Determination of sets of covariating gene expression using graph analysis on pairwise expression ratios | Zendy

Emmanuel Curis | Zendy; Cindie Courtin | Zendy; Pierre A. Geoffroy | Zendy; Jean Laplanche | Zendy; Bruno Saubaméa | Zendy; Cynthia MarieClaire | Zendy

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Determination of sets of covariating gene expression using graph analysis on pairwise expression ratios

Author(s) -

Emmanuel Curis,

Cindie Courtin,

Pierre A. Geoffroy,

Jean Laplanche,

Bruno Saubaméa,

Cynthia MarieClaire

Publication year - 2018

Publication title -

bioinformatics

Language(s) - English

Resource type - Journals

SCImago Journal Rank - 3.599

H-Index - 390

eISSN - 1367-4811

pISSN - 1367-4803

DOI - 10.1093/bioinformatics/bty629

Subject(s) - pairwise comparison , computer science , graph , r package , disjoint sets , data mining , set (abstract data type) , theoretical computer science , algorithm , mathematics , combinatorics , artificial intelligence , computational science , programming language

RNA quantification experiments result in compositional data, however usual methods for compositional data analysis [additive log ratio (alr), centered log ratio (clr), isometric log ratio (ilr)] do not apply easily and give results difficult to interpret. To handle this, a method based on disjoint subgraphs in a graph whose nodes are the quantified RNAs is proposed. Edges in the graph are defined by lack of change in ratios of the corresponding RNAs between conditions.

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