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MCL coexpression mm9:170: Difference between revisions

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|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0002370!1.88e-33!23;UBERON:0000974!1.88e-33!23;UBERON:0004807!1.88e-33!23;UBERON:0005058!1.88e-33!23;UBERON:0003351!1.88e-33!23;UBERON:0009113!1.88e-33!23;UBERON:0003295!1.88e-33!23;UBERON:0009722!1.88e-33!23;UBERON:0005562!1.88e-33!23;UBERON:0007690!1.88e-33!23;UBERON:0006562!6.85e-32!24;UBERON:0003408!6.85e-32!24;UBERON:0001557!6.85e-32!24;UBERON:0001042!6.85e-32!24;UBERON:0008814!6.85e-32!24;UBERON:0009145!6.85e-32!24;UBERON:0000072!6.72e-28!27;UBERON:0004177!1.07e-25!29;UBERON:0005057!1.07e-25!29;UBERON:0002193!2.93e-24!48;UBERON:0002405!2.93e-24!48;UBERON:0002390!7.41e-24!45;UBERON:0003061!7.41e-24!45;UBERON:0000077!3.25e-23!35;UBERON:0000063!1.34e-20!35;UBERON:0007811!6.46e-20!36;UBERON:0000065!5.36e-17!41;UBERON:0001004!1.70e-16!42;UBERON:0000153!5.08e-16!43;UBERON:0002384!1.08e-15!46;UBERON:0003929!3.11e-13!55;UBERON:0002368!8.80e-12!60;UBERON:0003081!3.31e-11!87;UBERON:0002530!1.48e-10!65;UBERON:0000490!2.47e-10!66;UBERON:0005911!1.05e-09!69;UBERON:0000949!3.96e-09!72;UBERON:0001041!8.25e-08!80;UBERON:0000926!9.10e-07!120;UBERON:0004120!9.10e-07!120;UBERON:0006603!9.10e-07!120
|ontology_enrichment_uberon=UBERON:0002370!1.88e-33!23;UBERON:0000974!1.88e-33!23;UBERON:0004807!1.88e-33!23;UBERON:0005058!1.88e-33!23;UBERON:0003351!1.88e-33!23;UBERON:0009113!1.88e-33!23;UBERON:0003295!1.88e-33!23;UBERON:0009722!1.88e-33!23;UBERON:0005562!1.88e-33!23;UBERON:0007690!1.88e-33!23;UBERON:0006562!6.85e-32!24;UBERON:0003408!6.85e-32!24;UBERON:0001557!6.85e-32!24;UBERON:0001042!6.85e-32!24;UBERON:0008814!6.85e-32!24;UBERON:0009145!6.85e-32!24;UBERON:0000072!6.72e-28!27;UBERON:0004177!1.07e-25!29;UBERON:0005057!1.07e-25!29;UBERON:0002193!2.93e-24!48;UBERON:0002405!2.93e-24!48;UBERON:0002390!7.41e-24!45;UBERON:0003061!7.41e-24!45;UBERON:0000077!3.25e-23!35;UBERON:0000063!1.34e-20!35;UBERON:0007811!6.46e-20!36;UBERON:0000065!5.36e-17!41;UBERON:0001004!1.70e-16!42;UBERON:0000153!5.08e-16!43;UBERON:0002384!1.08e-15!46;UBERON:0003929!3.11e-13!55;UBERON:0002368!8.80e-12!60;UBERON:0003081!3.31e-11!87;UBERON:0002530!1.48e-10!65;UBERON:0000490!2.47e-10!66;UBERON:0005911!1.05e-09!69;UBERON:0000949!3.96e-09!72;UBERON:0001041!8.25e-08!80;UBERON:0000926!9.10e-07!120;UBERON:0004120!9.10e-07!120;UBERON:0006603!9.10e-07!120
|tfbs_overrepresentation_for_novel_motifs=0.0368425,0.289095,0.531643,0.0549918,0.117992,0.554849,0.531771,0.275393,0.445059,0.00991314,0.224671,0.269937,0.178685,0.888555,0.583095,0,0.666151,0.669896,0.332291,0.422926,0.413456,0.134384,0.559718,0.209381,0.195571,0.631967,0.198884,0.190849,0.501436,0.149302,0.575329,0.148789,0.0177876,0.223302,0.252771,0.0694469,0.283525,0.494179,0.0680796,0.155254,0.330374,0.354139,0.147254,0.405175,0.191785,0.481193,0.86745,0.406662,0.170532,0.333782,0.303561,0.70312,0.848119,0.234657,0.688889,0.13559,0.213587,0.251353,0.172709,0.574727,0.427666,0.185146,0.505143,0.290468,0.144712,0.338619,0.344037,0.634194,0.421425,0.506486,0.289427,0.116427,0.0119773,0.269269,0.237217,0.544038,0.022969,0.22254,0.805526,0.138244,0.301478,0.345517,0.411335,1.34598,0.564631,0.0587607,0.824173,0.0531807,0.514672,0.781252,0.398019,0.571972,0.919879,0.535346,0.00217472,0.0483241,0.0541151,0.476333,0.505729,0.0149107,1.34796,0.454408,0.22324,0.63083,0.303022,0.179283,0.756342,0.205864,0.144639,0.880585,0.379909,0.63774,0.899307,0.231746,0.403606,0.0191115,0.257645,0.308594,0.668903,1.04186,0.273037,0.564014,0.636706,0.48189,0.447254,0.81383,0.300554,0.463067,0.34289,0.130862,0.609259,0.141084,0.320777,0.340315,0.420872,0.0170796,0.419895,0.357053,0.381878,1.13029,0.751949,0.347609,1.47132,0.469198,0.0877068,0.180371,0.237618,1.09202,0.0410569,0.216741,0.0291672,0.00238017,0.664207,0.0533224,0.0368708,0.292075,0.39903,1.79322,0.613938,0.239401,0.389333,0.563372,0.814832,0.0979978,0.291645,0.326774,0.816494,0.498991,0.0318099
}}
}}

Revision as of 17:55, 26 November 2012


Phase1 CAGE Peaks

 Short description
Mm9::chr10:128182501..128182522,-p@chr10:128182501..128182522
-
Mm9::chr10:18732348..18732353,-p@chr10:18732348..18732353
-
Mm9::chr10:18781687..18781698,-p@chr10:18781687..18781698
-
Mm9::chr10:20955283..20955294,+p@chr10:20955283..20955294
+
Mm9::chr10:3363575..3363598,+p@chr10:3363575..3363598
+
Mm9::chr11:105894898..105894916,+p@chr11:105894898..105894916
+
Mm9::chr11:32435982..32435997,+p@chr11:32435982..32435997
+
Mm9::chr11:5442142..5442173,-p2@Ccdc117
Mm9::chr12:109416693..109416707,+p@chr12:109416693..109416707
+
Mm9::chr13:110693261..110693272,+p31@Pde4d
Mm9::chr13:110693297..110693318,+p6@Pde4d
Mm9::chr13:110693331..110693341,+p33@Pde4d
Mm9::chr14:30299781..30299783,+p@chr14:30299781..30299783
+
Mm9::chr14:60796479..60796489,+p@chr14:60796479..60796489
+
Mm9::chr14:79935403..79935414,+p@chr14:79935403..79935414
+
Mm9::chr14:79935569..79935580,+p@chr14:79935569..79935580
+
Mm9::chr15:59973174..59973208,-p@chr15:59973174..59973208
-
Mm9::chr15:99871828..99871843,-p@chr15:99871828..99871843
-
Mm9::chr16:91545956..91545967,+p@chr16:91545956..91545967
+
Mm9::chr18:21121389..21121402,+p@chr18:21121389..21121402
+
Mm9::chr18:5594197..5594228,+p7@Zeb1
Mm9::chr18:56628893..56628932,+p2@Gramd3
Mm9::chr18:75527810..75527843,+p@chr18:75527810..75527843
+
Mm9::chr19:46694450..46694460,-p@chr19:46694450..46694460
-
Mm9::chr19:53258922..53258925,+p@chr19:53258922..53258925
+
Mm9::chr19:53495864..53495876,+p@chr19:53495864..53495876
+
Mm9::chr19:6400611..6400622,+p12@Rasgrp2
Mm9::chr1:185858332..185858352,+p1@Dusp10
Mm9::chr1:36364904..36364920,+p@chr1:36364904..36364920
+
Mm9::chr1:44159186..44159189,-p5@1700029F09Rik
Mm9::chr1:61034784..61034801,+p2@Icos
Mm9::chr2:32023450..32023498,-p@chr2:32023450..32023498
-
Mm9::chr2:59176806..59176817,+p@chr2:59176806..59176817
+
Mm9::chr2:91022340..91022369,+p@chr2:91022340..91022369
+
Mm9::chr3:130816799..130816810,+p@chr3:130816799..130816810
+
Mm9::chr3:51363691..51363703,+p2@5031434O11Rik
Mm9::chr3:87942813..87942826,+p@chr3:87942813..87942826
+
Mm9::chr4:102242670..102242729,+p5@Pde4b
Mm9::chr4:102242739..102242755,+p28@Pde4b
Mm9::chr4:106851921..106851931,-p14@2210012G02Rik
Mm9::chr4:153905378..153905379,+p@chr4:153905378..153905379
+
Mm9::chr4:59344603..59344615,-p@chr4:59344603..59344615
-
Mm9::chr4:59344643..59344658,-p@chr4:59344643..59344658
-
Mm9::chr4:59344867..59344881,+p@chr4:59344867..59344881
+
Mm9::chr4:8727359..8727384,+p@chr4:8727359..8727384
+
Mm9::chr5:114275427..114275442,-p@chr5:114275427..114275442
-
Mm9::chr5:123439357..123439375,+p1@ENSMUST00000148466
p1@uc008zmw.1
Mm9::chr5:124456124..124456163,-p@chr5:124456124..124456163
-
Mm9::chr5:124460721..124460727,-p@chr5:124460721..124460727
-
Mm9::chr5:124481027..124481031,-p@chr5:124481027..124481031
-
Mm9::chr5:124482223..124482299,-p1@Vps37b
Mm9::chr5:124529081..124529092,-p7@Abcb9
Mm9::chr5:124561794..124561804,-p@chr5:124561794..124561804
-
Mm9::chr5:138227879..138227896,-p1@Mepce
Mm9::chr5:31829478..31829485,+p5@Slc4a1ap
Mm9::chr7:46773162..46773172,+p2@Zfp619
Mm9::chr8:26712166..26712175,+p16@Whsc1l1
Mm9::chr8:35217716..35217740,+p@chr8:35217716..35217740
+
Mm9::chr8:35217753..35217784,+p@chr8:35217753..35217784
+
Mm9::chr8:74686848..74686859,-p@chr8:74686848..74686859
-
Mm9::chr8:75016122..75016164,+p@chr8:75016122..75016164
+
Mm9::chr8:84082901..84082910,+p@chr8:84082901..84082910
+
Mm9::chr8:87502021..87502042,-p@chr8:87502021..87502042
-
Mm9::chrX:131136047..131136052,-p4@Gla


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:00041143',5'-cyclic-nucleotide phosphodiesterase activity0.0324727093882639
GO:0004112cyclic-nucleotide phosphodiesterase activity0.0324727093882639



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>

Cell Type
Ontology termp-valuen
lymphoid lineage restricted progenitor cell5.18e-2712
mature alpha-beta T cell6.10e-259
alpha-beta T cell6.10e-259
immature T cell6.10e-259
mature T cell6.10e-259
immature alpha-beta T cell6.10e-259
lymphocyte9.40e-2513
common lymphoid progenitor9.40e-2513
T cell2.23e-2411
pro-T cell2.23e-2411
hematopoietic lineage restricted progenitor cell3.09e-2225
CD4-positive, alpha-beta T cell4.15e-228
hematopoietic cell1.41e-2132
hematopoietic oligopotent progenitor cell1.41e-2132
hematopoietic stem cell1.41e-2132
angioblastic mesenchymal cell1.41e-2132
hematopoietic multipotent progenitor cell1.41e-2132
nucleate cell1.14e-1916
leukocyte2.24e-1817
nongranular leukocyte2.24e-1817
thymocyte1.22e-166
double negative thymocyte1.22e-166
naive T cell1.22e-166
double-positive, alpha-beta thymocyte1.22e-166
CD4-positive, alpha-beta thymocyte1.22e-166
naive thymus-derived CD4-positive, alpha-beta T cell1.22e-166
DN4 thymocyte1.22e-166
DN1 thymic pro-T cell1.22e-166
DN2 thymocyte1.22e-166
DN3 thymocyte1.22e-166
immature single positive thymocyte1.22e-166
early T lineage precursor1.22e-166
mature CD4 single-positive thymocyte1.22e-166
resting double-positive thymocyte1.22e-166
double-positive blast1.22e-166
CD69-positive double-positive thymocyte1.22e-166
CD69-positive, CD4-positive single-positive thymocyte1.22e-166
CD4-positive, CD8-intermediate double-positive thymocyte1.22e-166
CD24-positive, CD4 single-positive thymocyte1.22e-166
connective tissue cell1.08e-1546
mesenchymal cell1.08e-1546
motile cell9.21e-1354
stem cell4.29e-0897
megakaryocyte progenitor cell2.44e-076
megakaryocyte2.44e-076

Uber Anatomy
Ontology termp-valuen
thymus1.88e-3323
neck1.88e-3323
respiratory system epithelium1.88e-3323
hemolymphoid system gland1.88e-3323
pharyngeal epithelium1.88e-3323
thymic region1.88e-3323
pharyngeal gland1.88e-3323
entire pharyngeal arch endoderm1.88e-3323
thymus primordium1.88e-3323
early pharyngeal endoderm1.88e-3323
pharynx6.85e-3224
gland of gut6.85e-3224
upper respiratory tract6.85e-3224
chordate pharynx6.85e-3224
pharyngeal arch system6.85e-3224
pharyngeal region of foregut6.85e-3224
segment of respiratory tract6.72e-2827
hemopoietic organ1.07e-2529
immune organ1.07e-2529
hemolymphoid system2.93e-2448
immune system2.93e-2448
hematopoietic system7.41e-2445
blood island7.41e-2445
mixed endoderm/mesoderm-derived structure3.25e-2335
organ segment1.34e-2035
craniocervical region6.46e-2036
respiratory tract5.36e-1741
respiratory system1.70e-1642
anterior region of body5.08e-1643
connective tissue1.08e-1546
gut epithelium3.11e-1355
endocrine gland8.80e-1260
lateral plate mesoderm3.31e-1187
gland1.48e-1065
unilaminar epithelium2.47e-1066
endo-epithelium1.05e-0969
endocrine system3.96e-0972
foregut8.25e-0880
mesoderm9.10e-07120
mesoderm-derived structure9.10e-07120
presumptive mesoderm9.10e-07120


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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