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

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\xa0mm vs. 12 to 16\xa0mm and 4–8\xa0mm vs. 8–12\xa0mm 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\xa0mm vs.12–16\xa0mm and 4–8\xa0mm vs. 8–12\xa0mm stage, respectively. Gene symbols for DEGs has recognized and identified that, 7 DEGs from 0–4\xa0mm vs. 12–16\xa0mm stage were coding for miRNAs. Gene classification searched 2 & 4 highly enriched groups of genes from up-down regulated DEGs of 0–4\xa0mm vs. 12–16\xa0mm stage, respectively and 19 & 6 groups of genes from up-down regulated DEGs of 4–8\xa0mm vs. 8–12\xa0mm 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\xa0mm vs. 12–16\xa0mm stage, respectively. For up-down regulated DEGs of 4–8\xa0mm vs. 8–12\xa0mm 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\xa0mm vs. 12–16\xa0mm 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\xa0mm vs. 8–12\xa0mm. These analyses would be helpful in the further characterization of interesting candidate genes that involve in the seed development of G. max.