In:
PLOS ONE, Public Library of Science (PLoS), Vol. 17, No. 4 ( 2022-4-21), p. e0266618-
Abstract:
Identifying differentially expressed genes between experimental conditions is still the gold-standard approach to interpret transcriptomic profiles. Alternative approaches based on diversity measures have been proposed to complement the interpretation of such datasets but are only used marginally. Methods Here, we reinvestigated diversity measures, which are commonly used in ecology, to characterize mice pregnancy microenvironments based on a public transcriptome dataset. Mainly, we evaluated the Tsallis entropy function to explore the potential of a collection of diversity measures for capturing relevant molecular event information. Results We demonstrate that the Tsallis entropy function provides additional information compared to the traditional diversity indices, such as the Shannon and Simpson indices. Depending on the relative importance given to the most abundant transcripts based on the Tsallis entropy function parameter, our approach allows appreciating the impact of biological stimulus on the inter-individual variability of groups of samples. Moreover, we propose a strategy for reducing the complexity of transcriptome datasets using a maximation of the beta diversity. Conclusions We highlight that a diversity-based analysis is suitable for capturing complex molecular events occurring during physiological events. Therefore, we recommend their use through the Tsallis entropy function to analyze transcriptomics data in addition to differential expression analyses.
Type of Medium:
Online Resource
ISSN:
1932-6203
DOI:
10.1371/journal.pone.0266618
DOI:
10.1371/journal.pone.0266618.g001
DOI:
10.1371/journal.pone.0266618.g002
DOI:
10.1371/journal.pone.0266618.g003
DOI:
10.1371/journal.pone.0266618.g004
DOI:
10.1371/journal.pone.0266618.g005
DOI:
10.1371/journal.pone.0266618.s001
DOI:
10.1371/journal.pone.0266618.s002
DOI:
10.1371/journal.pone.0266618.s003
DOI:
10.1371/journal.pone.0266618.s004
DOI:
10.1371/journal.pone.0266618.s005
DOI:
10.1371/journal.pone.0266618.s006
DOI:
10.1371/journal.pone.0266618.s007
DOI:
10.1371/journal.pone.0266618.r001
DOI:
10.1371/journal.pone.0266618.r002
DOI:
10.1371/journal.pone.0266618.r003
DOI:
10.1371/journal.pone.0266618.r004
Language:
English
Publisher:
Public Library of Science (PLoS)
Publication Date:
2022
detail.hit.zdb_id:
2267670-3
Bookmarklink