Single-shot determination of differential gene network on multiple disease subtypes

• Autorzy: Sadhu Arnab , Bhattacharyya Balaram , Mukhopadhyay Tathagato

Identyfikatory

DOI

10.7494/csci.2022.23.2.4339

• Języki publikacji: EN

Abstrakty

EN

A differential gene expressional network determines the prominent genes under altered phenotypes. The traditional approach requires n(n − 2)/2 comparisons for n phenotypes. We present a direct method for determining a differentia network under multiple phenotypes. We explore the non-discrete nature of gene expression as a pattern in a fuzzy rough set. An edge between a pair of genes represents a positive region of a fuzzy similarity relationship upon a phenotypic change. We apply a weight-ranking formula and obtain a directed ranked network; we label this as a phenotype interwoven network. Those nodes with large in-degree connectivity bubble up as significant genes under respective phenotypic changes. We tested the method on six diseases and achieved good corroboration with the results of previous studies in the two-step approach. The subgraphs of the isolated genes achieved good significance upon validation through an information theoretic approach. The top-ranking genes determined in all of our case studies are in consonance with the findings of the respective wet-lab tests.

Słowa kluczowe

EN

phenotype interwoven network; fuzzy rough set-based attribute selection; gene interaction network; differential co-expression

• Wydawca: Wydawnictwa AGH
• Czasopismo: Computer Science
• Rocznik: 2022
• Tom: T. 23 (2)
• Strony: 247--276
• Opis fizyczny: Bibliogr. 55 poz., rys., tab.

Twórcy

autor

Sadhu Arnab

• Visva-Bharati University, Department of Computer and System Sciences, Santiniketan, West Bengal 731235, India

autor

Bhattacharyya Balaram

• Visva-Bharati University, Department of Computer and System Sciences, Santiniketan, West Bengal 731235, India

autor

Mukhopadhyay Tathagato

• Visva-Bharati University, Department of Computer and System Sciences, Santiniketan, West Bengal 731235, India

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Uwagi

PL

Opracowanie rekordu ze środków MEiN, umowa nr SONP/SP/546092/2022 w ramach programu "Społeczna odpowiedzialność nauki" - moduł: Popularyzacja nauki i promocja sportu (2022-2023).