Clustering techniques are important for gene expression data analysis. However, efficient computational algorithms for clustering time-series data are still lacking. This work documents two improvements on an existing profile-based greedy algorithm for short time-series data; the first one is implementation of a scaling method on the pre-processing of the raw data to handle some extreme cases; the second improvement is modifying the strategy to generate better clusters. Simulation data and real microarray data were used to evaluate these improvements; this approach could efficiently generate more accurate clusters. A new feature-based algorithm was also developed in which steady state value; overshoot, rise time, settling time and peak time are generated by the 2nd order control system for the clustering purpose. This feature-based approach is much faster and more accurate than the existing profile-based algorithm for long time-series data.

The experimental factors such as the cell type and the treatment may have different impact on expression levels of individual genes which are quantitative measurements from microarrays. The measurements can be collected at a few unevenly spaced time points with replicates. The aim of this study is to consider cell type, treatment and short time series attributes and to infer about their effects on individual genes. A mixed effects model (LME) was proposed to model the gene expression data and the performance of the model was validated by a simulation study. Realistic data sets were generated preserving the structure of the sample real life data studied by Nymark et al. (2007). Predictive performance of the model was evaluated by performance measures, such as accuracy, sensitivity and specificity, as well as compared to the competing method by Smyth (2004), namely Limma. Both methods were also compared on real life data. Simulation results showed that the predictive performance of LME is as high as 99%, and it produces False Discovery Rate (FDR) as low as 0.4% whereas Limma has an FDR value of at least 32%. Moreover, LME has almost 99% predictive capability on the continuous time parameter where Limma has only about 67% and even it cannot handle continuous independent variables.

Au cours d'une infection lytique, le virus de l'herpès simplex de type 1 (VHS-1) doit entreprendre plusieurs étapes de fusion afin de se répliquer et se propager correctement. Ainsi, le virus a évolué afin de tirer avantage de la machinerie cellulaire en utilisant des protéines et facteurs de l’hôte à cet effet. Dans la littérature, les processus sous-jacents à l’entrée du VHS-1 ont été largement élucidés. Cependant, on ne sait toujours pas comment les particules virales nouvellement synthétisées sortent de la cellule hôte et quels facteurs cellulaires sont impliqués dans ce processus. Des résultats publiés par notre laboratoire indiquent que la protéine cellulaire, Extended Synaptotagmin 1 (E-Syt1), a un impact négatif sur la propagation globale du virus lorsqu’inhibée par de l’ARN d’interférence. Conséquemment, la présente étude a pour objectif de confirmer et d'approfondir le rôle d’E-Syt1 sur la propagation virale, en particulier sur la sortie du virus. Étant donné que l’activation d’E-Syt1 est liée à l’augmentation de la concentration de calcium cytoplasmique, nous avons également étudié l'implication du calcium au cours des stades ultérieurs de la réplication virale. Ici, nous avons démontré que la surexpression d’E-Syt1 n’a pas d’effet détectable sur la sortie du VHS-1, mais que le calcium a effet sur la propagation virale. Alors que la séquestration précoce du calcium (4 et 6 heures post-infection) à l'aide de chélateurs réprime la sortie virale, aucun effet significatif a été détecté lorsque les chélateurs ont été ajoutés à un stade avancé de l’infection (12 et 16 heures post-infection). Nos résultats fournissent des données intéressantes sur la nécessité de l’homéostasie du calcium intracellulaire afin que VHS-1 puisse assurer une médiation adéquate de la sortie virale. Ces résultats pourraient conduire à la découverte de nouveaux mécanismes ou protéines cellulaires régulées par le calcium et utilisés par le VHS-1 lors de réplications lytiques virales. / During a lytic infection, Herpes Simplex Virus type 1 (HSV-1) must go through multiple steps of fusion to replicate and propagate properly. For this purpose, the virus has evolved consequently by taking advantage of the cellular machinery using host factors and proteins. In the literature, processes underlying HSV-1’s entry have been extensively elucidated. However, it remains unclear how newly synthesized viral particles egress from the host cell, and what cellular factors are implicated in this process. Results published by our laboratory suggest that the cellular protein, Extended Synaptotagmin 1 (E-Syt1), has a negative and global impact on the viral propagation when down regulated by RNA interference. Consequently, this study aims to confirm and deepen our understanding of E-Syt1’s role on HSV-1, particularly during viral egress. Since activation of E-Syt1 is linked to the increase in cytoplasmic calcium concentration, we also investigated calcium involvement during later stages of viral propagation. Interestingly, overexpression of E-Syt1 had no measurable effect on HSV-1 propagation whereas calcium has a dual effect on viral propagation. While early calcium sequestering (4 and 6 hours post-infection) using chelators represses viral egress, no significant effect was detected when chelators were added at later time points (12 and 16 hours post-infection). Our results give interesting insights on how HSV-1 relies on intracellular calcium homeostasis to properly mediate viral egress. These results may lead to the discovery of new mechanisms or cellular proteins that are regulated by calcium and hijacked by HSV-1 during lytic replication.