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Clustering analysis was performed only on the genes identified after BPS treatments by using the Expression Profile data CLUSTering and analysis tool (EPCLUST, ), with average linkage (average distance, UPGMA) clustering based on Spearman's rank correlation-based distance.
Relative gene expression fold-change were expressed as Log_2(2^-ΔΔCt) and to visualize the obtained expression profiles we used heatmap graphing by EPCLUST – Expression Profile data CLUSTering and analysis software (www.bioinf.ebc.ee/EP/EP/EPCLUST/) [ 52].
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For the microarray data, clustering and statistical analysis were performed using SUMO and Genego (metacore) software packages.
Text (or data) clustering and processing; linguistic analysis (especially with French, German, Spanish, etc.).
TMeV software was used with this matrix for data clustering and template matching analysis [ 64].
Expression data were analyzed using Epclust, a generic data clustering, visualization and analysis tool [ 21].
STGB designed the study, organised the research trial, performed and processed samples and microarray hybridizations, data analysis, clustering and pathway/network analysis using IPA, qPCR validations and wrote the manuscript.
Burns, R. et al. The Open Connectome Project Data Cluster: Scalable Analysis and Vision for High-Throughput Neuroscience.
JMP Genomics provides a versatile analysis environment with workflows for performing quality control and data normalization, supervised and unsupervised clustering, and analysis of variance of gene expression profiles.
For microarray analysis the platform independent JAVA tools ArrayNorm [ 13] for normalization of microarray data and Genesis [ 14] for clustering and analysis of large scale gene expression datasets were made available.
For each release, all the derived data, including clustering and PFAM analysis, is regenerated and updated.
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