Supplementary Table II			

Results from FatiScan analysis of mRNA-level derived residuals for enrichment of GO terms. Terms significantly enriched (e) or depleted (e) towards high ranking (i.e. large positive) residuals are shown.			
"Residuals comprise all substrate classes, including non-substrates."			
"Note that, as optimal codons are defined by their enrichment in very highly expressed genes, and these gene include many ribosomal protein genes, enrichment of ribosome-associated functions amongst high-residual genes is expected and should not be overinterpreted."			

GO category and hierarchical level	GO term	Enriched/Depleted towards high positive residuals	Adjusted p value
biological process at level 4	protein metabolic process (GO:0019538)	e	2.39E-09
biological process at level 5	cellular protein metabolic process (GO:0044267)	e	5.60E-09
biological process at level 4	cellular macromolecule metabolic process (GO:0044260)	e	1.65E-07
cellular component  at level 7	cytoplasmic part (GO:0044444)	e	2.00E-07
biological process at level 6	translation (GO:0006412)	e	3.39E-07
cellular component  at level 5	intracellular part (GO:0044424)	e	4.04E-06
biological process at level 3	macromolecule metabolic process (GO:0043170)	e	2.88E-05
biological process at level 5	macromolecule biosynthetic process (GO:0009059)	e	3.64E-05
cellular component  at level 4	intracellular (GO:0005622)	e	1.12E-04
molecular function at level 3	structural constituent of ribosome (GO:0003735)	e	1.28E-04
cellular component  at level 6	cytoplasm (GO:0005737)	e	3.03E-04
cellular component  at level 6	ribonucleoprotein complex (GO:0030529)	e	4.83E-04
biological process at level 3	primary metabolic process (GO:0044238)	e	6.37E-04
molecular function at level 3	protein binding (GO:0005515)	e	8.53E-04
cellular component  at level 3	non-membrane-bound organelle (GO:0043228)	e	9.82E-04
molecular function at level 4	RNA binding (GO:0003723)	e	1.37E-03
molecular function at level 4	"ligase activity, forming carbon-oxygen bonds (GO:0016875)"	e	1.37E-03
cellular component  at level 7	intracellular non-membrane-bound organelle (GO:0043232)	e	2.03E-03
biological process at level 7	amino acid activation (GO:0043038)	e	4.12E-03
biological process at level 8	tRNA aminoacylation (GO:0043039)	e	4.31E-03
cellular component  at level 6	intracellular organelle (GO:0043229)	e	4.88E-03
molecular function at level 5	"ligase activity, forming aminoacyl-tRNA and related compounds (GO:0016876)"	e	5.38E-03
molecular function at level 3	ligase activity (GO:0016874)	e	5.83E-03
biological process at level 9	tRNA aminoacylation for protein translation (GO:0006418)	e	8.15E-03
biological process at level 7	purine nucleotide biosynthetic process (GO:0006164)	e	8.40E-03
molecular function at level 6	aminoacyl-tRNA ligase activity (GO:0004812)	e	1.14E-02
molecular function at level 5	rRNA binding (GO:0019843)	e	1.20E-02
molecular function at level 4	"translation factor activity, nucleic acid binding (GO:0008135)"	e	1.64E-02
molecular function at level 4	unfolded protein binding (GO:0051082)	e	1.87E-02
biological process at level 4	response to drug (GO:0042493)	e	2.53E-02
biological process at level 8	purine nucleoside monophosphate biosynthetic process (GO:0009127)	e	2.67E-02
biological process at level 8	purine ribonucleoside monophosphate metabolic process (GO:0009167)	e	2.67E-02
biological process at level 4	cellular localization (GO:0051641)	e	2.98E-02
biological process at level 8	purine ribonucleotide biosynthetic process (GO:0009152)	e	3.01E-02
biological process at level 4	cellular component disassembly (GO:0022411)	e	3.13E-02
biological process at level 10	purine nucleotide metabolic process (GO:0006163)	e	3.17E-02
biological process at level 7	purine nucleoside monophosphate metabolic process (GO:0009126)	e	3.47E-02
cellular component  at level 3	organelle part (GO:0044422)	e	3.81E-02
cellular component  at level 9	cytosolic part (GO:0044445)	e	4.00E-02
biological process at level 12	intracellular transport (GO:0046907)	e	4.51E-02
biological process at level 5	establishment of cellular localization (GO:0051649)	e	4.67E-02
cellular component  at level 7	integral to membrane (GO:0016021)	d	1.13E-05
biological process at level 5	cofactor biosynthetic process (GO:0051188)	d	2.91E-05
biological process at level 7	coenzyme biosynthetic process (GO:0009108)	d	1.18E-04
cellular component  at level 5	plasma membrane (GO:0005886)	d	2.29E-04
cellular component  at level 6	intrinsic to membrane (GO:0031224)	d	4.83E-04
cellular component  at level 5	membrane part (GO:0044425)	d	2.04E-03
biological process at level 4	cofactor metabolic process (GO:0051186)	d	8.55E-03
biological process at level 5	nitrogen compound biosynthetic process (GO:0044271)	d	1.12E-02
biological process at level 4	aromatic compound metabolic process (GO:0006725)	d	1.14E-02
biological process at level 8	hexitol metabolic process (GO:0006059)	d	1.25E-02
biological process at level 8	alditol catabolic process (GO:0019405)	d	1.25E-02
biological process at level 9	galactitol metabolic process (GO:0019402)	d	1.29E-02
biological process at level 9	hexitol catabolic process (GO:0019407)	d	1.29E-02
biological process at level 5	vitamin biosynthetic process (GO:0009110)	d	1.53E-02
biological process at level 4	heterocycle metabolic process (GO:0046483)	d	1.54E-02
cellular component  at level 5	flagellum (GO:0019861)	d	1.83E-02
cellular component  at level 5	cell projection part (GO:0044463)	d	1.83E-02
biological process at level 8	amine biosynthetic process (GO:0009309)	d	1.89E-02
cellular component  at level 7	flagellin-based flagellum part (GO:0044461)	d	2.20E-02
biological process at level 7	alditol metabolic process (GO:0019400)	d	2.41E-02
cellular component  at level 6	flagellin-based flagellum (GO:0009288)	d	2.62E-02
cellular component  at level 6	flagellum part (GO:0044460)	d	2.62E-02
biological process at level 9	water-soluble vitamin biosynthetic process (GO:0042364)	d	3.02E-02
biological process at level 11	polyol catabolic process (GO:0046174)	d	3.51E-02
biological process at level 4	vitamin metabolic process (GO:0006766)	d	4.36E-02
cellular component  at level 8	flagellin-based flagellum basal body (GO:0009425)	d	4.54E-02
biological process at level 5	coenzyme metabolic process (GO:0006732)	d	4.67E-02