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MCL coexpression mm9:112: Difference between revisions

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|coexpression_dpi_cluster_scores_median=0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.329579472089612,0.743062195690373,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.160047342874364,0.108252561213616,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0
|coexpression_dpi_cluster_scores_median=0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.329579472089612,0.743062195690373,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.160047342874364,0.108252561213616,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0
|gostat_on_MCL_coexpression=GO:0048856;anatomical structure development;0.000952200394169407;17295,15221,231532,192897,56443,11735,14176,243914,235379,12661,233752!GO:0007399;nervous system development;0.000952200394169407;17295,11735,14176,243914,235379,12661,233752!GO:0007275;multicellular organismal development;0.00129763837263494;17295,15221,231532,192897,108105,11735,14176,243914,235379,12661,233752!GO:0032502;developmental process;0.00212167718388141;17295,15221,231532,192897,108105,56443,11735,14176,243914,235379,12661,233752!GO:0009925;basal plasma membrane;0.00272932897512999;17295,192897!GO:0045178;basal part of cell;0.00292214534650913;17295,192897!GO:0048731;system development;0.0030665695854812;17295,15221,231532,11735,14176,235379,243914,12661,233752!GO:0043005;neuron projection;0.0155603656934145;11735,15165,12661!GO:0048869;cellular developmental process;0.0173731909726563;15221,231532,11735,14176,235379,243914,12661,233752!GO:0030154;cell differentiation;0.0173731909726563;15221,231532,11735,14176,235379,243914,12661,233752!GO:0022008;neurogenesis;0.020825909281943;11735,14176,243914,12661!GO:0042995;cell projection;0.0251860800119627;11735,15165,12661,56443!GO:0005008;hepatocyte growth factor receptor activity;0.0283642871491444;17295!GO:0008917;lipopolysaccharide N-acetylglucosaminyltransferase activity;0.0283642871491444;108105!GO:0001829;trophectodermal cell differentiation;0.0283642871491444;15221!GO:0030425;dendrite;0.0330954276798172;15165,12661!GO:0009653;anatomical structure morphogenesis;0.0330954276798172;11735,15221,231532,192897,12661,56443!GO:0032989;cellular structure morphogenesis;0.0377276756698914;11735,192897,12661,56443!GO:0000902;cell morphogenesis;0.0377276756698914;11735,192897,12661,56443!GO:0048666;neuron development;0.0386225960481618;11735,243914,12661!GO:0051450;myoblast proliferation;0.0402741059270088;17295!GO:0030424;axon;0.0402741059270088;11735,15165!GO:0032501;multicellular organismal process;0.0468740066234956;17295,15221,231532,192897,108105,11735,14176,243914,235379,12661,233752!GO:0016323;basolateral plasma membrane;0.0468740066234956;17295,192897!GO:0048012;hepatocyte growth factor receptor signaling pathway;0.0489103062839025;17295!GO:0032990;cell part morphogenesis;0.0489103062839025;11735,192897,12661!GO:0048858;cell projection morphogenesis;0.0489103062839025;11735,192897,12661!GO:0030030;cell projection organization and biogenesis;0.0489103062839025;11735,192897,12661!GO:0007411;axon guidance;0.0491670232970789;11735,12661!
|gostat_on_MCL_coexpression=GO:0048856;anatomical structure development;0.000952200394169407;17295,15221,231532,192897,56443,11735,14176,243914,235379,12661,233752!GO:0007399;nervous system development;0.000952200394169407;17295,11735,14176,243914,235379,12661,233752!GO:0007275;multicellular organismal development;0.00129763837263494;17295,15221,231532,192897,108105,11735,14176,243914,235379,12661,233752!GO:0032502;developmental process;0.00212167718388141;17295,15221,231532,192897,108105,56443,11735,14176,243914,235379,12661,233752!GO:0009925;basal plasma membrane;0.00272932897512999;17295,192897!GO:0045178;basal part of cell;0.00292214534650913;17295,192897!GO:0048731;system development;0.0030665695854812;17295,15221,231532,11735,14176,235379,243914,12661,233752!GO:0043005;neuron projection;0.0155603656934145;11735,15165,12661!GO:0048869;cellular developmental process;0.0173731909726563;15221,231532,11735,14176,235379,243914,12661,233752!GO:0030154;cell differentiation;0.0173731909726563;15221,231532,11735,14176,235379,243914,12661,233752!GO:0022008;neurogenesis;0.020825909281943;11735,14176,243914,12661!GO:0042995;cell projection;0.0251860800119627;11735,15165,12661,56443!GO:0005008;hepatocyte growth factor receptor activity;0.0283642871491444;17295!GO:0008917;lipopolysaccharide N-acetylglucosaminyltransferase activity;0.0283642871491444;108105!GO:0001829;trophectodermal cell differentiation;0.0283642871491444;15221!GO:0030425;dendrite;0.0330954276798172;15165,12661!GO:0009653;anatomical structure morphogenesis;0.0330954276798172;11735,15221,231532,192897,12661,56443!GO:0032989;cellular structure morphogenesis;0.0377276756698914;11735,192897,12661,56443!GO:0000902;cell morphogenesis;0.0377276756698914;11735,192897,12661,56443!GO:0048666;neuron development;0.0386225960481618;11735,243914,12661!GO:0051450;myoblast proliferation;0.0402741059270088;17295!GO:0030424;axon;0.0402741059270088;11735,15165!GO:0032501;multicellular organismal process;0.0468740066234956;17295,15221,231532,192897,108105,11735,14176,243914,235379,12661,233752!GO:0016323;basolateral plasma membrane;0.0468740066234956;17295,192897!GO:0048012;hepatocyte growth factor receptor signaling pathway;0.0489103062839025;17295!GO:0032990;cell part morphogenesis;0.0489103062839025;11735,192897,12661!GO:0048858;cell projection morphogenesis;0.0489103062839025;11735,192897,12661!GO:0030030;cell projection organization and biogenesis;0.0489103062839025;11735,192897,12661!GO:0007411;axon guidance;0.0491670232970789;11735,12661!
|ontology_enrichment_celltype=CL:0000217!1.66e-44!2;CL:0000328!1.66e-44!2;CL:0002573!1.66e-44!2;CL:0002376!1.66e-44!2;CL:0000218!1.66e-44!2;CL:0000692!1.66e-44!2;CL:0002377!1.66e-44!2;CL:0002375!1.66e-44!2;CL:0000215!4.03e-30!3;CL:0000630!4.03e-30!3;CL:0000325!1.13e-15!6;CL:0000107!1.26e-10!9;CL:0000333!7.63e-10!10;CL:0000095!7.63e-10!10;CL:0000243!7.63e-10!10;CL:0000123!7.63e-10!10;CL:0000125!7.63e-10!10;CL:0000030!7.63e-10!10;CL:0000339!7.63e-10!10;CL:0002319!6.31e-09!43;CL:0000221!9.66e-09!44;CL:0000133!9.66e-09!44;CL:0000055!6.29e-08!49
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0000010!3.07e-32!11;UBERON:0000011!1.54e-29!3;UBERON:0002410!1.26e-10!9
}}
}}

Revision as of 16:22, 11 October 2012


Phase1 CAGE Peaks

 Short description
Mm9::chr10:128359639..128359653,+p@chr10:128359639..128359653
+
Mm9::chr10:69209762..69209778,+p@chr10:69209762..69209778
+
Mm9::chr10:69209793..69209801,+p@chr10:69209793..69209801
+
Mm9::chr10:69248255..69248271,+p14@Ank3
Mm9::chr11:115835864..115835869,+p20@Itgb4
Mm9::chr11:115836221..115836231,+p10@Itgb4
Mm9::chr11:56925925..56925960,-p@chr11:56925925..56925960
-
Mm9::chr11:56942405..56942422,+p@chr11:56942405..56942422
+
Mm9::chr11:73026893..73026901,+p@chr11:73026893..73026901
+
Mm9::chr11:95431310..95431333,-p@chr11:95431310..95431333
-
Mm9::chr11:95431700..95431710,-p@chr11:95431700..95431710
-
Mm9::chr11:99720074..99720077,-p@chr11:99720074..99720077
-
Mm9::chr12:31569186..31569191,+p1@Fam150b
Mm9::chr12:45629895..45629920,+p@chr12:45629895..45629920
+
Mm9::chr12:53884241..53884258,+p@chr12:53884241..53884258
+
Mm9::chr12:53884275..53884286,+p@chr12:53884275..53884286
+
Mm9::chr12:86685402..86685408,-p@chr12:86685402..86685408
-
Mm9::chr12:86685417..86685445,-p@chr12:86685417..86685445
-
Mm9::chr13:118391116..118391132,+p2@Hcn1
Mm9::chr13:40779254..40779265,-p@chr13:40779254..40779265
-
Mm9::chr13:93453323..93453355,+p@chr13:93453323..93453355
+
Mm9::chr13:93463212..93463214,+p@chr13:93463212..93463214
+
Mm9::chr13:95819359..95819371,-p@chr13:95819359..95819371
-
Mm9::chr14:67691531..67691536,-p7@Ppp2r2a
Mm9::chr14:74279307..74279342,+p@chr14:74279307..74279342
+
Mm9::chr15:103345675..103345685,+p10@Pde1b
Mm9::chr15:6490258..6490270,+p@chr15:6490258..6490270
+
Mm9::chr15:87485402..87485411,+p@chr15:87485402..87485411
+
Mm9::chr15:87485433..87485449,+p@chr15:87485433..87485449
+
Mm9::chr15:87485458..87485465,+p@chr15:87485458..87485465
+
Mm9::chr15:90746400..90746406,-p@chr15:90746400..90746406
-
Mm9::chr16:19760918..19760929,+p8@B3gnt5
Mm9::chr16:19760995..19761002,+p15@B3gnt5
Mm9::chr16:32867596..32867603,-p@chr16:32867596..32867603
-
Mm9::chr16:45038561..45038571,+p@chr16:45038561..45038571
+
Mm9::chr17:35380038..35380095,+p@chr17:35380038..35380095
+
Mm9::chr17:35380097..35380121,+p@chr17:35380097..35380121
+
Mm9::chr17:71029236..71029253,-p@chr17:71029236..71029253
-
Mm9::chr17:73424057..73424098,-p@chr17:73424057..73424098
-
Mm9::chr18:21130153..21130163,+p@chr18:21130153..21130163
+
Mm9::chr18:57302436..57302450,+p8@Megf10
Mm9::chr18:57302477..57302482,+p21@Megf10
Mm9::chr18:57302491..57302512,+p12@Megf10
Mm9::chr1:112873900..112873909,-p3@Cdh19
Mm9::chr1:112873943..112873959,-p1@Cdh19
Mm9::chr1:122931854..122931863,+p@chr1:122931854..122931863
+
Mm9::chr1:135777494..135777503,+p@chr1:135777494..135777503
+
Mm9::chr1:135777519..135777524,+p@chr1:135777519..135777524
+
Mm9::chr1:88964576..88964593,+p@chr1:88964576..88964593
+
Mm9::chr1:92754564..92754577,+p@chr1:92754564..92754577
+
Mm9::chr1:92754583..92754595,+p@chr1:92754583..92754595
+
Mm9::chr2:108525989..108525997,-p@chr2:108525989..108525997
-
Mm9::chr2:131087778..131087783,+p9@Pank2
Mm9::chr2:13346379..13346390,-p@chr2:13346379..13346390
-
Mm9::chr2:13346395..13346412,-p@chr2:13346395..13346412
-
Mm9::chr2:142583784..142583792,-p@chr2:142583784..142583792
-
Mm9::chr2:163516416..163516431,-p@chr2:163516416..163516431
-
Mm9::chr2:163516500..163516503,-p@chr2:163516500..163516503
-
Mm9::chr2:163516561..163516571,-p@chr2:163516561..163516571
-
Mm9::chr2:91152821..91152832,-p@chr2:91152821..91152832
-
Mm9::chr2:92688875..92688880,+p@chr2:92688875..92688880
+
Mm9::chr3:129764403..129764426,-p13@Sec24b
Mm9::chr4:140480203..140480226,+p2@Padi2
Mm9::chr4:99323353..99323363,+p@chr4:99323353..99323363
+
Mm9::chr5:102910365..102910376,+p20@Arhgap24
Mm9::chr5:102910393..102910401,+p21@Arhgap24
Mm9::chr5:116856799..116856810,+p@chr5:116856799..116856810
+
Mm9::chr5:145651101..145651113,-p@chr5:145651101..145651113
-
Mm9::chr5:145865342..145865361,+p6@Arpc1a
Mm9::chr5:152054997..152055007,+p@chr5:152054997..152055007
+
Mm9::chr5:152055079..152055086,+p@chr5:152055079..152055086
+
Mm9::chr5:152055094..152055108,+p@chr5:152055094..152055108
+
Mm9::chr5:35996812..35996829,-p@chr5:35996812..35996829
-
Mm9::chr5:81113315..81113317,+p@chr5:81113315..81113317
+
Mm9::chr5:98683260..98683274,+p1@Fgf5
Mm9::chr5:98683341..98683353,+p2@Fgf5
Mm9::chr6:103460767..103460778,+p13@Chl1
Mm9::chr6:120953023..120953030,-p5@LOC100505050
Mm9::chr6:120953117..120953152,-p1@LOC100505050
Mm9::chr6:17413432..17413442,+p10@Met
Mm9::chr6:17413555..17413581,+p5@Met
Mm9::chr6:17414092..17414113,+p6@Met
Mm9::chr6:17441128..17441144,+p@chr6:17441128..17441144
+
Mm9::chr6:17441216..17441242,+p@chr6:17441216..17441242
+
Mm9::chr6:18763883..18763912,-p@chr6:18763883..18763912
-
Mm9::chr6:31038438..31038445,-p@chr6:31038438..31038445
-
Mm9::chr6:39508100..39508110,-p12@Dennd2a
Mm9::chr6:39508130..39508138,-p15@Dennd2a
Mm9::chr7:114809700..114809718,+p@chr7:114809700..114809718
+
Mm9::chr7:121897273..121897278,+p21@Insc
Mm9::chr7:121897294..121897307,+p16@Insc
Mm9::chr7:121897309..121897342,+p5@Insc
Mm9::chr7:121897346..121897351,+p20@Insc
Mm9::chr7:125737212..125737216,+p@chr7:125737212..125737216
+
Mm9::chr7:31844871..31844895,+p9@Lgi4
Mm9::chr7:31844925..31844939,+p11@Lgi4
Mm9::chr7:31844941..31844960,+p7@Lgi4
Mm9::chr8:113317485..113317497,-p@chr8:113317485..113317497
-
Mm9::chr8:74103312..74103347,+p21@Slc27a1
Mm9::chr9:108887208..108887226,+p@chr9:108887208..108887226
+
Mm9::chr9:108890352..108890409,+p@chr9:108890352..108890409
+
Mm9::chr9:14575600..14575609,-p8@1700012B09Rik
Mm9::chr9:21134801..21134809,+p@chr9:21134801..21134809
+
Mm9::chr9:38526609..38526640,+p4@Vwa5a
Mm9::chr9:54134286..54134301,+p1@Gldn
Mm9::chrX:143863732..143863735,-p2@Il13ra2
Mm9::chrX:149092014..149092030,-p@chrX:149092014..149092030
-


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:0048856anatomical structure development0.000952200394169407
GO:0007399nervous system development0.000952200394169407
GO:0007275multicellular organismal development0.00129763837263494
GO:0032502developmental process0.00212167718388141
GO:0009925basal plasma membrane0.00272932897512999
GO:0045178basal part of cell0.00292214534650913
GO:0048731system development0.0030665695854812
GO:0043005neuron projection0.0155603656934145
GO:0048869cellular developmental process0.0173731909726563
GO:0030154cell differentiation0.0173731909726563
GO:0022008neurogenesis0.020825909281943
GO:0042995cell projection0.0251860800119627
GO:0005008hepatocyte growth factor receptor activity0.0283642871491444
GO:0008917lipopolysaccharide N-acetylglucosaminyltransferase activity0.0283642871491444
GO:0001829trophectodermal cell differentiation0.0283642871491444
GO:0030425dendrite0.0330954276798172
GO:0009653anatomical structure morphogenesis0.0330954276798172
GO:0032989cellular structure morphogenesis0.0377276756698914
GO:0000902cell morphogenesis0.0377276756698914
GO:0048666neuron development0.0386225960481618
GO:0051450myoblast proliferation0.0402741059270088
GO:0030424axon0.0402741059270088
GO:0032501multicellular organismal process0.0468740066234956
GO:0016323basolateral plasma membrane0.0468740066234956
GO:0048012hepatocyte growth factor receptor signaling pathway0.0489103062839025
GO:0032990cell part morphogenesis0.0489103062839025
GO:0048858cell projection morphogenesis0.0489103062839025
GO:0030030cell projection organization and biogenesis0.0489103062839025
GO:0007411axon guidance0.0491670232970789



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><br>

Uber Anatomy
Ontology termp-valuen
peripheral nervous system3.07e-3211
parasympathetic nervous system1.54e-293
autonomic nervous system1.26e-109


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)

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