Dataset Information

MitoGenesisDB: an expression data mining tool to explore spatio-temporal dynamics of mitochondrial biogenesis.

ABSTRACT: 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/.

SUBMITTER: Gelly JC

PROVIDER: S-EPMC3013754 | biostudies-literature | 2011 Jan

REPOSITORIES: biostudies-literature

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MitoGenesisDB: an expression data mining tool to explore spatio-temporal dynamics of mitochondrial biogenesis.

Gelly Jean-Christophe JC Orgeur Mickael M Jacq Claude C Lelandais Gaëlle G

Nucleic acids research 20100909 Database issue

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 transcript ...[more]

PMID: 20833631

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Project description:Accurate estimation of traffic emissions and analysis of spatio-temporal distribution on urban roads play a crucial role in the development of low-carbon transportation system. Traditionally, a region's emission characteristics have been studied using numerous emission models with GPS-based spatio-temporal data. Due to the heavy data processing needs of GPS-based data, emission characteristics for a large region have been studied by dividing the region into a limited number of smaller areas or units. Additionally, GPS data are based on a few vehicles in the traffic which does not fully reflect road conditions. This paper proposed an approach that can be used to study and calculate the spatio-temporal emission pattern of a region at a roadway section level by using Baidu's online traffic data and COPERT model. The proposed method can be used to estimate road-level emission patterns while avoiding the impact of redundant data in large datasets, making the dataset more reliable, applicable, and scalable. The proposed approach has been demonstrated through a study of spatio-temporal emission patterns in the Qiaoxi district within city of Shijiazhuang, China. Online data crawling technology was used to obtain data on urban road traffic speed and driving distance. The linear reference technology was used to construct a two-layer road network model to conduct the coupling and matching of traffic data with the road network data. The COPERT model was implemented to calculate the average traffic emissions on each road in the road network, and a traffic emission intensity index was proposed to quantify the CO, VOC, NOx and CO2 emissions on urban roads in the study area. The analysis results show that the traffic emission intensity of the expressway, trunk road, secondary road, and branch road is high during the morning peak (7 AM-9 AM) and evening peak (5 PM-7 PM). The sections with higher traffic emission intensity are mainly concentrated on the main roads and secondary roads such as Jiefang South Street, Shitong Road and Xinhua Road. Nearly one-third of 2nd Ring and 3rd Ring roads also have relatively high emission intensity. The research results provide new ideas for estimating traffic emissions in urban road networks and analyzing the spatio-temporal distribution of traffic emissions. The research results can also provide a decision-making basis for traffic management departments to formulate energy-saving and emission-reduction measures and promote the development of urban green and low-carbon transportation.

Dataset Information

MitoGenesisDB: an expression data mining tool to explore spatio-temporal dynamics of mitochondrial biogenesis.

Publications

MitoGenesisDB: an expression data mining tool to explore spatio-temporal dynamics of mitochondrial biogenesis.

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