RapaNet: A Web Tool for the Co-Expression Analysis of Genes

Overview

Journal Evol Bioinform Online

Publisher Sage Publications

Specialty Biology

Date 2017 Jul 7

PMID 28680265

Citations 3

Authors

Jiye Kim

Kyong Mi Jun

Joung Sug Kim

Songhwa Chae

Yoon-Mok Pahk

Tae-Ho Lee

Soo-In Sohn

Soo In Lee

Myung-Ho Lim

Chang-Kug Kim

Yoonkang Hur

Baek Hie Nahm

Yeon-Ki Kim

Affiliations

Soon will be listed here.

Abstract

Accumulated microarray data are used for assessing gene function by providing statistical values for co-expressed genes; however, only a limited number of Web tools are available for analyzing the co-expression of genes of . We have developed a Web tool called RapaNet (http://bioinfo.mju.ac.kr/arraynet/brassica300k/query/), which is based on a data set of 143 microarrays compiled from various organs and at different developmental stages during exposure to biotic or abiotic stress. RapaNet visualizes correlated gene expression information via correlational networks and phylogenetic trees using Pearson correlation coefficient (). In addition, RapaNet provides hierarchical clustering diagrams, scatterplots of log ratio intensities, related pathway maps, and -element lists of promoter regions. To ascertain the functionality of RapaNet, the correlated genes encoding ribosomal protein (L7Ae), photosystem II protein D1 (psbA), and cytochrome P450 monooxygenase in glucosinolate biosynthesis (CYP79F1) were retrieved from RapaNet and compared with their homologues. An analysis of the co-expressed genes revealed their shared and unique features.

Citing Articles

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