MitoGenesisDB: Mitochondrial Spatio-Temporal Expression Database

DEFINITIONS

MLR: Mitochondrial Localization of mRNA (MLR). The mRNA localization is quantified by the percentage of yeast cells that exhibit a significant number of mRNAs to mitochondria proximity (see Saint-Georges et al., 2008 for more details). A threshold value of 7% distinguishes the mitochondria-localized mRNAs (7 to 100%, classes I and II), from the cytoplasmic free mRNAs (0 to 7%, class III).

mRNA classes: Four different classes (class I, II, III and IV) that distinguish the cellular sites where mRNAs are translated (see Saint-Georges et al., 2008 for more details).

Class I mRNAs: Nuclear-encoded mRNAs whose asymmetric localization to the vicinity of mitochondria depend on the mRNA-binding protein Puf3p (MLR > 7%); they are translated in close association with the outer membrane.
Class II mRNAs: Nuclear-encoded mRNAs whose asymmetric localization to the vicinity of mitochondria does not depend on the mRNA-binding protein Puf3p (MLR > 7%); they are translated in close association with the outer membrane.
Class III mRNAs: Nuclear-encoded mRNAs not specifically localized to the vicinity of mitochondria (MLR < 7%); they are translated on cytoplasmic free polysomes and the obtained protein is post-translationally imported into mitochondria.
Class IV mRNAs: mRNAs encoded in the mitochondrial genome. They are translated to the vicinity of the inner membrane, inside mitochondria.

EDPM: Expression Decomposition based on Periodic Models (EDPM). EDPM is an algorithm developed in order to better characterize, using Yeast Metabolic Cycle (YMC) data, spatio-temporal phases (see Lelandais et al., 2009 for more details). With the EDPM algorithm, the nuclear genes encoding mitochondria-localized proteins were classified into 6 different expression phases (named A to F).

YMC expression profile (phases R/B, R/C and Ox): The Yeast Metabolic Cycle (YMC) can be observed when yeast cell cultures are grown in special conditions that induce synchronized oscillations of oxygen consumption with a period of about 4 to 5 hours (see Tu et al., 2005 for more details). Cells successively progress through three major phases of the YMC: Reductive/Bulding (R/B), Reductive/Charging (R/C) and Oxidative (Ox).

Correlation level between TR and mRNA, the r-coefficient: Transcription Rate (TR) and mRNA level data were collected for all yeast genes in diverse responses to carbon source shifts (see Garcia-Martinez et al., 2004 for more details). The Pearson coefficient, r, for correlations of individual values of TR versus mRNA level, reflects the global nature of gene regulation. A negative r coefficient underscores the importance of post-transcriptional regulation processes, whereas a positive value highlights the role of the transcription rate.