SLC genes display different expression profiles along the rostral-caudal axis of the gut depending on species, digestive requirements and specialization of the sequential domains. Here, we report on the longitudinal expression profiles of SLC genes in the intestine of two simple-gutted teleost fish, zebrafish and Ballan wrasse (L. bergylta), using a subset of publicly available data from the GEO repository (zebrafish: [GSE20884]; Ballan wrasse: [GSE93191]). We explored intra-species/intra-dataset concordances/discordances in the expression profiles through Spearman simple correlation, which coefficients, even if heavily affected by the compositionality of the data, may be informative of which genes are co- or counter-expressed. Through hierarchical clustering on the correlation coefficients we defined groups of concordant and discordant profiles of SLC genes. An online app (freely available at: https://gianmarcopiccinno.shinyapps.io/zebrafish_wrasse_v2/) was developed that allows rapid display of the longitudinal patterns of the genes differentially expressed in the two datasets. All the analyses were performed through R programming language. To define differentially expressed genes, we performed multiple One-Way ANOVA tests, whose p-values were subjected to Benjamini-Hochberg correction. Genes were considered differentially expressed if the corresponding corrected p-value from the ANOVA test was lower than 0.05. The plots were prepared using the R package ggplot2. The online app was produced through the R package shiny, and is hosted by free servers of RStudio. Our tools allow comparative analysis of the longitudinal profiles of the genes expressed in simple guts, and can be extended to implement any new similar datasets.
|Titolo:||SoLute Carrier (SLC) genes expression along the rostro-caudal axis of adult teleost fish gut: a publicly available datasets analysis|
|Data di pubblicazione:||2019|
|Appare nelle tipologie:||Abstract (in Rivista)|