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MCL coexpression mm9:239: Difference between revisions

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{{MCL_coexpression_mm9
{{MCL_coexpression_mm9
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|coexpression_dpi_cluster_scores_median=0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.110544086345426,1.45535602179364,0.482861297633124,0.418153668255242,0.556194597731905,0.44593214273782,0.0570741246689917,0,0,0,0,0,0,0,0,0,0,0.16338070954688,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.276314229565956,0,0,0,0,0,0,0,0.0652566657696677,0.10536076625968,0,0,0.0489051668165172,0.097805083983237,0.133153884834288,0.170978156452844,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0
|gostat_on_MCL_coexpression=GO:0003939;L-iditol 2-dehydrogenase activity;0.0132825759081275;20322!GO:0003692;left-handed Z-DNA binding;0.0132825759081275;56417!GO:0005792;microsome;0.0132825759081275;56615,13105!GO:0042598;vesicular fraction;0.0132825759081275;56615,13105!GO:0016553;base conversion or substitution editing;0.0132825759081275;56417!GO:0003726;double-stranded RNA adenosine deaminase activity;0.0132825759081275;56417!GO:0003969;RNA editase activity;0.0151784233633089;56417!GO:0004000;adenosine deaminase activity;0.0265506003537321;56417!GO:0031047;RNA-mediated gene silencing;0.0320874135331278;56417!GO:0043169;cation binding;0.0320874135331278;20322,56417,213573,13105!GO:0006749;glutathione metabolic process;0.0320874135331278;56615!GO:0046872;metal ion binding;0.0320874135331278;20322,56417,213573,13105!GO:0009451;RNA modification;0.0320874135331278;56417!GO:0005624;membrane fraction;0.0320874135331278;56615,13105!GO:0043167;ion binding;0.0320874135331278;20322,56417,213573,13105!GO:0019239;deaminase activity;0.0320874135331278;56417!GO:0051287;NAD binding;0.0320874135331278;20322!GO:0004364;glutathione transferase activity;0.0320874135331278;56615!GO:0016814;hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in cyclic amidines;0.0320874135331278;56417!GO:0000267;cell fraction;0.0325170541772116;56615,13105!GO:0003725;double-stranded RNA binding;0.0325170541772116;56417!GO:0016458;gene silencing;0.0325170541772116;56417!GO:0050381;unspecific monooxygenase activity;0.0368429415700452;13105!GO:0016712;oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, reduced flavin or flavoprotein as one donor, and incorporation of one atom of oxygen;0.0419004765711758;13105!GO:0005783;endoplasmic reticulum;0.0488021084113138;56615,13105!GO:0043566;structure-specific DNA binding;0.0488021084113138;56417!
|gostat_on_MCL_coexpression=GO:0003939;L-iditol 2-dehydrogenase activity;0.0132825759081275;20322!GO:0003692;left-handed Z-DNA binding;0.0132825759081275;56417!GO:0005792;microsome;0.0132825759081275;56615,13105!GO:0042598;vesicular fraction;0.0132825759081275;56615,13105!GO:0016553;base conversion or substitution editing;0.0132825759081275;56417!GO:0003726;double-stranded RNA adenosine deaminase activity;0.0132825759081275;56417!GO:0003969;RNA editase activity;0.0151784233633089;56417!GO:0004000;adenosine deaminase activity;0.0265506003537321;56417!GO:0031047;RNA-mediated gene silencing;0.0320874135331278;56417!GO:0043169;cation binding;0.0320874135331278;20322,56417,213573,13105!GO:0006749;glutathione metabolic process;0.0320874135331278;56615!GO:0046872;metal ion binding;0.0320874135331278;20322,56417,213573,13105!GO:0009451;RNA modification;0.0320874135331278;56417!GO:0005624;membrane fraction;0.0320874135331278;56615,13105!GO:0043167;ion binding;0.0320874135331278;20322,56417,213573,13105!GO:0019239;deaminase activity;0.0320874135331278;56417!GO:0051287;NAD binding;0.0320874135331278;20322!GO:0004364;glutathione transferase activity;0.0320874135331278;56615!GO:0016814;hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in cyclic amidines;0.0320874135331278;56417!GO:0000267;cell fraction;0.0325170541772116;56615,13105!GO:0003725;double-stranded RNA binding;0.0325170541772116;56417!GO:0016458;gene silencing;0.0325170541772116;56417!GO:0050381;unspecific monooxygenase activity;0.0368429415700452;13105!GO:0016712;oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, reduced flavin or flavoprotein as one donor, and incorporation of one atom of oxygen;0.0419004765711758;13105!GO:0005783;endoplasmic reticulum;0.0488021084113138;56615,13105!GO:0043566;structure-specific DNA binding;0.0488021084113138;56417!
}}
}}

Revision as of 12:38, 11 October 2012


Phase1 CAGE Peaks

 Short description
Mm9::chr10:124988598..124988600,+p@chr10:124988598..124988600
+
Mm9::chr10:36958849..36958852,+p@chr10:36958849..36958852
+
Mm9::chr10:94173889..94173890,-p@chr10:94173889..94173890
-
Mm9::chr11:118377098..118377101,+p@chr11:118377098..118377101
+
Mm9::chr15:82282802..82282815,+p1@Cyp2d9
Mm9::chr16:18410871..18410893,-p@chr16:18410871..18410893
-
Mm9::chr16:22899291..22899297,+p@chr16:22899291..22899297
+
Mm9::chr16:22899461..22899472,+p@chr16:22899461..22899472
+
Mm9::chr16:22899486..22899494,+p@chr16:22899486..22899494
+
Mm9::chr16:77838388..77838392,+p@chr16:77838388..77838392
+
Mm9::chr17:15914532..15914535,+p@chr17:15914532..15914535
+
Mm9::chr17:32067507..32067510,+p@chr17:32067507..32067510
+
Mm9::chr18:87925672..87925680,+p1@ENSMUST00000091776
Mm9::chr1:13864450..13864458,+p@chr1:13864450..13864458
+
Mm9::chr1:7167752..7167760,+p1@ENSMUST00000029124
Mm9::chr1:94791475..94791478,+p@chr1:94791475..94791478
+
Mm9::chr2:122060569..122060577,+p2@Sord
Mm9::chr2:156282978..156282979,+p@chr2:156282978..156282979
+
Mm9::chr2:172984701..172984706,+p@chr2:172984701..172984706
+
Mm9::chr3:14864162..14864173,+p@chr3:14864162..14864173
+
Mm9::chr3:89539611..89539638,+p@chr3:89539611..89539638
+
Mm9::chr4:50498164..50498166,+p@chr4:50498164..50498166
+
Mm9::chr4:60016350..60016358,+p1@Mup6
Mm9::chr4:61335128..61335131,-p1@LOC100048884
p1@Mup14
Mm9::chr4:61443256..61443260,-p2@Mup12
p2@Mup16
p2@Mup17
p2@Mup19
p2@Mup9
Mm9::chr4:61715146..61715151,-p1@Mup20
Mm9::chr5:127887029..127887031,+p@chr5:127887029..127887031
+
Mm9::chr5:44194868..44194871,+p@chr5:44194868..44194871
+
Mm9::chr6:138096234..138096265,+p@chr6:138096234..138096265
+
Mm9::chr6:138105225..138105237,+p@chr6:138105225..138105237
+
Mm9::chr7:112744083..112744109,-p@chr7:112744083..112744109
-
Mm9::chr7:148648620..148648622,+p12@Efcab4a
Mm9::chr8:13012412..13012413,+p@chr8:13012412..13012413
+
Mm9::chr9:120730227..120730233,+p@chr9:120730227..120730233
+
Mm9::chrX:45409736..45409738,+p@chrX:45409736..45409738
+


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:0003939L-iditol 2-dehydrogenase activity0.0132825759081275
GO:0003692left-handed Z-DNA binding0.0132825759081275
GO:0005792microsome0.0132825759081275
GO:0042598vesicular fraction0.0132825759081275
GO:0016553base conversion or substitution editing0.0132825759081275
GO:0003726double-stranded RNA adenosine deaminase activity0.0132825759081275
GO:0003969RNA editase activity0.0151784233633089
GO:0004000adenosine deaminase activity0.0265506003537321
GO:0031047RNA-mediated gene silencing0.0320874135331278
GO:0043169cation binding0.0320874135331278
GO:0006749glutathione metabolic process0.0320874135331278
GO:0046872metal ion binding0.0320874135331278
GO:0009451RNA modification0.0320874135331278
GO:0005624membrane fraction0.0320874135331278
GO:0043167ion binding0.0320874135331278
GO:0019239deaminase activity0.0320874135331278
GO:0051287NAD binding0.0320874135331278
GO:0004364glutathione transferase activity0.0320874135331278
GO:0016814hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in cyclic amidines0.0320874135331278
GO:0000267cell fraction0.0325170541772116
GO:0003725double-stranded RNA binding0.0325170541772116
GO:0016458gene silencing0.0325170541772116
GO:0050381unspecific monooxygenase activity0.0368429415700452
GO:0016712oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, reduced flavin or flavoprotein as one donor, and incorporation of one atom of oxygen0.0419004765711758
GO:0005783endoplasmic reticulum0.0488021084113138
GO:0043566structure-specific DNA binding0.0488021084113138



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)

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