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MCL coexpression mm9:604: Difference between revisions

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{{MCL_coexpression_mm9
{{MCL_coexpression_mm9
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|gostat_on_MCL_coexpression=GO:0006865;amino acid transport;0.00742592749386153;26889,30962!GO:0015837;amine transport;0.00742592749386153;26889,30962!GO:0046942;carboxylic acid transport;0.00742592749386153;26889,30962!GO:0015849;organic acid transport;0.00742592749386153;26889,30962!GO:0051938;L-glutamate import;0.00742592749386153;26889!GO:0001306;age-dependent response to oxidative stress;0.00742592749386153;26889!GO:0007571;age-dependent general metabolic decline;0.00742592749386153;26889!GO:0051935;glutamate uptake during transmission of nerve impulse;0.00742592749386153;26889!GO:0043092;L-amino acid import;0.00742592749386153;26889!GO:0043090;amino acid import;0.00742592749386153;26889!GO:0051933;amino acid uptake during transmission of nerve impulse;0.00742592749386153;26889!GO:0043066;negative regulation of apoptosis;0.0227637367820043;17940,26889!GO:0043069;negative regulation of programmed cell death;0.0227637367820043;17940,26889!GO:0015813;L-glutamate transport;0.0233271231683103;26889!GO:0050881;musculoskeletal movement;0.0240092682974037;26889!GO:0015800;acidic amino acid transport;0.0240092682974037;26889!GO:0050879;multicellular organismal movement;0.0240092682974037;26889!GO:0050884;neuromuscular process controlling posture;0.0244854287352586;26889!GO:0021517;ventral spinal cord development;0.0244854287352586;26889!GO:0021522;spinal cord motor neuron differentiation;0.0244854287352586;26889!GO:0001504;neurotransmitter uptake;0.0259651260297395;26889!GO:0021515;cell differentiation in spinal cord;0.0259651260297395;26889!GO:0035176;social behavior;0.028379572271805;26889!GO:0060041;retina development in camera-type eye;0.0293680300337478;26889!GO:0060052;neurofilament cytoskeleton organization and biogenesis;0.0293680300337478;26889!GO:0015807;L-amino acid transport;0.0302090572509609;26889!GO:0045494;photoreceptor cell maintenance;0.0302090572509609;26889!GO:0021510;spinal cord development;0.0365453531738146;26889!GO:0007006;mitochondrial membrane organization and biogenesis;0.0365453531738146;26889!GO:0008306;associative learning;0.0380383978584187;26889!GO:0007040;lysosome organization and biogenesis;0.0394342539518126;26889!GO:0018024;histone-lysine N-methyltransferase activity;0.0395714715565424;67956!GO:0016278;lysine N-methyltransferase activity;0.0395714715565424;67956!GO:0045104;intermediate filament cytoskeleton organization and biogenesis;0.0395714715565424;26889!GO:0016279;protein-lysine N-methyltransferase activity;0.0395714715565424;67956!GO:0007033;vacuole organization and biogenesis;0.0429842832395465;26889!GO:0045103;intermediate filament-based process;0.0436800695348437;26889!GO:0042981;regulation of apoptosis;0.0436800695348437;17940,26889!GO:0043067;regulation of programmed cell death;0.0436800695348437;17940,26889!GO:0007628;adult walking behavior;0.0436800695348437;26889!GO:0051705;behavioral interaction between organisms;0.0436800695348437;26889!GO:0042054;histone methyltransferase activity;0.0465011535712391;67956!
|gostat_on_MCL_coexpression=GO:0006865;amino acid transport;0.00742592749386153;26889,30962!GO:0015837;amine transport;0.00742592749386153;26889,30962!GO:0046942;carboxylic acid transport;0.00742592749386153;26889,30962!GO:0015849;organic acid transport;0.00742592749386153;26889,30962!GO:0051938;L-glutamate import;0.00742592749386153;26889!GO:0001306;age-dependent response to oxidative stress;0.00742592749386153;26889!GO:0007571;age-dependent general metabolic decline;0.00742592749386153;26889!GO:0051935;glutamate uptake during transmission of nerve impulse;0.00742592749386153;26889!GO:0043092;L-amino acid import;0.00742592749386153;26889!GO:0043090;amino acid import;0.00742592749386153;26889!GO:0051933;amino acid uptake during transmission of nerve impulse;0.00742592749386153;26889!GO:0043066;negative regulation of apoptosis;0.0227637367820043;17940,26889!GO:0043069;negative regulation of programmed cell death;0.0227637367820043;17940,26889!GO:0015813;L-glutamate transport;0.0233271231683103;26889!GO:0050881;musculoskeletal movement;0.0240092682974037;26889!GO:0015800;acidic amino acid transport;0.0240092682974037;26889!GO:0050879;multicellular organismal movement;0.0240092682974037;26889!GO:0050884;neuromuscular process controlling posture;0.0244854287352586;26889!GO:0021517;ventral spinal cord development;0.0244854287352586;26889!GO:0021522;spinal cord motor neuron differentiation;0.0244854287352586;26889!GO:0001504;neurotransmitter uptake;0.0259651260297395;26889!GO:0021515;cell differentiation in spinal cord;0.0259651260297395;26889!GO:0035176;social behavior;0.028379572271805;26889!GO:0060041;retina development in camera-type eye;0.0293680300337478;26889!GO:0060052;neurofilament cytoskeleton organization and biogenesis;0.0293680300337478;26889!GO:0015807;L-amino acid transport;0.0302090572509609;26889!GO:0045494;photoreceptor cell maintenance;0.0302090572509609;26889!GO:0021510;spinal cord development;0.0365453531738146;26889!GO:0007006;mitochondrial membrane organization and biogenesis;0.0365453531738146;26889!GO:0008306;associative learning;0.0380383978584187;26889!GO:0007040;lysosome organization and biogenesis;0.0394342539518126;26889!GO:0018024;histone-lysine N-methyltransferase activity;0.0395714715565424;67956!GO:0016278;lysine N-methyltransferase activity;0.0395714715565424;67956!GO:0045104;intermediate filament cytoskeleton organization and biogenesis;0.0395714715565424;26889!GO:0016279;protein-lysine N-methyltransferase activity;0.0395714715565424;67956!GO:0007033;vacuole organization and biogenesis;0.0429842832395465;26889!GO:0045103;intermediate filament-based process;0.0436800695348437;26889!GO:0042981;regulation of apoptosis;0.0436800695348437;17940,26889!GO:0043067;regulation of programmed cell death;0.0436800695348437;17940,26889!GO:0007628;adult walking behavior;0.0436800695348437;26889!GO:0051705;behavioral interaction between organisms;0.0436800695348437;26889!GO:0042054;histone methyltransferase activity;0.0465011535712391;67956!
}}
}}

Revision as of 12:44, 11 October 2012


Phase1 CAGE Peaks

 Short description
Mm9::chr11:69780398..69780413,+p2@Cldn7
Mm9::chr13:101222804..101222815,-p1@Naip1
Mm9::chr14:52636491..52636519,+p2@G630016D24Rik
Mm9::chr1:172815273..172815329,-p3@Dusp12
Mm9::chr1:178927958..178928000,+p2@Sdccag8
Mm9::chr1:95057484..95057532,-p1@2310007B03Rik
Mm9::chr5:124901158..124901176,+p13@Setd8
Mm9::chr7:104979429..104979440,+p@chr7:104979429..104979440
+
Mm9::chr7:17507398..17507413,+p@chr7:17507398..17507413
+
Mm9::chr7:36234155..36234162,+p6@Slc7a9
Mm9::chr8:14888022..14888037,+p7@Cln8
Mm9::chr9:95715715..95715726,-p3@Pls1


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:0006865amino acid transport0.00742592749386153
GO:0015837amine transport0.00742592749386153
GO:0046942carboxylic acid transport0.00742592749386153
GO:0015849organic acid transport0.00742592749386153
GO:0051938L-glutamate import0.00742592749386153
GO:0001306age-dependent response to oxidative stress0.00742592749386153
GO:0007571age-dependent general metabolic decline0.00742592749386153
GO:0051935glutamate uptake during transmission of nerve impulse0.00742592749386153
GO:0043092L-amino acid import0.00742592749386153
GO:0043090amino acid import0.00742592749386153
GO:0051933amino acid uptake during transmission of nerve impulse0.00742592749386153
GO:0043066negative regulation of apoptosis0.0227637367820043
GO:0043069negative regulation of programmed cell death0.0227637367820043
GO:0015813L-glutamate transport0.0233271231683103
GO:0050881musculoskeletal movement0.0240092682974037
GO:0015800acidic amino acid transport0.0240092682974037
GO:0050879multicellular organismal movement0.0240092682974037
GO:0050884neuromuscular process controlling posture0.0244854287352586
GO:0021517ventral spinal cord development0.0244854287352586
GO:0021522spinal cord motor neuron differentiation0.0244854287352586
GO:0001504neurotransmitter uptake0.0259651260297395
GO:0021515cell differentiation in spinal cord0.0259651260297395
GO:0035176social behavior0.028379572271805
GO:0060041retina development in camera-type eye0.0293680300337478
GO:0060052neurofilament cytoskeleton organization and biogenesis0.0293680300337478
GO:0015807L-amino acid transport0.0302090572509609
GO:0045494photoreceptor cell maintenance0.0302090572509609
GO:0021510spinal cord development0.0365453531738146
GO:0007006mitochondrial membrane organization and biogenesis0.0365453531738146
GO:0008306associative learning0.0380383978584187
GO:0007040lysosome organization and biogenesis0.0394342539518126
GO:0018024histone-lysine N-methyltransferase activity0.0395714715565424
GO:0016278lysine N-methyltransferase activity0.0395714715565424
GO:0045104intermediate filament cytoskeleton organization and biogenesis0.0395714715565424
GO:0016279protein-lysine N-methyltransferase activity0.0395714715565424
GO:0007033vacuole organization and biogenesis0.0429842832395465
GO:0045103intermediate filament-based process0.0436800695348437
GO:0042981regulation of apoptosis0.0436800695348437
GO:0043067regulation of programmed cell death0.0436800695348437
GO:0007628adult walking behavior0.0436800695348437
GO:0051705behavioral interaction between organisms0.0436800695348437
GO:0042054histone methyltransferase activity0.0465011535712391



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}}}