Guidelines for correlation coefficient threshold settings in metabolite correlation networks exemplified on a potato association panel

Background Correlation network analysis has become an integral tool to study metabolite datasets. Networks are constructed by omitting correlations between metabolites based on two thresholds—namely the r and the associated p-values. While p-value threshold settings follow the rules of multiple hypotheses testing correction, guidelines for r-value threshold settings have not been defined. Results Here, we introduce a method that allows determining the r-value threshold based on an iterative approach, where different networks are constructed and their network topology is monitored. Once the network topology changes significantly, the threshold is set to the corresponding correlation coefficient value. The approach was exemplified on: (i) a metabolite and morphological trait dataset from a potato association panel, which was grown under normal irrigation and water recovery conditions; and validated (ii) on a metabolite dataset of hearts of fed and fasted mice. For the potato normal irrigation correlation network a threshold of Pearson’s |r|≥ 0.23 was suggested, while for the water recovery correlation network a threshold of Pearson’s |r|≥ 0.41 was estimated. For both mice networks the threshold was calculated with Pearson’s |r|≥ 0.84. Conclusions Our analysis corrected the previously stated Pearson’s correlation coefficient threshold from 0.4 to 0.41 in the water recovery network and from 0.4 to 0.23 for the normal irrigation network. Furthermore, the proposed method suggested a correlation threshold of 0.84 for both mice networks rather than a threshold of 0.7 as applied earlier. We demonstrate that the proposed approach is a valuable tool for constructing biological meaningful networks.

Editorial Volumen 23

It is a special satisfaction for the editorial committee of the journal of the Latin American Potato Association - LAPA- to publish the second issue of the year 2019. In this issue are articles by researchers from various Latin American countries in which various topics are addressed, among them, the production of seeds under the family farming system in Uruguay, the recognition of the contribution of research institutions in Bolivia, especially for the development and impact of new potato varieties in various producing regions, in the same way, results of the evaluation of new clones with special characteristics of disease resistance and good agronomic response in the Midwest of Brazil, the response in the content of phenols and enzymatic browning in important varieties of Argentine potatoes treated with antioxidant products in storage, the benefits of the clinics of plants in Peru and finally turned out Research data from the International Potato Center -IPC- related to the quantification of potato losses in the value chain, analyzed in Ecuador and Peru.

Visibility: The challenge of the Latin American Potato Journal

In this work, the “state of art” of the Latin American Potato Journal is analyzed, as a means of scientific and technical diffusion of the potato crop, which is published by the Latin American Potato Association (LAPA). The objectives of the document are: i) to make a current analysis of the Journal and its challenges in the world of information and ii) to share the strategy developed for achieving visibility. The journal has a biannual frequency (June and December). Original and unpublished articles are accepted in biotechnologies, genomics, physiology, nutrition and fertilization of crops, genetics and plant breeding,entomology, phytopathology, integrated phytoprotection, agroecology, malherbology, geomatics, soils, water and irrigation, postharvest and agro-industrialization, rural development and agro-business, agricultural economy and marketing of agriculturalproducts. Since 1988, the LAPA Journal has published 25 issues. Twelve invited articles, 170 scientific articles, 25 short communications and 8 reviews, totaling 215 publications. From this total, 29% are from Bolivia, 23% from Peru, 13% from Argentina, 8% from Colombia, 8% from Ecuador, 4% from Venezuela, 3% from Mexico and 4% from Brazil. Countries such as Spain, Costa Rica, Honduras, Panama, Nicaragua, Chile, USA and Denmark have contributed 1% each country. The main publication topics were in phytopathology, entomology, plant breeding, agronomy and physiology, agro-industry, genetics resources, participatory methodologies and economics, seed production, biotechnology and microbiology.