Personal tools

MCL coexpression mm9:841

From FANTOM5_SSTAR

Revision as of 21:20, 11 October 2012 by Autoedit (talk | contribs)
Jump to: navigation, search


Phase1 CAGE Peaks

 Short description
Mm9::chr1:34178286..34178303,+p11@Dst
Mm9::chr1:34178314..34178329,+p7@Dst
Mm9::chr5:122068874..122068934,-p1@Acad12
Mm9::chr6:86466214..86466234,-p1@uc009csb.1
Mm9::chr6:86466248..86466270,-p3@uc009csb.1
Mm9::chr6:86466277..86466290,-p4@uc009csb.1
Mm9::chr7:96781385..96781422,+p2@Me3
Mm9::chr7:96781461..96781503,+p5@Me3
Mm9::chrX:156576281..156576303,-p1@Pdha1


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:0030056hemidesmosome0.00928461847680428
GO:0004473malate dehydrogenase (oxaloacetate-decarboxylating) (NADP+) activity0.00928461847680428
GO:0004738pyruvate dehydrogenase activity0.00928461847680428
GO:0008090retrograde axon cargo transport0.00928461847680428
GO:0004739pyruvate dehydrogenase (acetyl-transferring) activity0.00928461847680428
GO:0044262cellular carbohydrate metabolic process0.00928461847680428
GO:0031122cytoplasmic microtubule organization and biogenesis0.00928461847680428
GO:0004470malic enzyme activity0.00928461847680428
GO:0006108malate metabolic process0.0103156775094049
GO:0005975carbohydrate metabolic process0.0104423344548168
GO:0016624oxidoreductase activity, acting on the aldehyde or oxo group of donors, disulfide as acceptor0.0104423344548168
GO:0016615malate dehydrogenase activity0.0104423344548168
GO:0009925basal plasma membrane0.0104423344548168
GO:0060053neurofilament cytoskeleton0.0104423344548168
GO:0045178basal part of cell0.0104423344548168
GO:0043648dicarboxylic acid metabolic process0.0104423344548168
GO:0008088axon cargo transport0.0109194899359178
GO:0031110regulation of microtubule polymerization or depolymerization0.0134045032055733
GO:0031109microtubule polymerization or depolymerization0.0136750999806115
GO:0006100tricarboxylic acid cycle intermediate metabolic process0.0139185353958062
GO:0051287NAD binding0.019434306341141
GO:0044444cytoplasmic part0.0241329633513848
GO:0016491oxidoreductase activity0.0246206447328127
GO:0030055cell-matrix junction0.0270341658124554
GO:0016903oxidoreductase activity, acting on the aldehyde or oxo group of donors0.0281726907363467
GO:0005739mitochondrion0.0293869201483859
GO:0006096glycolysis0.0293869201483859
GO:0007050cell cycle arrest0.0293869201483859
GO:0008017microtubule binding0.0293869201483859
GO:0006007glucose catabolic process0.0296262072510759
GO:0046365monosaccharide catabolic process0.0296262072510759
GO:0019320hexose catabolic process0.0296262072510759
GO:0051128regulation of cellular component organization and biogenesis0.0296262072510759
GO:0015631tubulin binding0.0296262072510759
GO:0046164alcohol catabolic process0.0296262072510759
GO:0000226microtubule cytoskeleton organization and biogenesis0.0329035671846674
GO:0044275cellular carbohydrate catabolic process0.0330111061329209
GO:0016323basolateral plasma membrane0.0340829371096963
GO:0016052carbohydrate catabolic process0.0341540971008432
GO:0007018microtubule-based movement0.0383646209931261
GO:0006006glucose metabolic process0.0431054408632943
GO:0030705cytoskeleton-dependent intracellular transport0.0431054408632943
GO:0016616oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor0.0472273373491732
GO:0050662coenzyme binding0.0475000923347259
GO:0045786negative regulation of progression through cell cycle0.0475000923347259
GO:0016614oxidoreductase activity, acting on CH-OH group of donors0.0475000923347259
GO:0045111intermediate filament cytoskeleton0.0475000923347259
GO:0019318hexose metabolic process0.0499452758871698



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><br>uberon_data<br><br>


Uber Anatomy
Ontology termp-valuen
cardiovascular system6.86e-0823
circulatory system6.86e-0823
primary circulatory organ4.71e-0718
heart4.71e-0718
primitive heart tube4.71e-0718
primary heart field4.71e-0718
anterior lateral plate mesoderm4.71e-0718
heart tube4.71e-0718
heart primordium4.71e-0718
cardiac mesoderm4.71e-0718
cardiogenic plate4.71e-0718
heart rudiment4.71e-0718


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}}}