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 4 Years necessary to generate a literature body of given FPE values

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

T	All genes					Genes with T0 in 1995 and later
T	Min	Max	Mean	Median	SD	Min	Max	Mean	Median	SD
(A)
T1	0	40	5.72	4	6.48	0	25	5.77	5	5.41
T5	1	56	15.55	14	9.21	1	27	12.26	12	5.44
T10	2	54	20.32	19	10.19	2	26	14.59	14	5.26
T15	2	57	23.03	22	10.49	3	27	15.70	16	5.04
T20	3	58	25.03	24	10.61	3	27	16.88	17	5.09
T25	3	60	26.49	26	10.86	4	27	17.12	17	4.80
T30	4	65	27.74	27	11.01	5	26	17.48	17	4.78
T35	4	76	28.72	29	11.13	6	26	17.91	18	4.73
T40	4	79	29.34	29	11.12	6	27	18.25	19	4.76
T45	5	82	30.15	30	11.24	7	27	18.74	18.5	4.78
T50	6	70	30.84	31	11.26	7	26	18.53	19	4.47
T75	7	64	32.58	33	11.27	8	26	18.94	19	4.52
T100	8	67	33.43	33	10.94	10	25	18.73	19	4.04
T500	16	54	39.56	41	8.38	25	25	25.00	25	NA

T	Genes with T0 in 1980 and later					Genes with T0 in 2000 and later
T	Min	Max	Mean	Median	SD	Min	Max	Mean	Median	SD
(B)
T1	0	36	3.95	2	4.89	0	21	5.09	4	4.42
T5	0	42	11.01	10	6.65	0	22	10.13	10	4.45
T10	0	41	14.05	13	7.34	1	22	11.98	12	4.45
T15	1	42	15.89	15	7.71	1	22	12.96	13	4.42
T20	1	41	17.11	17	7.94	1	22	13.42	14	4.39
T25	1	42	17.99	18	8.08	1	22	13.80	14	4.40
T30	2	42	18.71	18	8.18	2	22	13.97	14	4.32
T35	2	42	19.25	19	8.23	2	22	14.21	15	4.32
T40	2	41	19.80	20	8.34	2	22	14.32	15	4.29
T45	2	42	20.15	20	8.38	2	22	14.33	15	4.27
T50	2	42	20.50	20	8.38	2	22	14.42	15	4.22
T75	2	42	21.69	22	8.50	3	22	14.96	15	4.23
T100	2	42	22.46	22	8.53	4	22	15.16	15	4.14
T500	6	42	25.38	26	7.84	8	22	15.62	17	4.52

The letter “T” in abbreviations “T0, T1, etc.” stands for “threshold” applied to FPE values (see Table 2). We list the minimal (Min), maximal (Max), median and mean (together with the respective standard deviation—SD) numbers of years needed to accumulate the necessary FPEs for a given gene relative to the gene’s year for T0
Surprisingly, the data for the number of years necessary to generate a body of literature that corresponds to a given FPE bracket is quite similar for E. coli and for human genes despite the human system being so much more complex (and the research being correspondingly more expensive for the human systems). Also, we see the disproportionally large decrease of the number of years to achieve T75, T100, and T500 compared with lower FPE score ranges for both taxa in recent years. As a trend, the research progress is faster in human than in E. coli despite the latter being the much simpler system with still many gene functions to discover
(A) As the research technology has dramatically changed compared with the time when the first genes achieved T0 (the first recorded publication for b0344 is from 1939), we present the data for all eligible K-12 MG1655 genes as well as separately for those with their T0 event 1995 and later. The years necessary for getting into higher T ranges get smaller for more recently studied genes but still remain clearly above a decade. Notably, the median number of years needed to make a threshold dropped more dramatically for higher literature thresholds (> 14 years for T75, T100 and T500 versus a drop by just 5–7 years for T10, T15 and T20)
(B) Similar data for the body of literature for human genes with their T0 event 1980 (or later) and, separately, for those with first mentioning in 2000 (or later). The years necessary for getting into higher T ranges get smaller for more recently studied genes but still remain clearly above a decade. Notably, the median number of years needed to make a threshold dropped more dramatically for higher literature thresholds (> 7 years for T75, T100 and T500 versus a drop by just 1–3 years for T10, T15 and T20)

Back to article page

ISSN: 1745-6150

Contact us

General enquiries: journalsubmissions@springernature.com

Biology Direct

Contact us