Discovery of leaf region and time point related modules and genes in maize (Zea mays L.) leaves by Weighted Gene Co-expression Network analysis (WGCNA) of gene expression profiles of carbon metabolism
Maize (Zea mays L.) yield depends not only on the conversion and accumulation of carbohydrates in kernels, but also on the supply of carbohydrates by leaves. However, the carbon metabolism process in leaves can vary across different leaf regions and during the day and night. Hence, we used Weighted...
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KeAi Communications Co., Ltd.
2019-02-01
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| Series: | Journal of Integrative Agriculture |
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| Online Access: | http://www.sciencedirect.com/science/article/pii/S2095311918620295 |
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| author | Jing-lu WANG Ying ZHANG Xiao-di PAN Jian-jun DU Li-ming MA Xin-yu GUO |
| author_facet | Jing-lu WANG Ying ZHANG Xiao-di PAN Jian-jun DU Li-ming MA Xin-yu GUO |
| author_sort | Jing-lu WANG |
| collection | DOAJ |
| description | Maize (Zea mays L.) yield depends not only on the conversion and accumulation of carbohydrates in kernels, but also on the supply of carbohydrates by leaves. However, the carbon metabolism process in leaves can vary across different leaf regions and during the day and night. Hence, we used Weighted Gene Co-expression Network analysis (WGCNA) with the gene expression profiles of carbon metabolism to identify the modules and genes that may associate with particular regions in a leaf and time of day. There were a total of 45 samples of maize leaves that were taken from three different regions of a growing maize leaf at five time points. Robust Multi-array Average analysis was used to pre-process the raw data of GSE85963 (accession number), and quality control of data was based on Pearson correlation coefficients. We obtained eight co-expression network modules. The modules with the highest significance of association with LeafRegion and TimePoint were selected. Functional enrichment and gene-gene interaction analyses were conducted to acquire the hub genes and pathways in these significant modules. These results can support the findings of similar studies by providing evidence of potential module genes and enriched pathways associated with leaf development in maize. |
| format | Article |
| id | doaj-art-a2f0f8d9c7c541ddb0d442f085ec7c02 |
| institution | Matheson Library |
| issn | 2095-3119 |
| language | English |
| publishDate | 2019-02-01 |
| publisher | KeAi Communications Co., Ltd. |
| record_format | Article |
| series | Journal of Integrative Agriculture |
| spelling | doaj-art-a2f0f8d9c7c541ddb0d442f085ec7c022025-08-02T15:37:58ZengKeAi Communications Co., Ltd.Journal of Integrative Agriculture2095-31192019-02-01182350360Discovery of leaf region and time point related modules and genes in maize (Zea mays L.) leaves by Weighted Gene Co-expression Network analysis (WGCNA) of gene expression profiles of carbon metabolismJing-lu WANG0Ying ZHANG1Xiao-di PAN2Jian-jun DU3Li-ming MA4Xin-yu GUO5WANG Jing-lu, Tel: +86-10-51503618; Beijing Key Lab of Digital Plant/Beijing Research Center for Information Technology in Agriculture/National Engineering Research Center for Information Technology in Agriculture/Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, P.R.ChinaZHANG Ying, Tel: +86-10-51503618; Beijing Key Lab of Digital Plant/Beijing Research Center for Information Technology in Agriculture/National Engineering Research Center for Information Technology in Agriculture/Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, P.R.ChinaBeijing Key Lab of Digital Plant/Beijing Research Center for Information Technology in Agriculture/National Engineering Research Center for Information Technology in Agriculture/Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, P.R.ChinaBeijing Key Lab of Digital Plant/Beijing Research Center for Information Technology in Agriculture/National Engineering Research Center for Information Technology in Agriculture/Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, P.R.ChinaBeijing Key Lab of Digital Plant/Beijing Research Center for Information Technology in Agriculture/National Engineering Research Center for Information Technology in Agriculture/Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, P.R.ChinaCorrespondence GUO Xin-yu, Tel/Fax: +86-10-51503422; Beijing Key Lab of Digital Plant/Beijing Research Center for Information Technology in Agriculture/National Engineering Research Center for Information Technology in Agriculture/Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, P.R.ChinaMaize (Zea mays L.) yield depends not only on the conversion and accumulation of carbohydrates in kernels, but also on the supply of carbohydrates by leaves. However, the carbon metabolism process in leaves can vary across different leaf regions and during the day and night. Hence, we used Weighted Gene Co-expression Network analysis (WGCNA) with the gene expression profiles of carbon metabolism to identify the modules and genes that may associate with particular regions in a leaf and time of day. There were a total of 45 samples of maize leaves that were taken from three different regions of a growing maize leaf at five time points. Robust Multi-array Average analysis was used to pre-process the raw data of GSE85963 (accession number), and quality control of data was based on Pearson correlation coefficients. We obtained eight co-expression network modules. The modules with the highest significance of association with LeafRegion and TimePoint were selected. Functional enrichment and gene-gene interaction analyses were conducted to acquire the hub genes and pathways in these significant modules. These results can support the findings of similar studies by providing evidence of potential module genes and enriched pathways associated with leaf development in maize.http://www.sciencedirect.com/science/article/pii/S2095311918620295WGCNAmaize leafgene expressiongene modulespathways |
| spellingShingle | Jing-lu WANG Ying ZHANG Xiao-di PAN Jian-jun DU Li-ming MA Xin-yu GUO Discovery of leaf region and time point related modules and genes in maize (Zea mays L.) leaves by Weighted Gene Co-expression Network analysis (WGCNA) of gene expression profiles of carbon metabolism Journal of Integrative Agriculture WGCNA maize leaf gene expression gene modules pathways |
| title | Discovery of leaf region and time point related modules and genes in maize (Zea mays L.) leaves by Weighted Gene Co-expression Network analysis (WGCNA) of gene expression profiles of carbon metabolism |
| title_full | Discovery of leaf region and time point related modules and genes in maize (Zea mays L.) leaves by Weighted Gene Co-expression Network analysis (WGCNA) of gene expression profiles of carbon metabolism |
| title_fullStr | Discovery of leaf region and time point related modules and genes in maize (Zea mays L.) leaves by Weighted Gene Co-expression Network analysis (WGCNA) of gene expression profiles of carbon metabolism |
| title_full_unstemmed | Discovery of leaf region and time point related modules and genes in maize (Zea mays L.) leaves by Weighted Gene Co-expression Network analysis (WGCNA) of gene expression profiles of carbon metabolism |
| title_short | Discovery of leaf region and time point related modules and genes in maize (Zea mays L.) leaves by Weighted Gene Co-expression Network analysis (WGCNA) of gene expression profiles of carbon metabolism |
| title_sort | discovery of leaf region and time point related modules and genes in maize zea mays l leaves by weighted gene co expression network analysis wgcna of gene expression profiles of carbon metabolism |
| topic | WGCNA maize leaf gene expression gene modules pathways |
| url | http://www.sciencedirect.com/science/article/pii/S2095311918620295 |
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