Table 3. Correlation of GO CC Subcellular Location Annotations P, R, G and S with Nucleus (N) and Mitochondrion (M) Annotations and Experimental Data.

	GO CC annotation plasma membrane (P) number of proteins with N and/or M annotation
data set	M	M+N	N	neither	sum	R2 {m&n}a
{m}	10	2	10	80	102
{m&n}	10	9	40	60	119	0.27
{n}	3	2	20	21	46
sum	23	13	70	161	267

	selected{m} and {n} proteins
data set	gene	{N} peptides	{N} counts	{M} peptides	{M} counts
{n}	SRP72	20	31	0	0
	LRRK2	8	63	0	0
	ENAH	13	23	0	0
{m}	CAT	0	0	18	48
	RHOA	0	0	8	47
	LAMP2	0	0	5	36

	GO CC annotation endoplasmic reticulum (R) number of proteins with N and/or M annotation
data set	M	M+N	N	neither	sum	R2 {m&n}a
{m}	9	3	9	55	76
{m&n}	1	5	21	53	80	0.15
{n}	2	0	5	8	15
sum	12	8	35	116	171

	selected {m} and {n} proteins
data set	gene	{N} peptides	{N} counts	{M} peptides	{M} counts
{n}	PDCD6	7	11	0	0
	P4HA1	7	7	0	0
	RRS1	9	18	0	0
{m}	POR	0	0	26	61
	TMX1	0	0	11	40
	LMAN1	0	0	10	29

	GO CC annotation Golgi apparatus (G) number of proteins with N and/or M annotation
data set	M	M+N	N	neither	sum	R2 {m&n}a
{m}	3	1	9	47	60
{m&n}	3	0	13	37	53	−0.08
{n}	0	2	13	16	31
sum	6	3	35	100	144

	selected {m} and {n} proteins
data set	gene	{N} peptides	{N} counts	{M} peptides	{M} counts
{n}	AFGF1	6	9	0	0
	COPA	18	21	0	0
	GTPBP4	11	23	0	0
{m}	LMAN1	0	0	10	29
	LPCAT1	0	0	7	17
	SLC1A5	0	0	9	33

	GO CC annotation Cytosol (S) number of proteins with N and/or M annotation
data set	M	M+N	N	neither	sum	R2 {m&n}a
{m}	5	7	20	48	80
{m&n}	12	15	91	143	261	0.56
{n}	8	8	64	79	159
sum	25	30	175	270	500

	selected {m} and {n} proteins
data set	gene	{N} peptides	{N} counts	{M} peptides	{M} counts
{n}	DDX6	20	60	0	0
	SNRPB	6	87	0	0
	TRIM25	12	30	0	0
{m}	BAG6	0	0	10	14
	GGH	0	0	7	23
	PPT1	0	0	8	32

^aR²{m&n} is the correlation between the number of nuclear counts and the number of mitochondrial counts for proteins in subset {m&n}.