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Statistical Approaches to Omics Data: Searching for Biological Truth

A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Molecular Informatics".

Deadline for manuscript submissions: closed (20 June 2025) | Viewed by 1472

Special Issue Editor


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Guest Editor
Departamento de Bioquímica y Biología Molecular, Edificio Severo Ochoa, Campus de Rabanales, Universidad de Córdoba, 14071 Córdoba, Spain
Interests: bioremediation; biodegradation; proteomics; omics; cyanide; plastics; denitrification

Special Issue Information

Dear Colleagues,

Omics approaches are very powerful tools for generating new knowledge about molecular processes, especially those from shotgun analyses. However, the information obtained must be reliable. To achieve this, it is essential to implement correct analyzes and statistical treatments for each stage of an omics workflow, without forgetting that the results must represent, in the best possible way, a biological reality. Thus, in addition to justifying one type of analysis or another (transcriptome based on reference vs. de novo, choice between quantification and sequence normalization methods, protein quantification methods, etc.), or performing a hypothesis contrast test or an alternative (t-test, ANOVA, Limma, DEqMS, negative binomial models, etc.), it is essential to know if the omics results fit those obtained through other methodologies within the context of functional validation. Additionally, differences between statistical and biological significance should be considered. For this Special Issue, we welcome works that compare different types of analysis and statistical treatments to elucidate which ones best fit with the “biological reality”, demonstrated through the implementation of other methodological approaches.

Dr. Alfonso Olaya Abril
Guest Editor

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Keywords

  • omics
  • statistics
  • hypothesis contrast
  • statistical confidence

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Published Papers (1 paper)

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Research

22 pages, 16880 KiB  
Article
Research on the Molecular Mechanisms and Key Gene Discovery in Quercus variabilis Root Pruning Based on Transcriptomics and Hormone Profiling
by Hao Dou, Jiajia Sun, Xi Feng, Huyang Lyu, Zhen Qin, Ruoyi Ni, Yilin Wang, Huijuan Sun, Xin Zhou, Wu Tang, Jin’e Quan and Xitian Yang
Int. J. Mol. Sci. 2024, 25(21), 11541; https://doi.org/10.3390/ijms252111541 - 27 Oct 2024
Viewed by 1118
Abstract
Quercus variabilis (Q. variabilis), a significant broadleaf species used in afforestation across high, sandy, and mountainous regions, presents unique challenges for transplantation. This species is characterized by its slow above-ground growth and rapid taproot development, which suppresses the proliferation of lateral [...] Read more.
Quercus variabilis (Q. variabilis), a significant broadleaf species used in afforestation across high, sandy, and mountainous regions, presents unique challenges for transplantation. This species is characterized by its slow above-ground growth and rapid taproot development, which suppresses the proliferation of lateral and fibrous roots, negatively impacting post-transplant survival. Research indicates that targeted root pruning—specifically, the removal of one-third of the roots—promotes the development of lateral roots in these seedlings. This study involved pruning the root systems of Q. variabilis and assessing the subsequent root development in comparison to an unpruned control group. Our analysis, which included transcriptome sequencing and plant hormone metabolism assays conducted at 2, 12, and 25 days post-pruning, yielded 126.02 Gb of clean data and identified 7662 differentially expressed genes (DEGs). These genes were primarily enriched in the plant hormone signal transduction pathway. Further investigation of this pathway, along with hormone content measurements, elucidated the mechanisms that contribute to enhanced root growth following pruning. Additionally, through a weighted correlation network analysis (WGCNA), we identified 20 key genes that are instrumental in promoting root development in Q. variabilis saplings. This research advances the theoretical framework for forestry seedling production and afforestation, laying the groundwork for scientifically informed vegetation restoration techniques. Full article
(This article belongs to the Special Issue Statistical Approaches to Omics Data: Searching for Biological Truth)
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