Guide

Gene Search | Pathwsy Search | DEGs Search | Pathway Enrichment | Co-expression Analysis


Gene Search: It allows users to search the gene in Arabidopsis thaliana, Oryza sativa, Zea mays, Solanum lycopersicum, Glycine max, or Medicago truncatula After getting the basic gene information, users can do further analysis about the interested gene, include "microarray search", "pathway search" and "Co-expression analysis".








Pathway Search: It supplies users with the KEGG pathways map and the gene microarray expression profile. In this section, users can search the expression pattern of the enzymes and their coding genes under several conditions in the pathway that users is interested in. Also, the promoter analysis can be processed in a group of genes involved in a certain pathway.











Degs Search: It allows the user to search the significantly differentially expressed genes under the given conditions in Arabidopsis thaliana, Oryza sativa, Zea mays, Solanum lycopersicum, Glycine max, or Medicago truncatula. For identifying important genes in each developmental stage, stage-specific gene expression analysis is provided. The expression values of Arabidopsis thaliana and Oryza sativa were transformed to z-scores to normalize data across a wide range of expression levels.








Pathway/GO Enrichment Search:It allows users to identify the enriched KEGG pathways/GO of a group of genes, especially for those that are differentially expressed under various conditions. As we know, given a gene list involved in significant biological processes, signal transduction, or metabolic pathways, we can understand the pathogenicity of diseases and the roles of these genes. It helps researchers to determine biomarkers or treatments for specific diseases.







Co-expression Search:Co-expressed genes are a group of genes that express simultaneously under specific conditions. They tend to be controlled under similar transcriptional regulation and involve in identical biological processes or pathways. In this section, Pearson’s correlation coefficient and Spearman's rank correlation coefficient are applied to identify genes with co-expression patterns. Also, users can input a group of genes / transcripts and set parameters to view the correlation network. Based on the correlation network, users can find the candidate of the key gene / transcript.










Contact us:Wen-Chi Chang          E-mail:sarah321@mail.ncku.edu.tw