About the dark corners in the gene function space of Escherichia coli remaining without illumination by scientific literature

Tantoso, Erwin; Eisenhaber, Birgit; Sinha, Swati; Jensen, Lars Juhl; Eisenhaber, Frank

doi:10.1186/s13062-023-00362-0

Table 2 The growing trend of literature coverage for E. coli K-12 genes in various FPE score thresholds

From: About the dark corners in the gene function space of Escherichia coli remaining without illumination by scientific literature

FPE score threshold	Phase 1					Phase 2
FPE score threshold	Years	Slope	R²	ρ	P-value	Years	Slope	R²	ρ	P-value
0	–	–	–	–	–	–	–	–	–	–
T0 (0 < x < 1)	1960–2009 ↑	2.28	0.81	0.90	1.04E-18	2009–2021 ↓	− 11.37	0.94	0.97	3.95E-08
T1 (1 ≤ x < 5)	1965–2009 ↑	1.68	0.79	0.89	5.76E-16	2009–2021 ↓	− 3.63	0.57	0.75	2.93E-03
T5 (5 ≤ x < 10)	1970–2013 ↑	1.78	0.84	0.92	3.20E-18	2013–2021 ↓	− 2.33	0.36	0.60	9.00E-02
T10 (10 ≤ x < 15)	1973–2001 ↑	1.08	0.89	0.94	1.70E-14	2001–2021 ↑↑	3.46	0.79	0.89	7.07E-08
T15 (15 ≤ x < 20)	1973–2003 ↑	0.85	0.84	0.92	3.68E-12	2003–2021 ↑↑	3.61	0.77	0.88	7.79E-07
T20 (20 ≤ x < 25)	1973–2004 ↑	0.65	0.77	0.88	3.44E-11	2004–2021 ↑↑	3.88	0.87	0.93	1.83E-08
T25 (25 ≤ x < 30)	1975–2004 ↑	0.49	0.61	0.78	2.94E-07	2004–2021 ↑↑	3.81	0.91	0.95	8.04E-10
T30 (30 ≤ x < 35)	1975–2004 ↑	0.51	0.75	0.87	4.82E-10	2004–2021 ↑↑	3.42	0.89	0.94	5.23E-09
T35 (35 ≤ x < 40)	1975–2004 ↑	0.41	0.75	0.86	7.83E-10	2004–2021 ↑↑	3.06	0.91	0.95	1.26E-09
T40 (40 ≤ x < 45)	1975–2006 ↑	0.41	0.69	0.83	3.69E-09	2006–2021 ↑↑	2.65	0.81	0.90	2.08E-06
T45 (45 ≤ x < 50)	1975–2006 ↑	0.36	0.66	0.81	1.53E-08	2006–2021 ↑↑	2.83	0.90	0.95	1.55E-08
T50 (50 ≤ x < 75)	1975–2006 ↑	0.32	0.75	0.87	1.60E-10	2006–2021 ↑↑	2.82	0.88	0.94	6.96E-08
T75 (75 ≤ x < 100)	1980–2006 ↑	0.16	0.37	0.61	7.34E-04	2006–2021 ↑↑	2.33	0.93	0.96	2.71E-09
T100 (100 ≤ x < 500)	1980–2006 ↑	0.11	0.23	0.48	1.19E-02	2006–2021 ↑↑	2.02	0.78	0.88	6.81E-06
T500 (x ≥ 500)	1980–2021 ↑	0.09	0.56	0.75	1.53E-08	–	–	–	–	–

The slope is the most important information that was shown in bold
The letter “T” in abbreviations “T0, T1, etc.” stands for “threshold” applied to FPE values. Further, the curve of the number of new genes in the respective FPE range as a function of the year (see Fig. 2) is analyzed with linear regression methods. The trend of changes is generally identified through two phases, i. e. Phase 1 and Phase 2. The slopes, R², ρ and P-value in time intervals of Phase 1 and Phase 2 are listed based on linear regression model y_i ~ C + b.x_i; where y_i = total number of new genes reaching the specific FPE threshold at year i; x_i = year i; b is the slope and C is intercept. The slope (b) indicates the rate increase/decrease of the total number of new genes reaching a specific FPE score threshold throughout the years. A positive slope indicates that, as a trend, the total number of new genes reaching a specific FPE score threshold is larger than the previous year (or from year to year); a negative slope indicates otherwise. ρ is the linear correlation between the total number of new genes reaching a specific FPE score threshold and year. R² is the square of correlation or the goodness of fit of the linear regression. P-value is the statistical significance of the slope. The total number of genes reaching the specific FPE score threshold can then be estimated by: N_i ~ N_(i-1) + y_i; where N_i and N_(i-1) = total number of genes reaching the specific FPE score threshold at year i and (i-1) respectively. The symbol ↑ indicates growing trend, whereas the symbol ↓ indicates declining trend. The symbol ↑↑ indicates accelerating growth trend

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ISSN: 1745-6150

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