Table 2.

Significant predictors for retention of WGD, syntenic, non-syntenic, and CNS-associated genes

	WGD			CNS			Synteny			Non-syntenic
	Estimatea	SEb	Pr− > |z|c	Estimate	SE	Pr− > |z|	Estimate	SE	Pr− > |z|	Estimate	SE	Pr− > |z|
-Intercept	−0.75	0.04	0	0.63	0.05	0.63	−0.2	0.04	0	−1.46	0.07	0
ExpSpecific	1.3	0.06	0	1.82	0.08	0	1.47	0.07	0	−0.2	0.01	0
Length	0	0	0	0	0	0	0	0	0	−1.86	0.72	0
Phosphatase activity	0.72	0.31	0.02	N/A	N/A	N/A	1.83	0.73	0.01	0	N/A	N/A
Transporter activity	N/A	N/A	N/A	0.48	0.18	0.01	−0.49	0.14	0	0	N/A	N/A
Ion channel activity	N/A	N/A	N/A	N/A	N/A	N/A	−1.07	0.37	0	0	N/A	N/A
Protein kinase activity	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	0	N/A	N/A
Catalytic activity	N/A	N/A	N/A	N/A	N/A	N/A	−0.29	0.08	0	0.24	0.25	0.01
Stress response	0.46	0.24	0.05	0.68	0.32	0.03	N/A	N/A	N/A	0	N/A	N/A
Receptor activity	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	−0.55	0.11	0
Nucleic acid binding	0.17	0.08	0.03	N/A	N/A	N/A	0.53	0.11	0	0	N/A	N/A
Protease activity	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	−10.69	74.51	0.01
Ligase activity	1.01	0.57	0.08	N/A	N/A	N/A	N/A	N/A	N/A	−1.53	0.6	0.01
Cation binding	0.65	0.29	0.02	0.94	0.38	0.01	1.8	0.6	0	−1.7	0.18	0
Transcription factor	1.12	0.09	0	0.49	0.13	0	1.69	0.18	0	−0.11	0.05	0.02
Protein binding	0.17	0.03	0	0.17	0.05	0	0.09	0.05	0.04	−1.46	0.07	0

Logistic regression was used to identify significant predictors of occurrence of different gene categories, including genes related to CNS, synteny, and paralog retention. Candidate variables included gene ontology (GO) functional categories, gene length, and the tissue specificity score (ExpSpecific). Gene length was measured in bases between the start and stop codon, including all intron sequence

^aEstimate indicates the contribution of individual predictors, representing the change in the logit for each unit change in the predictor

^bSE indicates the standard error of regression coefficients estimation

^cThe significance of each variable