Objectives To uncover key genes and pathways regulated by SCL3, a GRAS transcription factor, in the context of gibberellin (GA) in the roots of the model plant Arabidopsis thaliana. Results Gene expression profiles of ga1-3 mutant and ga1-3 and scl3 double mutant are considerably similar to each other, revealed by Principal Component Analysis (PCA). More than 400 significantly Differentially Expressed Genes (DEGs) among the Arabidopsis thaliana roots of ga1-3 mutant, ga1-3 and scl3 double mutant and GA loss/SCL3 gain mutant were uncovered by comprehensive bioinformatics analyses. Protein synthesis pathway, including RPL proteins, RPS proteins, etc., and flavonoid biosynthesis pathway, including TT4, F3H, TT5, CHIL, etc. were significantly increased when SCL3 expression was higher than normal by means of pathway enrichment analysis and protein-protein interaction analysis, which is further supported by comparison analyses between wild type samples and SCL3 overexpressed roots. Conclusion Protein synthesis and flavonoid biosynthesis were regulated by SCL3 in the context of GA in Arabidopsis thaliana root system identified by comprehensive bioinformatic analyses.