MitoGenesisDB: an expression data mining tool to explore spatio-temporal dynamics of mitochondrial biogenesis.
Mitochondria constitute complex and flexible cellular entities, which play crucial roles in normal and pathological cell conditions. The database MitoGenesisDB focuses on the dynamic of mitochondrial protein formation through global mRNA analyses. Three main parameters confer a global view of mitochondrial biogenesis: (i) time-course of mRNA production in highly synchronized yeast cell cultures, (ii) microarray analyses of mRNA localization that define translation sites and (iii) mRNA transcription rate and stability which characterize genes that are more dependent on post-transcriptional regulation processes. MitoGenesisDB integrates and establishes cross-comparisons between these data. Several model organisms can be analyzed via orthologous relationships between interspecies genes. More generally this database supports the 'post-transcriptional operon' model, which postulates that eukaryotes co-regulate related mRNAs based on their functional organization in ribonucleoprotein complexes. MitoGenesisDB allows identifying such groups of post-trancriptionally regulated genes and is thus a useful tool to analyze the complex relationships between transcriptional and post-transcriptional regulation processes. The case of respiratory chain assembly factors illustrates this point. The MitoGenesisDB interface is available at http://www.dsimb.inserm.fr/dsimb_tools/mitgene/.
Gelly
Jean-Christophe
JC
Dynamique des Structures et Interactions des Macromolécules Biologiques, INSERM, U665, Paris F-75015, France. jean-christophe.gelly@univ-paris-diderot.fr
Orgeur
Mickael
M
Jacq
Claude
C
Lelandais
Gaëlle
G
D057225:Data Mining; D030562:Databases, Protein; D004579:Electron Transport; D050259:Genes, Mitochondrial; D008928:Mitochondria / Q000235:genetics* / Q000378:metabolism; D024101:Mitochondrial Proteins / Q000235:genetics* / Q000378:metabolism; D014176:Protein Biosynthesis; D020871:RNA Stability; D012333:RNA, Messenger / Q000032:analysis / Q000378:metabolism; D012441:Saccharomyces cerevisiae / Q000235:genetics / Q000378:metabolism; D029701:Saccharomyces cerevisiae Proteins / Q000235:genetics* / Q000378:metabolism; D012984:Software; D014158:Transcription, Genetic
D024101:Mitochondrial Proteins; D012333:RNA, Messenger; D029701:Saccharomyces cerevisiae Proteins