EXPath 2.0: An Updated Database for Integrating High-Throughput Gene Expression Data with Biological Pathways. (8th September 2020)

• Record Type: Journal Article
• Authors: Tseng, Kuan-Chieh; Li, Guan-Zhen; Hung, Yu-Cheng; Chow, Chi-Nga; Wu, Nai-Yun; Chien, Yi-Ying; Zheng, Han-Qin; Lee, Tzong-Yi; Kuo, Po-Li; Chang, Song-Bin; Chang, Wen-Chi
• Is Part Of: Plant & cell physiology. Volume 61:Number 10(2020)
• Page Start: 1818
• Page End: 1827
• Publication Date: 2020-09-08
• Subjects: Comparative gene expression analysis -- Gene regulation -- Metabolic pathways -- Promoter analysis -- Transcription factors; Plant physiology -- Periodicals; Microbiology -- Periodicals; Cytology -- Periodicals; Cell Physiology -- Periodicals; Plant Physiological Phenomena -- Periodicals; Cytology; Microbiology; Plant physiology; Periodicals; 571.205
• DOI: 10.1093/pcp/pcaa115
• Languages: English
• ISSNs: 0032-0781

Abstract

Abstract: Co-expressed genes tend to have regulatory relationships and participate in similar biological processes. Construction of gene correlation networks from microarray or RNA-seq expression data has been widely applied to study transcriptional regulatory mechanisms and metabolic pathways under specific conditions. Furthermore, since transcription factors (TFs) are critical regulators of gene expression, it is worth investigating TFs on the promoters of co-expressed genes. Although co-expressed genes and their related metabolic pathways can be easily identified from previous resources, such as EXPath and EXPath Tool, this information is not simultaneously available to identify their regulatory TFs. EXPath 2.0 is an updated database for the investigation of regulatory mechanisms in various plant metabolic pathways with 1, 881 microarray and 978 RNA-seq samples. There are six significant improvements in EXPath 2.0: (i) the number of species has been extended from three to six to include Arabidopsis, rice, maize, Medicago, soybean and tomato; (ii) gene expression at various developmental stages have been added; (iii) construction of correlation networks according to a group of genes is available; (iv) hierarchical figures of the enriched Gene Ontology (GO) terms are accessible; (v) promoter analysis of genes in a metabolic pathway or correlation network is provided; and (vi) user's gene expression data can be uploaded and analyzed. Thus, EXPath 2.0 is an updated platform for investigating gene expression profiles and metabolic pathways under specific conditions. It facilitates users to access the regulatory mechanisms of plant biological processes. The new version is available at http://EXPath.itps.ncku.edu.tw .