Computational analysis of microarray-based gene expression profiling and unveiling the functional traits in the developmental phases of Glycine max seed

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Research Articles | Published:

Print ISSN : 0970-4078.
Online ISSN : 2229-4473.
Website:www.vegetosindia.org
Pub Email: contact@vegetosindia.org
Doi: 10.1007/s42535-019-00008-5
First Page: 64
Last Page: 77
Views: 1690


Keywords: Glycine max , Differential gene expression, Gene clustering, R and bioconductor


Abstract

The Glycine max seed is an ultimate source of protein worldwide and plays the crucial role in crop development. This made us curious to insight the developmental stages of G. max seed at the genomic level with computational based microarray data analysis. The data analysis explored 10453 and 6085 significant DEGs from 0 to 4 mm vs. 12 to 16 mm and 4–8 mm vs. 8–12 mm stage, respectively and based on log2 FC, 407 & 2342 DEGs were regulating high expression and 340 & 1414 DEGs were low in expression at the 0–4 mm vs.12–16 mm and 4–8 mm vs. 8–12 mm stage, respectively. Gene symbols for DEGs has recognized and identified that, 7 DEGs from 0–4 mm vs. 12–16 mm stage were coding for miRNAs. Gene classification searched 2 & 4 highly enriched groups of genes from up-down regulated DEGs of 0–4 mm vs. 12–16 mm stage, respectively and 19 & 6 groups of genes from up-down regulated DEGs of 4–8 mm vs. 8–12 mm stage that were showing functional similarities. Analysis for functional characterization has found that 38% & 36% DEGs were annotating for BP, 42% & 67% DEGs were for CC and 53% & 46% DEGs were for MF in up-down regulated DEGs of 0–4 mm vs. 12–16 mm stage, respectively. For up-down regulated DEGs of 4–8 mm vs. 8–12 mm stage has drawn and 8% &10% DEGs were indicating BP, 4% & 3% for CC and 15% & 23% DEGs were annotating for MF, respectively. Top ten highly regulated genes with the ID 11998843, 11855572, 12189716, etc. from stage 0–4 mm vs. 12–16 mm were annotating 10 BP, 6 MF and 6 CC. While, up-regulated DEGs with the ID Gma.10969.1.S1_at, GmaAffx.92715.1.S1_s_at, etc. were annotating 19 MF, 7 BP and one term from CC for stage 4–8 mm vs. 8–12 mm. These analyses would be helpful in the further characterization of interesting candidate genes that involve in the seed development of G. max.


Glycine max , Differential gene expression, Gene clustering, R and bioconductor


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Acknowledgements

Authors are grateful to the Department of Computational Biology and Bioinformatics, Jacob Institute of Biotechnology and Bioengineering, Sam Higginbottom University of Agriculture, Technology and Sciences,  Prayagraj for providing infrastructure facilities. Ms Nivedita is also thankful to the Ministry of Social Justice and Empowerment, Govt. of India, New Delhi for providing fellowship.


Author Information

Yadav Nivedita
Jacob Institute of Biotechnology and Bioengineering, Department of Computational Biology and Bioinformatics, Sam Higginbottom University of Agriculture, Technology and Sciences, Prayagraj, India

Gautam Budhayash
Jacob Institute of Biotechnology and Bioengineering, Department of Computational Biology and Bioinformatics, Sam Higginbottom University of Agriculture, Technology and Sciences, Prayagraj, India


Yadav Pramod Kumar
Jacob Institute of Biotechnology and Bioengineering, Department of Computational Biology and Bioinformatics, Sam Higginbottom University of Agriculture, Technology and Sciences, Prayagraj, India

pramod.yadav@shiats.edu.in