Table 1.

Genes differentially expressed between Pde6b^rd1/rd1 and Pde6b^+/+ retinae at P90, grouped by broad function based on gene ontology terms annotated to the gene's entry on the gene ontology consortium database (two listed for each gene). Δ = change in expression compared to Pde6b^wt/wt (i.e. ‘+’ = up regulated; ‘-’ = down regulated) please see Table S2 for corresponding FDR adjusted p-values.

Symbol	Δ log2	Ontology term 1	Ontology term 2
A - Actin cytoskeleton, microtubules and intracellular transport
Ap3m2	−1.85	anterograde synaptic vesicle transport	intracellular protein transport
Cng	3.52	microtubule cytoskeleton organisation	microtubule binding
Sept4	1.54	cilium assembly	mitotic cytokinesis
Srm2	1.81	actin cytoskeleton organisation	melanosome organisation
Tmsb10	−2.15	actin cytoskeleton organisation	regulation of cell migration
B - Heparin sulphate proteoglycan metabolism
Extl3	−2.05	heparan sulphate proteoglycan biosynthesis	protein glycosylation
Slf2	1.43	heparan sulphate proteoglycan metabolic process	arylsulfatase activity
C - Cell signalling, calcium homeostasis
Anxa7	−1.56	calcium ion binding	membrane fusion
Cabyr	2.25	sperm capacitation	calcium-mediated signalling
Gabrg2	−1.56	gamma-aminobutyric acid signalling pathway	synaptic transmission, GABAergic
Pde1c	−1.96	signal transduction	response to calcium ion
Slc7a3	−2.87	amino acid transport	arginine transport
Unc13a	−2.11	neurotransmitter secretion	SNARE binding
D - Neural cell growth, survival & remodelling
Cntn1	−1.79	neuron projection development	nervous system development
Efnb1	2.15	axon guidance	presynapse assembly
Hdac9	−3.69	DNA repair	chromatin organisation
Lynx1	−8.26	synaptic transmission, cholinergic	acetylcholine receptor binding
Mif	−1.91	regulation of cell proliferation	positive regulation of axon regeneration
Nrm	−1.40	nuclear membrane	membrane
Pcdha7	−1.98	cell adhesion	cell-cell recognition
Phc1	1.93	cellular response to retinoic acid	histone ubiquitination
Ptprr	−3.72	negative regulation of ERK1 and ERK2 cascade	ERBB2 signalling pathway
Sfrs1	1.72	mRNA 5′-splice site recognition	regulation of transcription, DNA-templated
Socs5	−1.64	regulation of growth	JAK-STAT cascade
Yaf2	−2.54	regulation of transcription, DNA-templated	transcription, DNA-templated
E - Aerobic and anaerobic respiration, cellular response to stress
Atox1	−1.62	transition metal ion binding	response to oxidative stress
Clip1	−2.75	transition metal ion binding	microtubule bundle formation
Cox3	−1.83	aerobic electron transport chain	aerobic respiration
Msrb2	3.03	transition metal ion binding	cellular response to stress
Mt1	−10.73	transition metal ion binding	cellular metal ion homeostasis
Ndufb2	−1.55	mitochondrial respiratory chain complex I	oxidation-reduction process
Pgk1	−2.30	glycolytic process	carbohydrate metabolic process
F - Miscellaneous
Abca1	−3.10	cholesterol homeostasis	cellular response to retinoic acid
Fam19a3	1.87	positive regulation of microglial cell activation	negative regulation of microglial cell activation
Naa11	−3.83	n-terminal protein amino acid acetylation	n-terminal peptidyl-glutamic acid acetylation
Rnf11	−1.75	protein autoubiquitination	ubiquitin-dependent protein catabolic process