Journal Article

Finite mixture clustering of human tissues with different levels of IGF-1 splice variants mRNA transcripts

Martella, Francesca, Alfò, Marco, Pappalardo, Elisa, Musarò, Antonio, Pelosi, Michele

2015

Overview

Background This study addresses a recurrent biological problem, that is to define a formal clustering structure for a set of tissues on the basis of the relative abundance of multiple alternatively spliced isoforms mRNAs generated by the same gene. To this aim, we have used a model-based clustering approach, based on a finite mixture of multivariate Gaussian densities. However, given we had more technical replicates from the same tissue for each quantitative measurement, we also employed a finite mixture of linear mixed models, with tissue-specific random effects. Results A panel of human tissues was analysed through quantitative real-time PCR methods, to quantify the relative amount of mRNA encoding different IGF-1 alternative splicing variants. After an appropriate, preliminary, equalization of the quantitative data, we provided an estimate of the distribution of the observed concentrations for the different IGF-1 mRNA splice variants in the cohort of tissues by employing suitable kernel density estimators. We observed that the analysed IGF-1 mRNA splice variants were characterized by multimodal distributions, which could be interpreted as describing the presence of several sub-population, i.e. potential tissue clusters. In this context, a formal clustering approach based on a finite mixture model (FMM) with Gaussian components is proposed. Due to the presence of potential dependence between the technical replicates (originated by repeated quantitative measurements of the same mRNA splice isoform in the same tissue) we have also employed the finite mixture of linear mixed models (FMLMM), which allowed to take into account this kind of within-tissue dependence. Conclusions The FMM and the FMLMM provided a convenient yet formal setting for a model-based clustering of the human tissues in sub-populations, characterized by homogeneous values of concentrations of the mRNAs for one or multiple IGF-1 alternative splicing isoforms. The proposed approaches can be applied to any cohort of tissues expressing several alternatively spliced mRNAs generated by the same gene, and can overcome the limitations of clustering methods based on simple comparisons between splice isoform expression levels.

• Publisher: BioMed Central,BioMed Central Ltd
• Subject: Algorithms / Alternative Splicing - genetics / Analysis / Bioinformatics / Biomedical and Life Sciences / Cluster Analysis / Computational Biology/Bioinformatics / Computer Appl. in Life Sciences / Female / Gene expression / Gene Expression Profiling / Humans / Insulin-Like Growth Factor I - genetics / Life Sciences / Male / Messenger RNA / Methodology / Methodology Article / Microarrays / Normal Distribution / Protein Isoforms / Real-Time Polymerase Chain Reaction / RNA Isoforms / RNA, Messenger - genetics / Transcriptome analysis