Table 2.

Differentially expressed proteins in PKD1 and normal ELVs

UniProt ID	Section	Normal Mean	PKD Mean	PKD/Normal	Corrected P Value	q Value	Function
PKD1	A	55.5×106	29.8×106	0.537	0.011	0.0036	PKD1 gene product PC1
PKD2	A	18.7×106	9.9×106	0.529	0.0004	0.0003	PKD2 gene product PC2
TMEM2	B	4.0×106	8.2×106	2.057	0.02	0.0109	Similar to fibrocystin
SAHH3	D	2.4×105	1.6×105	0.662	0.002	0.0016	Similar to SAHH2 (IRBIT)
SAHH2	E	2.0×106	1.4×106	0.684	0.005	0.0042	IRBIT interacts with IP3 receptor, CFTR, NBC1, and NHE3 channels; REDOX sensitive
SBP1	F	19.1×106	11.2×106	0.583	0.01	0.0075	Antioxidant metabolism
CU062	G	2.49×105	1.10×105	0.440	0.001	0.0001	Small secreted glycoprotein
RCL	I	13.3×106	7.7×106	0.578	0.02	0.0097	2′-deoxynucleoside 5′-phosphate N-hydrolase 1 (C6orf108)
FABPH	J	61.9×106	26.9×106	0.434	0.001	0.0007	Mammary-derived growth inhibitor (MDGI)

The discovery phase of the study yielded eight proteins that were reduced and one that was increased in ELVs from PKD1 individuals versus normals (P<0.03). Loess corrected intensities were compared using a Welch t test to yield the P value, and these were then adjusted for multiple testing using Bonferroni correction (m=number of proteins per gel slice) to yield corrected P value. q values were obtained from the uncorrected P value using the BioConductor q-value package.