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MCL coexpression mm9:760: Difference between revisions

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{{MCL_coexpression_mm9
{{MCL_coexpression_mm9
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|coexpression_dpi_cluster_scores_median=0.064513712786576,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.115321149766792,0,0,0,0.0862481039219708,0.0771606661507038,0.107200755467032,0,0,0,0,0.180274689346406,0.109421078997306,0,0,0,0.213207239280454,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.551017298218583,0.641198182396786,0.540751926847053,0,1.40452636520987,0.785052424066859,0,0,0,0,0,0,0,0.0694776635602275,0,0,0,0,0,0,0,0,0.121735003810417,0.0866592903778752,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0509235292940968,0,0,0,0.0898705446131073,0,0,0,0.0523528812100954,0.0388988969149198,0,0,0.0752205997629372,0.0703892716151147,0.0860734338295156,0.106546909924599,0.12977112683364,0.0812688455295622,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.127993717815825,0,0,0,0.0294389011296462,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0543491846550801,0,0,0,0,0,0,0,0,0,0,0,0,0.12315552345362,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0661577744756082,0,0,0,0,0,0,0.0254340553719351,0.0489745727197172,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.034489466458534,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0424616899933645,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0945084131504676,0,0.073294297058821,0,0.081359932135904,0.120876255993453,0,0,0,0.0388749848471105,0.0523284672130554,0.0690411384905589,0,0.0476191773904887,0,0,0,0,0.0709519923534245,0,0.0589368614163519,0.0390607415003592,0.0678996586311492,0,0.101427320830301,0,0,0.0486884105045233,0.0780974029773103,0,0.0625582350728301,0.0766064454112358,0,0.091291089277545,0,0,0,0
|gostat_on_MCL_coexpression=GO:0005085;guanyl-nucleotide exchange factor activity;0.0242392330827444;102075,110596!GO:0048666;neuron development;0.0242392330827444;110596,18742!GO:0007417;central nervous system development;0.0242392330827444;110596,18742!GO:0030182;neuron differentiation;0.0242392330827444;110596,18742!GO:0030695;GTPase regulator activity;0.0242392330827444;102075,110596!GO:0048699;generation of neurons;0.0242392330827444;110596,18742!GO:0060052;neurofilament cytoskeleton organization and biogenesis;0.0242392330827444;110596!GO:0021955;central nervous system neuron axonogenesis;0.0242392330827444;110596!GO:0022008;neurogenesis;0.0242392330827444;110596,18742!GO:0030901;midbrain development;0.0262535463198016;18742!GO:0045104;intermediate filament cytoskeleton organization and biogenesis;0.0368669614433751;110596!GO:0045103;intermediate filament-based process;0.038522481583093;110596!GO:0021954;central nervous system neuron development;0.038522481583093;110596!GO:0021953;central nervous system neuron differentiation;0.0408709206211934;110596!GO:0007275;multicellular organismal development;0.0421558894881009;110596,18742,14051!GO:0007399;nervous system development;0.0447041300673786;110596,18742!
|gostat_on_MCL_coexpression=GO:0005085;guanyl-nucleotide exchange factor activity;0.0242392330827444;102075,110596!GO:0048666;neuron development;0.0242392330827444;110596,18742!GO:0007417;central nervous system development;0.0242392330827444;110596,18742!GO:0030182;neuron differentiation;0.0242392330827444;110596,18742!GO:0030695;GTPase regulator activity;0.0242392330827444;102075,110596!GO:0048699;generation of neurons;0.0242392330827444;110596,18742!GO:0060052;neurofilament cytoskeleton organization and biogenesis;0.0242392330827444;110596!GO:0021955;central nervous system neuron axonogenesis;0.0242392330827444;110596!GO:0022008;neurogenesis;0.0242392330827444;110596,18742!GO:0030901;midbrain development;0.0262535463198016;18742!GO:0045104;intermediate filament cytoskeleton organization and biogenesis;0.0368669614433751;110596!GO:0045103;intermediate filament-based process;0.038522481583093;110596!GO:0021954;central nervous system neuron development;0.038522481583093;110596!GO:0021953;central nervous system neuron differentiation;0.0408709206211934;110596!GO:0007275;multicellular organismal development;0.0421558894881009;110596,18742,14051!GO:0007399;nervous system development;0.0447041300673786;110596,18742!
}}
}}

Revision as of 12:46, 11 October 2012


Phase1 CAGE Peaks

 Short description
Mm9::chr10:23069666..23069687,-p5@Eya4
Mm9::chr10:37035191..37035196,+p@chr10:37035191..37035196
+
Mm9::chr13:98786130..98786139,-p11@Rgnef
Mm9::chr14:112177430..112177435,-p@chr14:112177430..112177435
-
Mm9::chr3:66023831..66023849,+p2@Ptx3
Mm9::chr3:66023864..66023873,+p3@Ptx3
Mm9::chr3:66029440..66029442,+p@chr3:66029440..66029442
+
Mm9::chr4:140268695..140268697,+p@chr4:140268695..140268697
+
Mm9::chr8:107897165..107897177,+p1@Plekhg4


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:0005085guanyl-nucleotide exchange factor activity0.0242392330827444
GO:0048666neuron development0.0242392330827444
GO:0007417central nervous system development0.0242392330827444
GO:0030182neuron differentiation0.0242392330827444
GO:0030695GTPase regulator activity0.0242392330827444
GO:0048699generation of neurons0.0242392330827444
GO:0060052neurofilament cytoskeleton organization and biogenesis0.0242392330827444
GO:0021955central nervous system neuron axonogenesis0.0242392330827444
GO:0022008neurogenesis0.0242392330827444
GO:0030901midbrain development0.0262535463198016
GO:0045104intermediate filament cytoskeleton organization and biogenesis0.0368669614433751
GO:0045103intermediate filament-based process0.038522481583093
GO:0021954central nervous system neuron development0.038522481583093
GO:0021953central nervous system neuron differentiation0.0408709206211934
GO:0007275multicellular organismal development0.0421558894881009
GO:0007399nervous system development0.0447041300673786



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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