Use of biplots and partial least squares regression in microarray data analysis for assessing association between genes involved in different biological pathways

Niccoló Bassani, Federico Ambrogi, Danila Coradini, Elia Biganzoli

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Abstract

Microarrays are widely used to study expression profiles for thousand of transcripts simultaneously and to explore inter-relationships between sets of genes. Visualization techniques and Partial Least Squares (PLS) regression have thus gained relevance in genomic. Biplots provide an aid to understand relationships between genes and samples and among genes, whereas passive projections of variables are helpful for understanding conditional relationships between sets of genes to be quantitatively evaluated via PLS regression. 62 genes involved in loss of cell polarity and 8 involved in Epithelial-Mesenchymal Transition (EMT), were selected from a study on 49 mesothelioma samples, and analysis considered EMT genes as conditioning and polarity genes as conditioned variables. PLS regression results are consistent with the PCA-based biplot of EMT genes and with passive projections of polarity genes. Future work will address sparsity in PCA and PLS regression. PLS path modeling will be considered after specification of a detailed dependency network.

Original languageEnglish
Title of host publicationLecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
Pages123-134
Number of pages12
Volume6685 LNBI
DOIs
Publication statusPublished - 2011
Event7th International Meeting on Computational Intelligence Methods for Bioinformatics and Biostatistics, CIBB 2010 - Palermo, Italy
Duration: Sep 16 2010Sep 18 2010

Publication series

NameLecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
Volume6685 LNBI
ISSN (Print)03029743
ISSN (Electronic)16113349

Other

Other7th International Meeting on Computational Intelligence Methods for Bioinformatics and Biostatistics, CIBB 2010
CountryItaly
CityPalermo
Period9/16/109/18/10

ASJC Scopus subject areas

  • Computer Science(all)
  • Theoretical Computer Science

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    Bassani, N., Ambrogi, F., Coradini, D., & Biganzoli, E. (2011). Use of biplots and partial least squares regression in microarray data analysis for assessing association between genes involved in different biological pathways. In Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics) (Vol. 6685 LNBI, pp. 123-134). (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); Vol. 6685 LNBI). https://doi.org/10.1007/978-3-642-21946-7_10