Table 1.

A summary of the search for candidate molecular markers of plant advantages related to Arabidopsis thaliana proximal promoter SNPs using the Ensembl Plant database [31] along with Plant_SNP_TATA_Z-tester [24], as schematically shown in Figure 1, the result of which is freely available in the AtSNP_TATAdb database created within this work (https://www.sysbio.ru/AtSNP_TATAdb/), as illustrated in Figure 2.

#	Indicator	Result
Genome-wide analysis in silico:
1	Total number of the Arabidopsis thaliana genes documented in the Ensembl Plants database [31] and, thus, taken into account	32,833 (100%)
2	Total number of the Arabidopsis thaliana protein-coding genes, which were selected for further analysis	27,628 (80.04%)
3	Total number of the transcripts from the Arabidopsis thaliana genes taken into account	54,013 (100%)
4	Total number of the protein-coding transcripts selected from the above amount of the Arabidopsis thaliana transcripts, which were selected for further analysis	48,321 (89.46%)
5	Total number of the nucleotide substitutions (SNPs) localized in the proximal region of 90 bp in length just before TSS for the analyzed transcripts	871,707 (100%)
6	Total number of candidate SNP markers having significant changes in the TBP binding affinity identified in this work	54,993 (6.31%)
7	Total number of candidate SNP markers that down-regulated gene expression	27,568 (3.16%)
8	Total number of candidate SNP markers that up-regulated gene expression	27,425 (3.15%)
9	Total number of A. thaliana genes whose expression may be significantly altered by the promoter proximal SNPs changing the TBP binding affinity	18,636 (56.78%)
10	The arithmetic mean estimate and its standard error rate of the equilibrium dissociation constant (KD) expressed in nanomoles per liter (nM) of the complexes between the TBP and only the ancestral alleles of the promoters of the Arabidopsis thaliana genes (Mean ± SEM)	3.96 ± 0.01 nM
11	The arithmetic mean estimate and its standard error rate of the same KD-values in the case of only the minor alleles of the Arabidopsis thaliana promoters	4.07 ± 0.01 nM
12	Statistical significance of the difference between ancestral and minor alleles of the Arabidopsis thaliana promoters examined by the arithmetic mean of the KD-values in question according to the following:
	Student’s t-test, t-value (PADJ)	8.07 (10−7)
	Fisher’s Z-test, Z-score (PADJ)	7.78 (10−2)
13	The standard deviation of the same KD-values in the case of only the ancestral alleles of the Arabidopsis thaliana promoters	1.95 nM
14	The standard deviation of the same KD-values in the case of only the minor alleles of the Arabidopsis thaliana promoters	1.90 nM
15	Significance of the difference between ancestral and minor alleles of the A. thaliana promoters studied by the standard deviation of the KD-values by means of Fisher’s F-test and F-score (PADJ)	1.06 (10−2)
16	Statistical significance of the difference between ancestral and minor alleles of the Arabidopsis thaliana promoters examined as the difference between the distributions of the KD-values according to the following:
	Pearson’s chi-squared test, χ2-value (PADJ)	298.17 (10−9)
	Kolmogorov–Smirnov test, D-score (PADJ)	0.04 (10−9)
17	Total number of the Arabidopsis thaliana protein-coding genes whose SNP-related expression changes were hand annotated (Supplementary Materials: Table S1)	109
18	Total number of the plant benefits annotated within this work	173
19	Total number of the plant species whose gene expression changes were taken into account within the framework of our hand-curated annotation	17
20	Total number of the original articles on experimental observations of benefits from gene expression alterations cited in this work	83
21	Total number of the proximal promoter SNPs, which can statistically significantly alter expression of the Arabidopsis thaliana genes and their paralogs annotated within this work	2426

Notes. P_ADJ, significance level according to Bonferroni correction for multiple comparisons.