Gene Co-Expression Network Tools and Databases for Crop Improvement
Transcriptomics has significantly grown as a functional genomics tool for understanding the expression of biological systems. The generated transcriptomics data can be utilised to produce a gene co-expression network that is one of the essential downstream omics data analyses. To date, several gene...
| Main Authors: | , , , , |
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| Format: | Article |
| Language: | English |
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MDPI AG
2022-06-01
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| Series: | Plants |
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| Online Access: | https://www.mdpi.com/2223-7747/11/13/1625 |
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| author | Rabiatul-Adawiah Zainal-Abidin Sarahani Harun Vinothienii Vengatharajuloo Amin-Asyraf Tamizi Nurul Hidayah Samsulrizal |
| author_facet | Rabiatul-Adawiah Zainal-Abidin Sarahani Harun Vinothienii Vengatharajuloo Amin-Asyraf Tamizi Nurul Hidayah Samsulrizal |
| author_sort | Rabiatul-Adawiah Zainal-Abidin |
| collection | DOAJ |
| description | Transcriptomics has significantly grown as a functional genomics tool for understanding the expression of biological systems. The generated transcriptomics data can be utilised to produce a gene co-expression network that is one of the essential downstream omics data analyses. To date, several gene co-expression network databases that store correlation values, expression profiles, gene names and gene descriptions have been developed. Although these resources remain scattered across the Internet, such databases complement each other and support efficient growth in the functional genomics area. This review presents the features and the most recent gene co-expression network databases in crops and summarises the present status of the tools that are widely used for constructing the gene co-expression network. The highlights of gene co-expression network databases and the tools presented here will pave the way for a robust interpretation of biologically relevant information. With this effort, the researcher would be able to explore and utilise gene co-expression network databases for crops improvement. |
| first_indexed | 2024-03-09T10:26:22Z |
| format | Article |
| id | doaj.art-536ea92bf9cd48698e7c07bfde363e2a |
| institution | Directory Open Access Journal |
| issn | 2223-7747 |
| language | English |
| last_indexed | 2024-03-09T10:26:22Z |
| publishDate | 2022-06-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Plants |
| spelling | doaj.art-536ea92bf9cd48698e7c07bfde363e2a2023-12-01T21:38:37ZengMDPI AGPlants2223-77472022-06-011113162510.3390/plants11131625Gene Co-Expression Network Tools and Databases for Crop ImprovementRabiatul-Adawiah Zainal-Abidin0Sarahani Harun1Vinothienii Vengatharajuloo2Amin-Asyraf Tamizi3Nurul Hidayah Samsulrizal4Biotechnology and Nanotechnology Research Centre, Malaysian Agricultural Research and Development Institute (MARDI), Serdang 43400, Selangor, MalaysiaCentre for Bioinformatics Research, Institute of Systems Biology, Universiti Kebangsaan Malaysia (UKM), Bangi 43600, Selangor, MalaysiaCentre for Bioinformatics Research, Institute of Systems Biology, Universiti Kebangsaan Malaysia (UKM), Bangi 43600, Selangor, MalaysiaBiotechnology and Nanotechnology Research Centre, Malaysian Agricultural Research and Development Institute (MARDI), Serdang 43400, Selangor, MalaysiaDepartment of Plant Science, Kulliyyah of Science, International Islamic Universiti Malaysia (IIUM), Jalan Sultan Ahmad Shah, Bandar Indera Mahkota, Kuantan 25200, Pahang, MalaysiaTranscriptomics has significantly grown as a functional genomics tool for understanding the expression of biological systems. The generated transcriptomics data can be utilised to produce a gene co-expression network that is one of the essential downstream omics data analyses. To date, several gene co-expression network databases that store correlation values, expression profiles, gene names and gene descriptions have been developed. Although these resources remain scattered across the Internet, such databases complement each other and support efficient growth in the functional genomics area. This review presents the features and the most recent gene co-expression network databases in crops and summarises the present status of the tools that are widely used for constructing the gene co-expression network. The highlights of gene co-expression network databases and the tools presented here will pave the way for a robust interpretation of biologically relevant information. With this effort, the researcher would be able to explore and utilise gene co-expression network databases for crops improvement.https://www.mdpi.com/2223-7747/11/13/1625bioinformatics toolcropdatabasegene co-expression networktranscriptomics |
| spellingShingle | Rabiatul-Adawiah Zainal-Abidin Sarahani Harun Vinothienii Vengatharajuloo Amin-Asyraf Tamizi Nurul Hidayah Samsulrizal Gene Co-Expression Network Tools and Databases for Crop Improvement Plants bioinformatics tool crop database gene co-expression network transcriptomics |
| title | Gene Co-Expression Network Tools and Databases for Crop Improvement |
| title_full | Gene Co-Expression Network Tools and Databases for Crop Improvement |
| title_fullStr | Gene Co-Expression Network Tools and Databases for Crop Improvement |
| title_full_unstemmed | Gene Co-Expression Network Tools and Databases for Crop Improvement |
| title_short | Gene Co-Expression Network Tools and Databases for Crop Improvement |
| title_sort | gene co expression network tools and databases for crop improvement |
| topic | bioinformatics tool crop database gene co-expression network transcriptomics |
| url | https://www.mdpi.com/2223-7747/11/13/1625 |
| work_keys_str_mv | AT rabiatuladawiahzainalabidin genecoexpressionnetworktoolsanddatabasesforcropimprovement AT sarahaniharun genecoexpressionnetworktoolsanddatabasesforcropimprovement AT vinothieniivengatharajuloo genecoexpressionnetworktoolsanddatabasesforcropimprovement AT aminasyraftamizi genecoexpressionnetworktoolsanddatabasesforcropimprovement AT nurulhidayahsamsulrizal genecoexpressionnetworktoolsanddatabasesforcropimprovement |