Table 1.
| a. Proteins with increased expression in the ventral prostate (VP) of 16-month-old animals | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| IPI ID | Gene Name |
Protein Name | MW | GB#a | No. of Unique Peptide b |
Coverage (%) |
No. of measurement for protein quantitation c |
O/Y (Mean) |
O/Y (Median) |
CV (%)d |
| Detoxification/Oxidative stress | ||||||||||
| IPI00231639.7 | GSTM1 | Glutathione S-transferase Mu 1e | 25897 | 17–22 | 3 | 23 | 31 | 2.59 | 2.49 | 26 |
| IPI00230942.5 | GSTM3 | Glutathione S-transferase Mu 3 | 25664 | 17,18,21–23 | 4 | 37 | 5 | 3.99 | 3.72 | 36 |
| IPI00214299.6 | CBS | Cystathionine beta-synthase | 61327 | 1,5 | 1 | 5 | 3 | 3.65 | 2.91 | 35 |
| IPI00382226.1 IPI00679203.3 |
RGD1306939 FTL1 |
Hypothetical protein LOC306934 (Ferritin_Like) Ferritin light chain |
144619 | 22 | 1 | 1 11 |
2 | 2.53 | 2.53 | 3.1 |
| IPI00373143.1 | FTH1 | Ferritin heavy chain | 21019 | 22 | 1 | 13 | 1 | 4.73 | 4.73 | – |
| IPI00371286.2 | ASNA1 | Predicted: Similar to ARSA (bacterial) arsenite transporter | 38993 | 13 | 1 | 6 | 3 | 2.07 | 2.19 | 10 |
| Cell Signaling | ||||||||||
| IPI00205606.3 | SEL1L | Sel1h Sel-1 homolog precursor | 88627 | 25 | 1 | 3 | 3 | 1.98 | 1.97 | 0.87 |
| IPI00203390.3 | PPP1CB | Serine/threonine-protein phosphatase PP1-b catalytic subunit | 37163 | 11,12 | 1 | 4 | 3 | 2.53 | 3.14 | 43 |
| IPI00198667.7 | CLU | Clusterin | 51342 | 11,14,16,20 | 1 | 5 | 3 | 2.99 | 3.47 | 48 |
| Protease inhibitor | ||||||||||
| IPI00679245.1 IPI00327182.4 |
MGC108747 KNG1 |
T-kininogen II (Major acute phase protein) T-kininogen I |
48076 47764 |
6 | 2 | 4 | 3 | 2.39 | 2.65 | 38.3 |
| Protein-lipid modification | ||||||||||
| IPI00208382.1 | PPT1 | Palmitoyl-protein thioesterase 1 | 34432 | 11–15 | 2 | 12 | 15 | 2.56 | 2.39 | 30 |
| Metabolism | ||||||||||
| IPI00372407.3 | Apoa1bp_predicted | Predicted: similar to apolipoprotein A-I binding protein | 30871 | 16–18 | 1 | 8 | 3 | 2.09 | 2.37 | 41 |
| IPI00194562.3 | HNRPR | Heterogeneous nuclear ribonucleoprotein R | 70831 | 1,3 | 1 | 2 | 2 | 2.54 | 2.54 | 32 |
| IPI00189991.1 | MAT2A | S-adenosylmethionine synthetase isoform type-2d | 43688 | 10–12 | 1 | 6 | 7 | 2.47 | 2.04 | 31 |
| IPI00188850.3 | RPIA_predicted | Predicted: Ribose-5-phosphate isomerase | 32452 | 18,20 | 1 | 6 | 3 | 1.99 | 2.07 | 7.3 |
| IPI00188330.1 | NDUFS8_predicted | Predicted: NADH dehydrogenase (ubiquinone) Fe-S protein 8 | 23955 | 18 | 1 | 8 | 3 | 2.34 | 2.34 | 25 |
| Immune response | ||||||||||
| IPI00558849.1 | DEFB50 | Beta-defensin 50 | 7895 | 31, 32 | 1 | 32 | 2 | 2.32 | 2.32 | 21 |
| IPI00388002.2 | LOC500180 LOC500183 |
Ig kappa chain | 34455 | 15–17,20,22 | 1 | 7 | 10 | 3.72 | 3.58 | 18 |
| b. Proteins with decreased expression in the VP of 16-month-old animals | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| IPI ID | Gene Name |
Protein Name | MW | GB# | No. of unique Peptide a |
Coverage (%) |
No. of measurement for protein quantitationb |
O/Y (Mean) |
O/Y (Median) |
CVc (%) |
| Protein folding | ||||||||||
| IPI00213644.3 | PPIB | Peptidyl-prolyl cis-trans isomerase B (Cyclophilin B) | 23803 | 21,22 | 1 | 6 | 5 | 0.58 | 0.53 | 18 |
| IPI00206660.2 | DNAJC3 | Protein kinase inhibitor p58, DnaJ (HSP40)C3 homolog | 57563 | 3,5,6 | 2 | 7 | 11 | 0.57 | 0.58 | 22 |
| IPI00210566.3 | HSPCA | Heat shock protein HSP 1, alpha (HSP 86), HSP 90 alpha | 84818 | 1–4 | 5 | 13 | 5 | 0.55 | 0.42 | 44 |
| IPI00210975.1 | HYOU1 | 150kDa oxygen-regulated protein, hypoxia up regulated protein 1 | 111291 | 38,1 | 2 | 2 | 3 | 0.55 | 0.57 | 27 |
| IPI00198887.1 | P4HB | Protein disulfide-isomerase, prolyl-4-hydroxyl -β peptide | 56916 | 5–7,9–14,16,17 | 2 | 2 | 22 | 0.48 | 0.5 | 31 |
| Metabolism | ||||||||||
| IPI00421357.2 | EPRS | Glutamyl-prolyl-tRNA synthetase | 169980 | 1,6 | 2 | 4 | 3 | 0.49 | 0.43 | 41 |
| IPI00230830.5 | EIF2S1 | Eukaryotic translation initiation factor 2 (eif-2) subunit 1 alpha | 36086 | 12–14 | 1 | 5 | 6 | 0.57 | 0.55 | 20 |
| IPI00206789.1 | RPL36 | Ribosomal protein L36 [Rattus norvegicus] | 12219 | 27–29 | 1 | 8 | 4 | 0.54 | 0.53 | 18 |
| IPI00197952.1 | SRM | Spermidine synthase | 33975 | 12–15 | 1 | 7 | 11 | 0.62 | 0.57 | 22 |
| IPI00188158.1 | HMGCS1 | Hydroxymethylglutaryl-CoA synthase, cytoplasmic | 57398 | 2,3,6 | 1 | 2 | 3 | 0.62 | 0.55 | 24 |
| Vesicle transport/Intracellular trafficking/Cytoskeleton | ||||||||||
| IPI00364707.1 | TMED9 | Transmembrane emp24 protein transport domain containing 9 | 27011 | 18 | 1 | 8 | 2 | 0.31 | 0.31 | 27 |
| IPI00231965.5 | ARF4 ARF5 |
ADP-ribosylation factor 4 ADP-ribosylation factor 5 |
20517 | 21,22 | 1 | 8 | 3 | 0.35 | 0.36 | 16 |
| IPI00200773.1 | ACTN1 ACTN2 ACTN3 ACTN4 |
Alpha-actinin alpha 1 Predicted similar to actinin alpha 2 Actinin alpha 3 Actinin alpha 4 |
102948 | 38,2,3,6 | 2 | 4 | 7 | 0.47 | 0.50 | 20 |
| IPI00231275.7 | LGALS1 | Beta-galactoside-binding lectin (galectin) | 14847 | 25 | 2 | 20 | 5 | 0.66 | 0.57 | 18 |
| Miscellaneous | ||||||||||
| IPI00198604.2 | RGD1563144_predicted | Preducted_similar to glucosamine 6-phosphate N-acetyltransferase | 42849 | 20–22 | 2 | 8 | 4 | 0.44 | 0.36 | 43 |
| IPI00197723.4 | RGD1565681_predicted | Predicted similar to proline rich 6 | 27499 | 14,15 | 1 | 4 | 2 | 0.58 | 0.58 | 22 |
| IPI00362395.4 | Esd | Esterase D/formylglutathione hydrolase | 31543 | 13,14 | 2 | 14 | 3 | 0.49 | 0.49 | 37 |
a)
Number of unique peptides (same amino acid sequence that may have modification (heavy/light labeled, oxidation) identified according to the criteria of XCorr values of 1.5 (1+), 2.0 (2+) and 2.5 (3+), DelCN =/> 0.1, and two missed cleavages allowed. Detailed information regarding peptide identification of the differentially expressed proteins is included in Supplementary Table S4.
b)
Number of quantifiable peptides used in ratio calculation: peptides that have labeled cysteines (including those with modification and/or were measured repeatedly).
c)
CV (%): coefficient of variation = standard deviation/mean. CVs (%) were calculated for proteins having 2 or more quantifiable peptides.
d)
Proteins whose transcript was found to be differentially expressed in our previous microarray study were italiced.
e)
Proteins that have an antibody available are highlighted in grey.