,12950,403395!GO:0005615;extracellular space;0.00306266264442543;12824,12845,17180,12950,12839,12815!GO:0005539;glycosaminoglycan binding;0.00374314072995;11595,12950!GO:0030247;polysaccharide binding;0.0042839181942941;11595,12950!GO:0001871;pattern binding;0.00451696322521827;11595,12950!GO:0001501;skeletal development;0.0189008761426242;12824,11595!GO:0005529;sugar binding;0.0193667460790394;11595,403395!GO:0016337;cell-cell adhesion;0.0231487892777975;12824,11595!GO:0006811;ion transport;0.0260616293747252;12824,12839,12815!GO:0030166;proteoglycan biosynthetic process;0.0285255231838653;11595!GO:0044262;cellular carbohydrate metabolic process;0.0292110437925668;12824,11595!GO:0009888;tissue development;0.0345915528954376;12824,11595!GO:0005921;gap junction;0.039418383839295;208098!GO:0005975;carbohydrate metabolic process;0.0473343727651521;12824,11595!
}}
}}

Revision as of 12:38, 11 October 2012


Phase1 CAGE Peaks

 Short description
Mm9::chr10:34822425..34822426,+p@chr10:34822425..34822426
+
Mm9::chr12:8954768..8954786,+p1@Matn3
Mm9::chr13:24247072..24247085,-p6@Lrrc16a
Mm9::chr13:89680450..89680470,+p1@Hapln1
Mm9::chr15:97806343..97806352,-p@chr15:97806343..97806352
-
Mm9::chr15:97806491..97806499,-p@chr15:97806491..97806499
-
Mm9::chr15:97806555..97806573,-p@chr15:97806555..97806573
-
Mm9::chr15:97806587..97806603,-p@chr15:97806587..97806603
-
Mm9::chr15:97807109..97807127,-p@chr15:97807109..97807127
-
Mm9::chr15:97807155..97807166,-p@chr15:97807155..97807166
-
Mm9::chr15:97807173..97807191,-p@chr15:97807173..97807191
-
Mm9::chr15:97807229..97807247,-p@chr15:97807229..97807247
-
Mm9::chr15:97807283..97807309,-p@chr15:97807283..97807309
-
Mm9::chr15:97807708..97807732,-p@chr15:97807708..97807732
-
Mm9::chr15:97808264..97808278,-p@chr15:97808264..97808278
-
Mm9::chr15:97808333..97808351,-p@chr15:97808333..97808351
-
Mm9::chr15:97835065..97835083,-p1@Col2a1
Mm9::chr17:34176407..34176426,+p1@Col11a2
Mm9::chr1:24184528..24184550,+p2@Col9a1
Mm9::chr1:89366833..89366856,+p1@3110079O15Rik
Mm9::chr1:89366868..89366879,+p3@3110079O15Rik
Mm9::chr1:89366883..89366905,+p2@3110079O15Rik
Mm9::chr2:29713767..29713788,+p@chr2:29713767..29713788
+
Mm9::chr2:77459335..77459343,-p@chr2:77459335..77459343
-
Mm9::chr3:113820930..113820931,+p@chr3:113820930..113820931
+
Mm9::chr3:144955680..144955740,+p1@Col24a1
Mm9::chr3:96449502..96449531,+p1@Itga10
Mm9::chr4:130500292..130500306,+p1@Matn1
Mm9::chr5:139882400..139882420,+p2@C130050O18Rik
Mm9::chr7:86198101..86198120,+p1@Acan
Mm9::chr7:86198122..86198151,+p2@Acan
Mm9::chr7:86198174..86198187,+p3@Acan
Mm9::chr7:86229411..86229424,+p@chr7:86229411..86229424
+
Mm9::chr8:116941895..116941911,+p1@Clec3a
Mm9::chr8:72897440..72897457,+p1@Comp
Mm9::chr9:37476743..37476752,-p2@Panx3
Mm9::chr9:37476755..37476811,-p1@Panx3
Mm9::chrX:147261468..147261472,+p1@ENSMUST00000145639


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:0005578proteinaceous extracellular matrix9.94805947125308e-09
GO:0005201extracellular matrix structural constituent9.94805947125308e-09
GO:0022610biological adhesion4.72297215510633e-07
GO:0007155cell adhesion4.72297215510633e-07
GO:0030198extracellular matrix organization and biogenesis6.55853841387458e-07
GO:0044420extracellular matrix part3.81878223203534e-06
GO:0043062extracellular structure organization and biogenesis4.39897247315514e-06
GO:0030020extracellular matrix structural constituent conferring tensile strength7.75836238883046e-06
GO:0005581collagen1.23252054246797e-05
GO:0005518collagen binding6.5611849078916e-05
GO:0044421extracellular region part6.68622318005401e-05
GO:0006817phosphate transport6.68622318005401e-05
GO:0001502cartilage condensation0.000108032930554557
GO:0030199collagen fibril organization0.000233644177338014
GO:0005540hyaluronic acid binding0.000249129426871181
GO:0006029proteoglycan metabolic process0.000332456786598914
GO:0015698inorganic anion transport0.000429192999854446
GO:0006820anion transport0.000671512432102679
GO:0051216cartilage development0.00182731708572627
GO:0030246carbohydrate binding0.00238614933504166
GO:0005615extracellular space0.00306266264442543
GO:0005539glycosaminoglycan binding0.00374314072995
GO:0030247polysaccharide binding0.0042839181942941
GO:0001871pattern binding0.00451696322521827
GO:0001501skeletal development0.0189008761426242
GO:0005529sugar binding0.0193667460790394
GO:0016337cell-cell adhesion0.0231487892777975
GO:0006811ion transport0.0260616293747252
GO:0030166proteoglycan biosynthetic process0.0285255231838653
GO:0044262cellular carbohydrate metabolic process0.0292110437925668
GO:0009888tissue development0.0345915528954376
GO:0005921gap junction0.039418383839295
GO:0005975carbohydrate metabolic process0.0473343727651521



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>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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