Assessment of Hierarchical Clustering Methodologies for Proteomic Data Mining

Meunier, Bruno; Dumas, Émilie; Piec, Isabelle; Béchet, Daniel; Hébraud, Michel; Hocquette, Jean-François

doi:10.1021/pr060343h

Cited by 136 publications

(117 citation statements)

References 29 publications

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“…Missing values and protein profile normalization were managed as described earlier (Meunier et al, 2007). Briefly, to achieve comparable profiles, each protein value (%volume) was divided (then logged) by the mean of all replicate values of this protein.…”

Section: Image Analysismentioning

confidence: 99%

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Proteome dynamics during contractile and metabolic differentiation of bovine foetal muscle

Chaze

Meunier

Chambon³

et al. 2009

Animal

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Contractile and metabolic properties of bovine muscles play an important role in meat sensorial quality, particularly tenderness. Earlier studies based on Myosin heavy chain isoforms analyses and measurements of glycolytic and oxidative enzyme activities have demonstrated that the third trimester of foetal life in bovine is characterized by contractile and metabolic differentiation. In order to complete this data and to obtain a precise view of this phase and its regulation, we performed a proteomic analysis of Semitendinosus muscle from Charolais foetuses analysed at three stages of the third trimester of gestation (180, 210 and 260 days). The results complete the knowledge of important changes in the profiles of proteins from metabolic and contractile pathways. They provide new insights about proteins such as Aldehyde dehydrogenase family, Enolase, Dihydrolipoyl dehydrogenase, Troponin T or Myosin light chains isoforms. These data have agronomical applications not only for the management of beef sensorial quality but also in medical context, as bovine myogenesis appears very similar to human one.

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Section: Image Analysismentioning

confidence: 99%

“…HCA of the quantitative matrices was processed according to the Pearson distance. The Ward aggregation procedure was then used to construct the resulting dendrogram, as described in Meunier et al (2007). PMF of unidentified proteins (using bovine database) were compared to the nrMammalia database (06/2007, 819370 seq).…”

Section: Image Analysismentioning

confidence: 99%

Proteome dynamics during contractile and metabolic differentiation of bovine foetal muscle

Chaze

Meunier

Chambon³

et al. 2009

Animal

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“…The animal genomics community has contributed to the development of microarray analysis methods by adapting the use of mixed model analysis to microarray experimentation (Reverter et al, 2003;PfisterGenskow et al, 2005). In proteomics, research by INRA scientists has also allowed improvement in statistical analyses by adapting the SAM (significance analysis of microarray) method (Meunier et al, 2005) and clustering methodologies (Meunier et al, 2007) to two-dimensional gel electrophoresis experiments.…”

Section: Potential Benefits Of Genomicsmentioning

confidence: 99%

Recent advances in cattle functional genomics and their application to beef quality

Hocquette

Lehnert

Barendse

et al. 2007

Animal

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The advent of high-throughput DNA sequencing techniques, array technology and protein analysis has increased the efficiency of research in bovine muscle physiology, with the ultimate objective of improving beef quality either by breeding or rearing factors. For genetic purposes, polymorphisms in some key genes have been reported for their association with beef quality traits. The sequencing of the bovine genome has dramatically increased the number of available gene polymorphisms. The association of these new polymorphisms with the variability in beef quality (e.g. tenderness, marbling) for different breeds in different rearing systems will be a very important issue. For rearing purposes, global gene expression profiling at the mRNA or protein level has already shown that previously unsuspected genes may be associated either with muscle development or growth, and may lead to the development of new molecular indicators of tenderness or marbling. Some of these genes are specifically regulated by genetic and nutritional factors or differ between different beef cuts. In recognition of the potential economic benefits of genomics, public institutions in association with the beef industry are developing livestock genomics projects around the world. From the scientific, technical and economical points of view, genomics is thus reshaping research on beef quality.

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“…The second objective of gel-based proteomics data mining is to use clustering approach to group or classify the proteins. This is important for understanding the complex biological systems, such as classification of tumor according to the expression of proteins, for the diagnostics and therapeutics purposes (Meunier et al, 2007). This approach can be achieved by applying the bioinformatics tools on both differential expression and global expression profile.…”

Section: Dataset In Gel-based Proteomicsmentioning

confidence: 99%