Buffering by gene duplicates: an analysis of molecular correlates and evolutionary conservation

BMC Genomics

Table 2 Characteristics of buffering and non-buffering yeast two-gene families

Feature	Source	Buffering gene pair – average	Buffering gene pair – count	Non-buffering gene pair – average	Non-buffering gene pair – count	t-score
Across genes
mRNA abundance (molecules/cell)	[67]	4.948	91	0.906	14	4.04*
Protein abundance (molecules/cell)	[67]	35040	29	2116	4	2.84
Molecular weight (Da)	[66]	66299.9	99	91885.0	16	-2.33
Codon Adaptation Index	[66]	0.232	99	0.134	16	4.97*
Codon Bias Index	[66]	0.187	99	0.051	16	5.18*
Protein production rate (s ^-1 )	[68]	0.632	90	0.056	12	3.45*
Proteins produced per mRNA	[68]	5.733	85	1.388	11	4.07*
Transcription rate (s ^-1 )	[68]	0.109	85	0.040	11	2.87
Protein half-life (min)	[69]	108.5	74	177.1	13	-0.50
dN/dS	[70]	0.056	56	0.113	8	-1.95
No. orthologs in 14 organisms	[32]	8.1	94	5.8	15	1.52
No. protein-protein interactions	[71]	15.2	84	4.3	14	4.50*
Between genes
Sequence similarity (%)	BLAST output	54.3	50	32.5	8	4.91*
Shortest path – Functional network	[31]	1.27	48	1.63	8	-1.26
Vector similarity – Functional interactions	[31]	0.15	23	0.04	7	2.04
Vector similarity – Physical interactions	[30]	0.13	25	0.03	8	2.01
Vector similarity – Genetic interactions	See methods	0.01	26	0.07	7	-1.49
Vector similarity – KO phenotypes	[63]	0.17	10	0.11	2	0.27
Worm two-gene families (subset)
Length (nt)	[66]	1556	254	1359	32	1.10
Codon Adaptation Index	[64]	0.396	254	0.326	32	2.46
dN (Ka)	Analysis by [33]	0.34		0.50

The table lists a selection of characteristics tested for the two sets of buffering and non-buffering yeast two-gene families, respectively. Also see Table 3 for description of the data. A small number of characteristics could also be tested for worm two-gene families, identified in published work [33]. Due to multiple hypothesis testing, a t-score > 3.26 should be considered significant at an adjusted P-value of 0.05 (Bonferroni); significant scores are marked with *. An E-value of '0' signifies an E-value that is smaller than 10^-360.

ISSN: 1471-2164