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pmid:29286311

Comparative Proteomics Analysis of Urine Reveals Down-Regulation of Acute Phase Response Signaling and LXR/RXR Activation Pathways in Prostate Cancer.

Katarina Davalieva · Sanja Kiprijanovska · Ivana Maleva Kostovska · Sotir Stavridis · Oliver Stankov · Selim Komina · Gordana Petrusevska · Momir Polenakovic

Proteomes · 2017 doi:10.3390/proteomes6010001

Paper

complete

Experiment

complete

Data

partial

Analysis

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Execution

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Record details sci_version · id · kind · revision · content_hash · schema · created_at · updated_at · generator
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2026-11-01T15:40:30Z
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2026-11-01T22:43:13Z
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paper object · 10 fields
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title
Comparative Proteomics Analysis of Urine Reveals Down-Regulation of Acute Phase Response Signaling and LXR/RXR Activation Pathways in Prostate Cancer.
doi
10.3390/proteomes6010001
pmid
29286311
authors array · 8 items
[0]
Katarina Davalieva
[1]
Sanja Kiprijanovska
[2]
Ivana Maleva Kostovska
[3]
Sotir Stavridis
[4]
Oliver Stankov
[5]
Selim Komina
[6]
Gordana Petrusevska
[7]
Momir Polenakovic
journal
Proteomes
year
2017
abstract
Detecting prostate cancer (PCa) using non-invasive diagnostic markers still remains a challenge. The aim of this study was the identification of urine proteins that are sufficiently sensitive and specific to detect PCa in the early stages. Comparative proteomics profiling of urine from patients with PCa, benign prostate hyperplasia, bladder cancer, and renal cancer, coupled with bioinformatics analysis, were performed. Statistically significant difference in abundance showed 20 and 85 proteins in the 2-D DIGE/MS and label-free LC-MS/MS experiments, respectively. In silico analysis indicated activation, binding, and cell movement of subset of immune cells as the top affected cellular functions in PCa, together with the down-regulation of Acute Phase Response Signaling and Liver X Receptor/ Retinoid X Receptor (LXR/RXR) activation pathways. The most promising biomarkers were 35, altered in PCa when compared to more than one group. Half of these have confirmed localization in normal or PCa tissues. Twenty proteins (CD14, AHSG, ENO1, ANXA1, CLU, COL6A1, C3, FGA, FGG, HPX, PTGDS, S100A9, LMAN2, ITIH4, ACTA2, GRN, HBB, PEBP1, CTSB, SPP1) are oncogenes, tumor suppressors, and multifunctional proteins with highly confirmed involvement in PCa, while 9 (AZU1, IGHG1, RNASE2, PZP, REG1A, AMY1A, AMY2A, ACTG2, COL18A1) have been associated with different cancers, but not with PCa so far, and may represent novel findings. LC-MS/MS data are available via ProteomeXchange with identifier PXD008407.
claims array · 2 items
[0] object · 6 fields
id
claim-data-access
statement
The mass spectrometry proteomics data have been deposited in the ProteomeXchange Consortium (http://proteomecentral.proteomexchange.org) via the PRIDE partner repository [20] with data set identifier PXD008407 and 10.6019/PXD008407.
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evidence array · 1 item
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sections[6] "2.4. Label-Free LC-MS/MS Analysis" paragraph 3
quote
The mass spectrometry proteomics data have been deposited in the ProteomeXchange Consortium (http://proteomecentral.proteomexchange.org) via the PRIDE partner repository [20] with data set identifier PXD008407 and 10.6019/PXD008407.
state
complete
[1] object · 6 fields
id
claim-target-result
statement
The study identified 20 and 85 significantly differentially abundant urine proteins by 2-D DIGE/MS and label-free LC-MS/MS, respectively, using fold-change and ANOVA thresholds with t-tests and false-discovery-rate correction; the mass-spectrometry data were deposited in ProteomeXchange via PRIDE under identifier PXD008407.
kind
qualitative
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null
evidence array · 3 items
[0] object · 3 fields
asset
source:pmid:29286311
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sections[0] "Abstract" paragraph 1
quote
Statistically significant difference in abundance showed 20 and 85 proteins in the 2-D DIGE/MS and label-free LC-MS/MS experiments, respectively.
[1] object · 3 fields
asset
source:pmid:29286311
locator
sections[7] "2.5. Analysis of the Proteomics Data" paragraph 2
quote
Proteins with differential abundance among the four groups were considered with fold change ≥ 1.5 and Anova ≤ 0.05. p-values between groups were calculated using t-test (independent, 2-tailed, unequal variance) and subsequently false discovery rate (FDR) correction for multiple testing [21] was applied.
[2] object · 3 fields
asset
source:pmid:29286311
locator
sections[6] "2.4. Label-Free LC-MS/MS Analysis" paragraph 3
quote
The mass spectrometry proteomics data have been deposited in the ProteomeXchange Consortium (http://proteomecentral.proteomexchange.org) via the PRIDE partner repository [20] with data set identifier PXD008407 and 10.6019/PXD008407.
state
complete
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experiment object · 8 fields
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complete
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The study identified 20 and 85 significantly differentially abundant urine proteins by 2-D DIGE/MS and label-free LC-MS/MS, respectively, using fold-change and ANOVA thresholds with t-tests and false-discovery-rate correction; the mass-spectrometry data were deposited in ProteomeXchange via PRIDE under identifier PXD008407.
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[0] object · 13 fields
id
read_published_estimate
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1
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Read the published estimate from the source
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other
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complete
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null
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The claim, method and evidence span published with the source article.
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inputs array · 1 item
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source:pmid:29286311
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the published estimate and its evidence
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Obtain the source data from the named repository
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The GEO series accession resolves and its sample accessions are listed. This lane did not download the dataset or read its licence.
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the source data with its repository provenance
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Run the published analysis
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Apply the paper's statistical method to the resolved series and compare the result with the published target.
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the replicated result and its comparison
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source:pmid:29286311
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https://doi.org/10.3390/proteomes6010001
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identifier
10.3390/proteomes6010001
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Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.
structure object · 4 fields
pmcid
PMC5874760
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europe_pmc_fulltext
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whole_body
text_hash_scope
rendered_section_body
[1] object · 15 fields
id
data:geo:PXD008407
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raw
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geo-series
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application/vnd.ncbi.geo-series+json
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https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=PXD008407
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null
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The mass spectrometry proteomics data have been deposited in the ProteomeXchange Consortium (http://proteomecentral.proteomexchange.org) via the PRIDE partner repository [20] with data set identifier PXD008407 and 10.6019/PXD008407.
structure object · 15 fields
repository
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GEO accession URL
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The mass spectrometry proteomics data have been deposited in the ProteomeXchange Consortium (http://proteomecentral.proteomexchange.org) via the PRIDE partner repository [20] with data set identifier PXD008407 and 10.6019/PXD008407.
access_statement_kind
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sample_accessions array · 0 items
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title
LC-MSMS analysis of human urine to identify early diagnostic biomarkers for prostate cancer
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2026-10-31T18:35:55Z
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identifier_resolution_only_no_download_no_licence_read
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[2] object · 16 fields
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List of proteins with differential abundance in prostate cancer (PCa) as compared to benign prostate hyperplasia (BPH,) bladder cancer (BC), and renal cancer (RC) obtained by two-dimensional Difference Gel Electrophoresis/Mass Spectrometry (2-D DIGE) and identified by MALDI-TOF MS.
structure object · 5 fields
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PMC5874760
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9
section_title
3.1. 2-D DIGE Analysis
row_count
56
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16
table object · 8 fields
label
Table 1
caption
List of proteins with differential abundance in prostate cancer (PCa) as compared to benign prostate hyperplasia (BPH,) bladder cancer (BC), and renal cancer (RC) obtained by two-dimensional Difference Gel Electrophoresis/Mass Spectrometry (2-D DIGE) and identified by MALDI-TOF MS.
rows array · 56 items
[0] array · 13 items
[0]
Reff. Spot No.
[1]
PCa/BPH
[2]
PCa/BC
[3]
PCa/RC
[4]
Protein Name
[5]
Gene Name
[6]
Mw (kDa) b
[7]
pl
[8]
Mascot Protein Score
[9]
p Value
[10]
RMS Error (ppm)
[11]
Matched Peptides/Total
[12]
% of Sequence Coverage
[1] array · 6 items
[0]
t-Test
[1]
Fold Change
[2]
t-Test
[3]
Fold Change
[4]
t-Test
[5]
Fold Change
[2] array · 16 items
[0]
1
[1]
[2]
[3]
4.0 × 10−2
[4]
−3.8
[5]
[6]
[7]
Serotransferrin
[8]
TF
[9]
79.3
[10]
6.81
[11]
205
[12]
6.4 × 10−17
[13]
35
[14]
20/23
[15]
35
[3] array · 16 items
[0]
2
[1]
[2]
[3]
8.5 × 10−3
[4]
−3.6
[5]
[6]
[7]
Serotransferrin
[8]
TF
[9]
79.3
[10]
6.81
[11]
203
[12]
1.0 × 10−16
[13]
33
[14]
21/27
[15]
31
[4] array · 16 items
[0]
3
[1]
[2]
[3]
2.7 × 10−2
[4]
−3.6
[5]
[6]
[7]
Serotransferrin
[8]
TF
[9]
79.3
[10]
6.81
[11]
190
[12]
2.0 × 10−15
[13]
46
[14]
23/37
[15]
37
[5] array · 16 items
[0]
4
[1]
[2]
[3]
3.7 × 10−2
[4]
−3.0
[5]
[6]
[7]
Serotransferrin
[8]
TF
[9]
79.3
[10]
6.81
[11]
287
[12]
4.0 × 10−25
[13]
39
[14]
29/36
[15]
41
[6] array · 16 items
[0]
5
[1]
[2]
[3]
4.5 × 10−2
[4]
−3.6
[5]
[6]
[7]
Serotransferrin
[8]
TF
[9]
79.3
[10]
6.81
[11]
148
[12]
3.2 × 10−11
[13]
44
[14]
17/34
[15]
23
[7] array · 16 items
[0]
6
[1]
[2]
[3]
3.1 × 10−3
[4]
−6.5
[5]
[6]
[7]
Serotransferrin
[8]
TF
[9]
79.3
[10]
6.81
[11]
70
[12]
1.8 × 10−3
[13]
99
[14]
8/11
[15]
13
[8] array · 16 items
[0]
7
[1]
2.3 × 10−2
[2]
3.5
[3]
[4]
[5]
[6]
[7]
Kininogen-1
[8]
KNG1
[9]
73.0
[10]
6.34
[11]
94
[12]
7.9 × 10−6
[13]
88
[14]
9/13
[15]
18
[9] array · 16 items
[0]
8
[1]
4.3 × 10−2
[2]
2.6
[3]
6.2 × 10−5
[4]
3.0
[5]
[6]
[7]
Kininogen-1
[8]
KNG1
[9]
73.0
[10]
6.34
[11]
156
[12]
5.1 × 10−12
[13]
43
[14]
17/24
[15]
24
[10] array · 16 items
[0]
9
[1]
[2]
[3]
2.2 × 10−2
[4]
2.4
[5]
[6]
[7]
Kininogen-1
[8]
KNG1
[9]
73.0
[10]
6.34
[11]
139
[12]
2.5 × 10−10
[13]
56
[14]
14/20
[15]
24
[11] array · 16 items
[0]
10
[1]
[2]
[3]
3.4 × 10−2
[4]
2.6
[5]
[6]
[7]
Kininogen-1
[8]
KNG1
[9]
73.0
[10]
6.34
[11]
131
[12]
1.6 × 10−9
[13]
101
[14]
11/12
[15]
18
[12] array · 16 items
[0]
11
[1]
4.5 × 10−2
[2]
2.5
[3]
6.9 × 10−3
[4]
4.4
[5]
[6]
[7]
Kininogen-1
[8]
KNG1
[9]
73.0
[10]
6.34
[11]
111
[12]
1.6 × 10−7
[13]
35
[14]
10/14
[15]
19
[13] array · 16 items
[0]
12
[1]
[2]
[3]
5.5 × 10−3
[4]
3.1
[5]
[6]
[7]
Kininogen-1
[8]
KNG1
[9]
73.0
[10]
6.34
[11]
90
[12]
5.6 × 10−6
[13]
58
[14]
9/14
[15]
18
[14] array · 16 items
[0]
13
[1]
1.3 × 10−2
[2]
−2.8
[3]
3.7 × 10−2
[4]
−2.6
[5]
[6]
[7]
mix (Ig alpha-1 chain C region/Ig alpha-2 chain C region)
[8]
IGHA1/ IGHA2
[9]
38.5/ 37.3
[10]
6.08/ 5.71
[11]
65/81
[12]
2.4 × 10−3/ 1.1 × 10−4
[13]
48/45
[14]
6/6/8
[15]
14/20
[15] array · 16 items
[0]
14
[1]
3.9 × 10−2
[2]
−2.4
[3]
1.9 × 10−2
[4]
−2.7
[5]
[6]
[7]
mix (Ig alpha-1 chain C region/Ig alpha-2 chain C region)
[8]
IGHA1/ IGHA2
[9]
38.5/ 37.3
[10]
6.08/ 5.71
[11]
59/82
[12]
2.4 × 10−2/ 1.3 × 10−4
[13]
48/45
[14]
5/6/8
[15]
13/20
[16] array · 16 items
[0]
15
[1]
2.2 × 10−2
[2]
−2.9
[3]
1.3 × 10−2
[4]
−2.5
[5]
[6]
[7]
Ig alpha-1 chain C region
[8]
IGHA1
[9]
38.5
[10]
6.08
[11]
84
[12]
8.8 × 10−5
[13]
13
[14]
7/13
[15]
31
[17] array · 16 items
[0]
16
[1]
[2]
[3]
8.3 × 10−3
[4]
−2.1
[5]
[6]
[7]
mix (Ig alpha-1 chain C region/Ig alpha-2 chain C region)
[8]
IGHA1/ IGHA2
[9]
38.5/ 37.3
[10]
6.08/ 5.71
[11]
111/84
[12]
1.6 × 10−7/ 7.7 × 10−5
[13]
59/63
[14]
10/8/19
[15]
38/27
[18] array · 16 items
[0]
17
[1]
2.1 × 10−2
[2]
−2.7
[3]
3.5 × 10−2
[4]
−2.5
[5]
[6]
[7]
mix (Ig alpha-1 chain C region/Ig alpha-2 chain C region)
[8]
IGHA1/ IGHA2
[9]
38.5/ 37.3
[10]
6.08/ 5.71
[11]
102/84
[12]
1.3 × 10−6/ 7.7 × 10−5
[13]
89/93
[14]
9/8/19
[15]
33/27
[19] array · 16 items
[0]
18
[1]
3.1 × 10−2
[2]
−2.2
[3]
1.2 × 10−2
[4]
−2.1
[5]
5.1 × 10−3
[6]
−1.6
[7]
mix (Ig alpha-1 chain C region/Ig alpha-2 chain C region)
[8]
IGHA1
[9]
38.5/ 37.3
[10]
6.08/ 5.71
[11]
92/56
[12]
1.2 × 10−5/ 5.0 × 10−2
[13]
23/28
[14]
7/6/20
[15]
28/26
[20] array · 16 items
[0]
19
[1]
1.4 × 10−2
[2]
−2.4
[3]
[4]
[5]
5.6 × 10−2
[6]
−1.6
[7]
mix (Ig alpha-1 chain C region/Ig alpha-2 chain C region)
[8]
IGHA1/ IGHA2
[9]
38.5/ 37.3
[10]
6.08/ 5.71
[11]
97/69
[12]
3.8 × 10−6/ 2.4 × 10−3
[13]
37/37
[14]
10/8/38
[15]
38/27
[21] array · 16 items
[0]
20
[1]
2.9 × 10−2
[2]
−2.0
[3]
6.4 × 10−3
[4]
−2.0
[5]
6.7 × 10−2
[6]
−1.7
[7]
mix (Ig alpha-1 chain C region/Ig alpha-2 chain C region)
[8]
IGHA1/ IGHA2
[9]
38.5/ 37.3
[10]
6.08/ 5.71
[11]
122/82
[12]
1.3 × 10−8/ 1.4 × 10−4
[13]
11/12
[14]
9/8/12
[15]
26/21
[22] array · 16 items
[0]
21 a
[1]
[2]
[3]
2.0 × 10−2
[4]
−3.2
[5]
[6]
[7]
Arginyl-tRNA-protein transferase 1
[8]
ATE1
[9]
60.0
[10]
8.17
[11]
98
[12]
3.6 × 10−6
[13]
67
[14]
9/16
[15]
28
[23] array · 16 items
[0]
22
[1]
[2]
[3]
1.8 × 10−2
[4]
−2.0
[5]
[6]
[7]
Fibrinogen gamma chain
[8]
FGG
[9]
52.1
[10]
5.37
[11]
121
[12]
1.6 × 10−8
[13]
43
[14]
12/23
[15]
38
[24] array · 16 items
[0]
23
[1]
[2]
[3]
2.1 × 10−2
[4]
−5.3
[5]
[6]
[7]
Fibrinogen gamma chain
[8]
FGG
[9]
52.1
[10]
5.37
[11]
174
[12]
8.0 × 10−14
[13]
39
[14]
14/18
[15]
42
[25] array · 16 items
[0]
24
[1]
[2]
[3]
3.4 × 10−2
[4]
−5.7
[5]
[6]
[7]
Fibrinogen gamma chain
[8]
FGG
[9]
52.1
[10]
5.37
[11]
117
[12]
4.0 × 10−8
[13]
83
[14]
12/19
[15]
31
[26] array · 16 items
[0]
25
[1]
[2]
[3]
3.5 × 10−2
[4]
−7.1
[5]
[6]
[7]
Fibrinogen gamma chain
[8]
FGG
[9]
52.1
[10]
5.37
[11]
107
[12]
4.0 × 10−7
[13]
35
[14]
12/26
[15]
32
[27] array · 16 items
[0]
26
[1]
[2]
[3]
4.1 × 10−2
[4]
−5.8
[5]
[6]
[7]
Fibrinogen gamma chain
[8]
FGG
[9]
52.1
[10]
5.37
[11]
139
[12]
2.5 × 10−10
[13]
39
[14]
13/25
[15]
37
[28] array · 16 items
[0]
27
[1]
[2]
[3]
2.0 × 10−3
[4]
2.1
[5]
[6]
[7]
Zinc-alpha-2-glycoprotein
[8]
AZGP1
[9]
34.5
[10]
5.71
[11]
102
[12]
1.3 × 10−6
[13]
45
[14]
13/27
[15]
30
[29] array · 16 items
[0]
28
[1]
[2]
[3]
2.0 × 10−2
[4]
−4.7
[5]
[6]
[7]
Haptoglobin
[8]
HP
[9]
45.9
[10]
6.13
[11]
87
[12]
3.8 × 10−5
[13]
104
[14]
8/17
[15]
18
[30] array · 16 items
[0]
29
[1]
[2]
[3]
1.9 × 10−2
[4]
−6.7
[5]
[6]
[7]
Haptoglobin
[8]
HP
[9]
45.9
[10]
6.13
[11]
108
[12]
3.2 × 10−7
[13]
11
[14]
13/25
[15]
27
[31] array · 16 items
[0]
30
[1]
[2]
[3]
2.2 × 10−2
[4]
−6.3
[5]
[6]
[7]
Haptoglobin
[8]
HP
[9]
45.9
[10]
6.13
[11]
107
[12]
4.0 × 10−7
[13]
53
[14]
16/37
[15]
28
[32] array · 16 items
[0]
31
[1]
[2]
[3]
2.6 × 10−2
[4]
−7.5
[5]
[6]
[7]
Haptoglobin
[8]
HP
[9]
45.9
[10]
6.13
[11]
98
[12]
3.1 × 10−6
[13]
47
[14]
12/27
[15]
27
[33] array · 16 items
[0]
32
[1]
[2]
[3]
2.6 × 10−2
[4]
−8.1
[5]
[6]
[7]
Haptoglobin
[8]
HP
[9]
45.9
[10]
6.13
[11]
86
[12]
5.0 × 10−5
[13]
55
[14]
13/30
[15]
28
[34] array · 16 items
[0]
33
[1]
[2]
[3]
2.1 × 10−2
[4]
−7.7
[5]
[6]
[7]
Haptoglobin
[8]
HP
[9]
45.9
[10]
6.13
[11]
129
[12]
2.5 × 10−9
[13]
44
[14]
12/16
[15]
30
[35] array · 16 items
[0]
34
[1]
[2]
[3]
1.8 × 10−3
[4]
3.4
[5]
[6]
[7]
Fibrinogen alpha chain (fragment)
[8]
FGA
[9]
95.7 (45)
[10]
5.7
[11]
125
[12]
6.4 × 10−9
[13]
72
[14]
12/16
[15]
15
[36] array · 16 items
[0]
35
[1]
[2]
[3]
2.6 × 10−3
[4]
5.3
[5]
[6]
[7]
Inter-alpha-trypsin inhibitor heavy chain H4 (fragment)
[8]
ITIH4
[9]
103.5 (45)
[10]
6.57
[11]
69
[12]
2.5 × 10−3
[13]
47
[14]
9/26
[15]
12
[37] array · 16 items
[0]
36
[1]
2.2 × 10−2
[2]
2.5
[3]
[4]
[5]
[6]
[7]
Hemoglobin subunit beta
[8]
HBB
[9]
16.1
[10]
6.75
[11]
141
[12]
1.6 × 10−10
[13]
88
[14]
11/22
[15]
69
[38] array · 16 items
[0]
37
[1]
8.4 × 10−3
[2]
2.5
[3]
5.0 × 10−4
[4]
4.3
[5]
[6]
[7]
Inter-alpha-trypsin inhibitor heavy chain H4 (fragment)
[8]
ITIH4
[9]
103.5 (45)
[10]
6.57
[11]
90
[12]
2.1 × 10−5
[13]
59
[14]
13/23
[15]
15
[39] array · 16 items
[0]
38
[1]
[2]
[3]
1.6 × 10−2
[4]
4.8
[5]
[6]
[7]
Protein AMBP
[8]
AMBP
[9]
39.9
[10]
5.95
[11]
94
[12]
8.0 × 10−6
[13]
66
[14]
11/30
[15]
24
[40] array · 16 items
[0]
39
[1]
[2]
[3]
1.5 × 10−2
[4]
5.0
[5]
[6]
[7]
Protein AMBP
[8]
AMBP
[9]
39.9
[10]
5.95
[11]
135
[12]
6.4 × 10−10
[13]
37
[14]
13/18
[15]
32
[41] array · 16 items
[0]
40
[1]
[2]
[3]
1.4 × 10−2
[4]
5.2
[5]
[6]
[7]
Protein AMBP
[8]
AMBP
[9]
39.9
[10]
5.95
[11]
108
[12]
3.2 × 10−7
[13]
91
[14]
10/19
[15]
18
[42] array · 16 items
[0]
41
[1]
5.3 × 10−3
[2]
2.0
[3]
[4]
[5]
[6]
[7]
Protein AMBP
[8]
AMBP
[9]
39.9
[10]
5.95
[11]
74
[12]
7.3 × 10−4
[13]
12
[14]
9/17
[15]
26
[43] array · 16 items
[0]
42
[1]
[2]
[3]
3.3 × 10−3
[4]
4.0
[5]
[6]
[7]
Prostaglandin-H2 D-isomerase
[8]
PTGDS
[9]
21.2
[10]
7.66
[11]
64
[12]
7.3 × 10−3
[13]
63
[14]
7/15
[15]
33
[44] array · 16 items
[0]
43
[1]
[2]
[3]
6.2 × 10−3
[4]
4.0
[5]
[6]
[7]
Prostaglandin-H2 D-isomerase
[8]
PTGDS
[9]
21.2
[10]
7.66
[11]
70
[12]
2.3 × 10−3
[13]
72
[14]
8/25
[15]
27
[45] array · 16 items
[0]
44
[1]
[2]
[3]
8.9 × 10−3
[4]
3.3
[5]
[6]
[7]
Prostaglandin-H2 D-isomerase
[8]
PTGDS
[9]
21.2
[10]
7.66
[11]
60
[12]
1.9 × 10−2
[13]
93
[14]
7/26
[15]
26
[46] array · 16 items
[0]
45 a
[1]
[2]
[3]
4.6 × 10−2
[4]
1.9
[5]
[6]
[7]
Ig kappa chain C region
[8]
IGKC
[9]
11.8
[10]
5.58
[11]
83
[12]
1.1 × 10−4
[13]
51
[14]
5/10
[15]
56
[47] array · 16 items
[0]
46
[1]
[2]
[3]
4.1 × 10−2
[4]
−1.9
[5]
[6]
[7]
Serum amyloid P-component
[8]
APCS
[9]
25.5
[10]
6.1
[11]
106
[12]
5.1 × 10−7
[13]
31
[14]
10/27
[15]
34
[48] array · 16 items
[0]
47 a
[1]
[2]
[3]
7.3 × 10−4
[4]
6.9
[5]
[6]
[7]
Vitelline membrane outer layer protein 1 homolog
[8]
VMO1
[9]
22.0
[10]
4.9
[11]
82
[12]
1.3 × 10−4
[13]
101
[14]
7/24
[15]
57
[49] array · 16 items
[0]
48
[1]
[2]
[3]
5.4 × 10−4
[4]
8.2
[5]
[6]
[7]
CD59 glycoprotein
[8]
CD59
[9]
14.8
[10]
6.02
[11]
67
[12]
4.1 × 10−3
[13]
17
[14]
4/5
[15]
21
[50] array · 16 items
[0]
49
[1]
[2]
[3]
4.8 × 10−2
[4]
3.4
[5]
[6]
[7]
Retinol-binding protein 4
[8]
RBP4
[9]
23.3
[10]
5.76
[11]
111
[12]
1.6 × 10−7
[13]
76
[14]
9/11
[15]
41
[51] array · 16 items
[0]
50
[1]
[2]
[3]
3.4 × 10−2
[4]
−7.8
[5]
[6]
[7]
Haptoglobin (fragment)
[8]
HP
[9]
45.9 (20)
[10]
6.13
[11]
71
[12]
2.4 × 10−3
[13]
50
[14]
6/11
[15]
12
[52] array · 16 items
[0]
51
[1]
[2]
[3]
3.8 × 10−2
[4]
−8.9
[5]
[6]
[7]
Haptoglobin (fragment)
[8]
HP
[9]
45.9 (20)
[10]
6.13
[11]
73
[12]
1.1 × 10−3
[13]
16
[14]
6/9
[15]
12
[53] array · 16 items
[0]
52
[1]
[2]
[3]
3.2 × 10−2
[4]
−10.4
[5]
[6]
[7]
Haptoglobin (fragment)
[8]
HP
[9]
45.9 (20)
[10]
6.13
[11]
72
[12]
1.3 × 10−3
[13]
49
[14]
6/9
[15]
14
[54] array · 16 items
[0]
53
[1]
2.7 × 10−2
[2]
4.5
[3]
3.7 × 10−3
[4]
11.0
[5]
[6]
[7]
Mannan-binding lectin serine protease 2 (fragment)
[8]
MASP2
[9]
77.2 (19.5)
[10]
5.39
[11]
125
[12]
6.4 × 10−9
[13]
104
[14]
12/16
[15]
18
[55] array · 16 items
[0]
54
[1]
[2]
[3]
1.7 × 10−2
[4]
4.5
[5]
[6]
[7]
Chain A, Laminin G Like Domain 3 From Human Perlecan
[8]
HSPG2 (gi|361131590)
[9]
20.7
[10]
5.47
[11]
181
[12]
2.5 × 10−13
[13]
55
[14]
11/15
[15]
73
row_count
56
column_count
16
numeric_cells
589
header_rows
2
locator
section[9]/table-wrap[1]#proteomes-06-00001-t001
[3] object · 16 fields
id
asset:table:pmid:29286311:2
role
table
format
jats-table
media_type
application/vnd.jats.table+json
uri
null
sha256
sha256:e248c23a63e291bc57a080e22c0624a37458cb7e7d4763ee943e7487dc1893c4
bytes
14187
access
open
state
verified
reader
read_table
reader_status
available
identifier
section[10]/table-wrap[1]#proteomes-06-00001-t002
version
null
note
List of identified proteins with differential abundance in PCa when compared to the three groups (BPH, BC, and RC) by LC-MS/MS.
structure object · 5 fields
pmcid
PMC5874760
section_index
10
section_title
3.2. LC-MS/MS Analysis
row_count
122
column_count
13
table object · 8 fields
label
Table 2
caption
List of identified proteins with differential abundance in PCa when compared to the three groups (BPH, BC, and RC) by LC-MS/MS.
rows array · 122 items
[0] array · 13 items
[0]
Uniprot Accession No.
[1]
Protein Name
[2]
Gene Name
[3]
Peptide Count
[4]
Unique Peptides
[5]
Confidence Score
[6]
ANOVA
[7]
Max Fold Change
[8]
Highest Mean Condition
[9]
Lowest Mean Condition
[10]
Group Comparison
[11]
p-Value a
[12]
Ratio
[1] array · 13 items
[0]
P08571
[1]
Monocyte differentiation antigen
[2]
CD14
[3]
8
[4]
7
[5]
75.64
[6]
8.87 × 10−10
[7]
2.70
[8]
PCa
[9]
Bc
[10]
PCa vs. BC
[11]
2.71 × 10−4
[12]
2.7
[2] array · 13 items
[0]
[1]
CD14
[2]
[3]
[4]
[5]
[6]
[7]
[8]
[9]
[10]
PCa vs. BPH
[11]
4.67 × 10−3
[12]
1.8
[3] array · 13 items
[0]
[1]
[2]
[3]
[4]
[5]
[6]
[7]
[8]
[9]
[10]
PCa vs. RC
[11]
2.61 × 10−2
[12]
1.6
[4] array · 13 items
[0]
P62736
[1]
Actin_ aortic smooth muscle
[2]
ACTA2
[3]
3
[4]
3
[5]
24.21
[6]
1.75 × 10−9
[7]
5.89
[8]
Bc
[9]
PCa
[10]
PCa vs. BC
[11]
3.40 × 10−4
[12]
0.2
[5] array · 13 items
[0]
[1]
[2]
[3]
[4]
[5]
[6]
[7]
[8]
[9]
[10]
PCa vs. BPH
[11]
1.75 × 10−2
[12]
0.4
[6] array · 13 items
[0]
P02765
[1]
Alpha-2-HS-glycoprotein
[2]
AHSG
[3]
9
[4]
9
[5]
94.63
[6]
5.73 × 10−4
[7]
2.70
[8]
PCa
[9]
Bc
[10]
PCa vs. BC
[11]
9.03 × 10−3
[12]
2.7
[7] array · 13 items
[0]
[1]
[2]
[3]
[4]
[5]
[6]
[7]
[8]
[9]
[10]
PCa vs. BPH
[11]
4.14 × 10−2
[12]
2.1
[8] array · 13 items
[0]
P04745
[1]
Alpha-amylase 1
[2]
AMY1A
[3]
9
[4]
5
[5]
101.49
[6]
1.42 × 10−7
[7]
3.46
[8]
PCa
[9]
Bc
[10]
PCa vs. BC
[11]
3.40 × 10−4
[12]
3.5
[9] array · 13 items
[0]
[1]
[2]
[3]
[4]
[5]
[6]
[7]
[8]
[9]
[10]
PCa vs. BPH
[11]
4.14 × 10−2
[12]
1.7
[10] array · 13 items
[0]
P19961
[1]
Alpha-amylase 2B
[2]
AMY2B
[3]
3
[4]
1
[5]
21.24
[6]
3.52 × 10−6
[7]
12.86
[8]
Rc
[9]
Bc
[10]
PCa vs. BC
[11]
1.25 × 10−2
[12]
11.9
[11] array · 13 items
[0]
[1]
[2]
[3]
[4]
[5]
[6]
[7]
[8]
[9]
[10]
PCa vs. BPH
[11]
4.32 × 10−2
[12]
4.1
[12] array · 13 items
[0]
P06733
[1]
Alpha-enolase
[2]
ENO1
[3]
2
[4]
2
[5]
14.73
[6]
3.64 × 10−5
[7]
1.78
[8]
BPH
[9]
PCa
[10]
PCa vs. BC
[11]
1.54 × 10−2
[12]
0.7
[13] array · 13 items
[0]
[1]
[2]
[3]
[4]
[5]
[6]
[7]
[8]
[9]
[10]
PCa vs. BPH
[11]
7.97 × 10−3
[12]
0.6
[14] array · 13 items
[0]
P04083
[1]
Annexin A1
[2]
ANXA1
[3]
5
[4]
5
[5]
41.02
[6]
5.95 × 10−12
[7]
5.45
[8]
Rc
[9]
Bc
[10]
PCa vs. BC
[11]
1.08 × 10−3
[12]
3.8
[15] array · 13 items
[0]
[1]
[2]
[3]
[4]
[5]
[6]
[7]
[8]
[9]
[10]
PCa vs. BPH
[11]
1.20 × 10−2
[12]
2.2
[16] array · 13 items
[0]
P20160
[1]
Azurocidin
[2]
AZU1
[3]
2
[4]
2
[5]
13.76
[6]
7.34 × 10−5
[7]
2.80
[8]
BPH
[9]
PCa
[10]
PCa vs. BC
[11]
3.35 × 10−2
[12]
0.6
[17] array · 13 items
[0]
[1]
[2]
[3]
[4]
[5]
[6]
[7]
[8]
[9]
[10]
PCa vs. BPH
[11]
8.89 × 10−3
[12]
0.4
[18] array · 13 items
[0]
P10909
[1]
Clusterin
[2]
CLU
[3]
10
[4]
10
[5]
99.24
[6]
6.33 × 10−6
[7]
2.26
[8]
BPH
[9]
PCa
[10]
PCa vs. BC
[11]
5.24 × 10−3
[12]
0.6
[19] array · 13 items
[0]
[1]
[2]
[3]
[4]
[5]
[6]
[7]
[8]
[9]
[10]
PCa vs. BPH
[11]
2.55 × 10−2
[12]
0.4
[20] array · 13 items
[0]
P12109
[1]
Collagen alpha-1(VI)
[2]
COL6A1
[3]
6
[4]
4
[5]
46.91
[6]
2.05 × 10−7
[7]
3.44
[8]
BPH
[9]
PCa
[10]
PCa vs. BC
[11]
7.15 × 10−4
[12]
0.4
[21] array · 13 items
[0]
[1]
chain
[2]
[3]
[4]
[5]
[6]
[7]
[8]
[9]
[10]
PCa vs. BPH
[11]
8.66 × 10−3
[12]
0.3
[22] array · 13 items
[0]
P39060
[1]
Collagen alpha-1(XVIII)
[2]
COL18A1
[3]
2
[4]
2
[5]
14.39
[6]
2.92 × 10−9
[7]
14.26
[8]
Rc
[9]
Bc
[10]
PCa vs. BC
[11]
6.21 × 10−3
[12]
7.1
[23] array · 13 items
[0]
[1]
chain
[2]
[3]
[4]
[5]
[6]
[7]
[8]
[9]
[10]
PCa vs. BPH
[11]
2.30 × 10−2
[12]
4.2
[24] array · 13 items
[0]
P01024
[1]
Complement C3
[2]
C3
[3]
57
[4]
57
[5]
545.51
[6]
2.30 × 10−7
[7]
3.43
[8]
Rc
[9]
Bc
[10]
PCa vs. BC
[11]
6.30 × 10−3
[12]
2.9
[25] array · 13 items
[0]
[1]
[2]
[3]
[4]
[5]
[6]
[7]
[8]
[9]
[10]
PCa vs. BPH
[11]
2.77 × 10−2
[12]
2.2
[26] array · 13 items
[0]
P24855
[1]
Deoxyribonuclease-1
[2]
DNASE1
[3]
3
[4]
3
[5]
23.62
[6]
1.84 × 10−10
[7]
4.85
[8]
Rc
[9]
Bc
[10]
PCa vs. BC
[11]
6.30 × 10−3
[12]
3.6
[27] array · 13 items
[0]
[1]
[2]
[3]
[4]
[5]
[6]
[7]
[8]
[9]
[10]
PCa vs. BPH
[11]
3.55 × 10−2
[12]
2.3
[28] array · 13 items
[0]
O94919
[1]
Endonuclease domain-containing 1
[2]
ENDOD1
[3]
3
[4]
3
[5]
24.51
[6]
1.64 × 10−7
[7]
2.97
[8]
PCa
[9]
Bc
[10]
PCa vs. BC
[11]
1.01 × 10−3
[12]
3.0
[29] array · 13 items
[0]
[1]
protein
[2]
[3]
[4]
[5]
[6]
[7]
[8]
[9]
[10]
PCa vs. BPH
[11]
4.67 × 10−3
[12]
2.8
[30] array · 13 items
[0]
P02671
[1]
Fibrinogen alpha chain
[2]
FGA
[3]
24
[4]
24
[5]
293.54
[6]
7.67 × 10−6
[7]
2.72
[8]
BPH
[9]
Rc
[10]
PCa vs. BC
[11]
2.94 × 10−3
[12]
0.6
[31] array · 13 items
[0]
[1]
[2]
[3]
[4]
[5]
[6]
[7]
[8]
[9]
[10]
PCa vs. BPH
[11]
3.15 × 10−2
[12]
0.4
[32] array · 13 items
[0]
P02679
[1]
Fibrinogen gamma chain
[2]
FGG
[3]
20
[4]
20
[5]
251.65
[6]
1.07 × 10−4
[7]
2.32
[8]
BPH
[9]
Rc
[10]
PCa vs. BC
[11]
2.48 × 10−2
[12]
0.5
[33] array · 13 items
[0]
[1]
[2]
[3]
[4]
[5]
[6]
[7]
[8]
[9]
[10]
PCa vs. BPH
[11]
4.25 × 10−2
[12]
0.5
[34] array · 13 items
[0]
P28799
[1]
Granulins
[2]
GRN
[3]
2
[4]
2
[5]
18.13
[6]
2.87 × 10−8
[7]
3.92
[8]
BPH
[9]
PCa
[10]
PCa vs. BC
[11]
2.32 × 10−3
[12]
0.5
[35] array · 13 items
[0]
[1]
[2]
[3]
[4]
[5]
[6]
[7]
[8]
[9]
[10]
PCa vs. BPH
[11]
8.89 × 10−3
[12]
0.3
[36] array · 13 items
[0]
P68871
[1]
Hemoglobin subunit beta
[2]
HBB
[3]
10
[4]
10
[5]
138.23
[6]
1.54 × 10−5
[7]
4.62
[8]
Bc
[9]
PCa
[10]
PCa vs. BC
[11]
2.96 × 10−2
[12]
0.2
[37] array · 13 items
[0]
[1]
[2]
[3]
[4]
[5]
[6]
[7]
[8]
[9]
[10]
PCa vs. BPH
[11]
1.75 × 10−2
[12]
0.3
[38] array · 13 items
[0]
P02790
[1]
Hemopexin
[2]
HPX
[3]
16
[4]
16
[5]
164.63
[6]
4.66 × 10−6
[7]
2.44
[8]
BPH
[9]
PCa
[10]
PCa vs. BC
[11]
6.60 × 10−3
[12]
0.6
[39] array · 13 items
[0]
[1]
[2]
[3]
[4]
[5]
[6]
[7]
[8]
[9]
[10]
PCa vs. BPH
[11]
1.30 × 10−2
[12]
0.4
[40] array · 13 items
[0]
P01857
[1]
Ig gamma-1 chain C region
[2]
IGHG1
[3]
6
[4]
6
[5]
76.08
[6]
6.40 × 10−4
[7]
3.29
[8]
BPH
[9]
PCa
[10]
PCa vs. BC
[11]
6.71 × 10−3
[12]
0.5
[41] array · 13 items
[0]
[1]
[2]
[3]
[4]
[5]
[6]
[7]
[8]
[9]
[10]
PCa vs. BPH
[11]
4.14 × 10−2
[12]
0.3
[42] array · 13 items
[0]
P05451
[1]
Lithostathine-1-alpha
[2]
REG1A
[3]
5
[4]
4
[5]
35.95
[6]
3.83 × 10−4
[7]
3.96
[8]
PCa
[9]
BPH
[10]
PCa vs. BC
[11]
6.30 × 10−3
[12]
3.8
[43] array · 13 items
[0]
[1]
[2]
[3]
[4]
[5]
[6]
[7]
[8]
[9]
[10]
PCa vs. BPH
[11]
1.50 × 10−2
[12]
4.0
[44] array · 13 items
[0]
P11117
[1]
Lysosomal acid
[2]
ACP2
[3]
5
[4]
4
[5]
45.84
[6]
5.59 × 10−6
[7]
2.11
[8]
BPH
[9]
PCa
[10]
PCa vs. BC
[11]
7.15 × 10−4
[12]
0.6
[45] array · 13 items
[0]
[1]
phosphatase
[2]
[3]
[4]
[5]
[6]
[7]
[8]
[9]
[10]
PCa vs. BPH
[11]
6.07 × 10−3
[12]
0.5
[46] array · 13 items
[0]
P08246
[1]
Neutrophil elastase
[2]
ELANE
[3]
3
[4]
3
[5]
39.04
[6]
6.45 × 10−3
[7]
3.25
[8]
BPH
[9]
PCa
[10]
PCa vs. BC
[11]
2.74 × 10−2
[12]
0.5
[47] array · 13 items
[0]
[1]
[2]
[3]
[4]
[5]
[6]
[7]
[8]
[9]
[10]
PCa vs. BPH
[11]
4.99 × 10−2
[12]
0.3
[48] array · 13 items
[0]
P10153
[1]
Non-secretory
[2]
RNASE2
[3]
4
[4]
3
[5]
51.80
[6]
3.38 × 10−8
[7]
5.21
[8]
PCa
[9]
Bc
[10]
PCa vs. BC
[11]
8.08 × 10−3
[12]
5.2
[49] array · 13 items
[0]
[1]
ribonuclease
[2]
[3]
[4]
[5]
[6]
[7]
[8]
[9]
[10]
PCa vs. BPH
[11]
2.55 × 10−2
[12]
3.9
[50] array · 13 items
[0]
P10451
[1]
Osteopontin
[2]
SPP1
[3]
12
[4]
11
[5]
164.02
[6]
1.10 × 10−11
[7]
15.72
[8]
Rc
[9]
Bc
[10]
PCa vs. BC
[11]
2.32 × 10−3
[12]
8.4
[51] array · 13 items
[0]
[1]
[2]
[3]
[4]
[5]
[6]
[7]
[8]
[9]
[10]
PCa vs. BPH
[11]
2.55 × 10−2
[12]
2.6
[52] array · 13 items
[0]
P04746
[1]
Pancreatic alpha-amylase
[2]
AMY2A
[3]
3
[4]
1
[5]
27.44
[6]
3.66 × 10−6
[7]
5.06
[8]
PCa
[9]
Bc
[10]
PCa vs. BC
[11]
4.27 × 10−3
[12]
5.1
[53] array · 13 items
[0]
[1]
[2]
[3]
[4]
[5]
[6]
[7]
[8]
[9]
[10]
PCa vs. BPH
[11]
4.32 × 10−2
[12]
2.3
[54] array · 13 items
[0]
P30086
[1]
Phosphatidylethanolamine-
[2]
PEBP1
[3]
3
[4]
3
[5]
27.16
[6]
2.93 × 10−5
[7]
3.38
[8]
BPH
[9]
PCa
[10]
PCa vs. BC
[11]
7.15 × 10−4
[12]
0.5
[55] array · 13 items
[0]
[1]
binding protein 1
[2]
[3]
[4]
[5]
[6]
[7]
[8]
[9]
[10]
PCa vs. BPH
[11]
1.75 × 10−2
[12]
0.3
[56] array · 13 items
[0]
P20742
[1]
Pregnancy zone protein
[2]
PZP
[3]
7
[4]
7
[5]
82.62
[6]
4.09 × 10−8
[7]
2.27
[8]
Bc
[9]
Rc
[10]
PCa vs. BC
[11]
2.32 × 10−3
[12]
0.5
[57] array · 13 items
[0]
[1]
[2]
[3]
[4]
[5]
[6]
[7]
[8]
[9]
[10]
PCa vs. BPH
[11]
4.76 × 10−2
[12]
0.7
[58] array · 13 items
[0]
P41222
[1]
Prostaglandin-H2
[2]
PTGDS
[3]
9
[4]
7
[5]
140.59
[6]
4.51 × 10−11
[7]
5.56
[8]
PCa
[9]
Bc
[10]
PCa vs. BC
[11]
3.40 × 10−4
[12]
5.6
[59] array · 13 items
[0]
[1]
D-isomerase
[2]
[3]
[4]
[5]
[6]
[7]
[8]
[9]
[10]
PCa vs. BPH
[11]
1.75 × 10−2
[12]
1.8
[60] array · 13 items
[0]
P06702
[1]
Protein S100-A9
[2]
S100A9
[3]
3
[4]
3
[5]
26.61
[6]
1.49 × 10−6
[7]
6.46
[8]
BPH
[9]
PCa
[10]
PCa vs. BC
[11]
1.22 × 10−3
[12]
0.5
[61] array · 13 items
[0]
[1]
[2]
[3]
[4]
[5]
[6]
[7]
[8]
[9]
[10]
PCa vs. BPH
[11]
5.03 × 10−2
[12]
0.2
[62] array · 13 items
[0]
Q8WZ75
[1]
Roundabout homolog 4
[2]
ROBO4
[3]
7
[4]
7
[5]
55.71
[6]
3.32 × 10−3
[7]
2.27
[8]
BPH
[9]
PCa
[10]
PCa vs. BC
[11]
1.47 × 10−2
[12]
0.6
[63] array · 13 items
[0]
[1]
[2]
[3]
[4]
[5]
[6]
[7]
[8]
[9]
[10]
PCa vs. BPH
[11]
2.96 × 10−2
[12]
0.4
[64] array · 13 items
[0]
Q12907
[1]
Vesicular integral-membrane
[2]
LMAN2
[3]
9
[4]
8
[5]
94.66
[6]
1.64 × 10−6
[7]
2.48
[8]
Rc
[9]
Bc
[10]
PCa vs. BC
[11]
2.32 × 10−3
[12]
2.4
[65] array · 13 items
[0]
[1]
protein VIP36
[2]
[3]
[4]
[5]
[6]
[7]
[8]
[9]
[10]
PCa vs. BPH
[11]
2.55 × 10−2
[12]
1.7
[66] array · 13 items
[0]
Q14624
[1]
Inter-alpha-trypsin inhibitor heavy
[2]
ITIH4
[3]
9
[4]
9
[5]
94.01
[6]
3.21 × 10−13
[7]
5.55
[8]
Rc
[9]
Bc
[10]
PCa vs. BC
[11]
5.07 × 10−5
[12]
3.5
[67] array · 13 items
[0]
[1]
chain H4
[2]
[3]
[4]
[5]
[6]
[7]
[8]
[9]
[10]
PCa vs. BPH
[11]
4.67 × 10−3
[12]
1.6
[68] array · 13 items
[0]
P63267
[1]
Actin_ gamma-enteric
[2]
ACTG2
[3]
3
[4]
3
[5]
19.63
[6]
4.29 × 10−2
[7]
1.79
[8]
PCa
[9]
Rc
[10]
PCa vs. BC
[11]
1.08 × 10−3
[12]
1.7
[69] array · 13 items
[0]
[1]
smooth muscle
[2]
[3]
[4]
[5]
[6]
[7]
[8]
[9]
[10]
PCa vs. RC
[11]
2.56 × 10−3
[12]
1.8
[70] array · 13 items
[0]
P07858
[1]
Cathepsin B
[2]
CTSB
[3]
3
[4]
2
[5]
19.04
[6]
5.87 × 10−3
[7]
3.16
[8]
Bc
[9]
PCa
[10]
PCa vs. BC
[11]
3.10 × 10−2
[12]
0.3
[71] array · 13 items
[0]
[1]
[2]
[3]
[4]
[5]
[6]
[7]
[8]
[9]
[10]
PCa vs. RC
[11]
3.14 × 10−2
[12]
0.4
[72] array · 13 items
[0]
P01023
[1]
Alpha-2-macroglobulin
[2]
A2M
[3]
38
[4]
38
[5]
491.82
[6]
1.42 × 10−4
[7]
2.29
[8]
BPH
[9]
PCa
[10]
PCa vs. BPH
[11]
6.07 × 10−3
[12]
0.4
[73] array · 13 items
[0]
P15144
[1]
Aminopeptidase N
[2]
ANPEP
[3]
2
[4]
2
[5]
14.55
[6]
3.31 × 10−4
[7]
1.70
[8]
BPH
[9]
PCa
[10]
PCa vs. BPH
[11]
4.20 × 10−2
[12]
0.6
[74] array · 13 items
[0]
P07355
[1]
Annexin A2
[2]
ANXA2
[3]
2
[4]
2
[5]
16.06
[6]
9.99 × 10−5
[7]
4.27
[8]
Rc
[9]
BPH
[10]
PCa vs. BPH
[11]
4.76 × 10−2
[12]
4.1
[75] array · 13 items
[0]
P06727
[1]
Apolipoprotein A-IV
[2]
APOA4
[3]
3
[4]
3
[5]
31.32
[6]
3.77 × 10−3
[7]
2.28
[8]
BPH
[9]
PCa
[10]
PCa vs. BPH
[11]
5.03 × 10−2
[12]
0.4
[76] array · 13 items
[0]
Q8NFZ8
[1]
Cell adhesion molecule 4
[2]
CADM4
[3]
8
[4]
7
[5]
60.30
[6]
1.09 × 10−3
[7]
2.26
[8]
BPH
[9]
PCa
[10]
PCa vs. BPH
[11]
3.15 × 10−2
[12]
0.4
[77] array · 13 items
[0]
P17900
[1]
Ganglioside GM2 activator
[2]
GM2A
[3]
4
[4]
3
[5]
40.41
[6]
4.80 × 10−2
[7]
1.81
[8]
BPH
[9]
PCa
[10]
PCa vs. BPH
[11]
4.97 × 10−2
[12]
0.6
[78] array · 13 items
[0]
P69905
[1]
Hemoglobin subunit alpha
[2]
HBA1
[3]
5
[4]
5
[5]
56.91
[6]
9.41 × 10−3
[7]
4.36
[8]
Bc
[9]
PCa
[10]
PCa vs. BPH
[11]
4.67 × 10−3
[12]
0.6
[79] array · 13 items
[0]
P02042
[1]
Hemoglobin subunit delta
[2]
HBD
[3]
3
[4]
3
[5]
29.39
[6]
1.38 × 10−5
[7]
13.11
[8]
Bc
[9]
Rc
[10]
PCa vs. BPH
[11]
4.20 × 10−2
[12]
0.5
[80] array · 13 items
[0]
P01859
[1]
Ig gamma-2 chain C region
[2]
IGHG2
[3]
7
[4]
7
[5]
67.03
[6]
6.75 × 10−5
[7]
2.18
[8]
BPH
[9]
Bc
[10]
PCa vs. BPH
[11]
6.07 × 10−3
[12]
0.5
[81] array · 13 items
[0]
P01861
[1]
Ig gamma-4 chain C region
[2]
IGHG4
[3]
6
[4]
6
[5]
72.40
[6]
9.74 × 10−4
[7]
2.05
[8]
BPH
[9]
Rc
[10]
PCa vs. BPH
[11]
4.32 × 10−2
[12]
0.6
[82] array · 13 items
[0]
P01772
[1]
Ig heavy chain V-III region KOL
[2]
IGHV3-33
[3]
2
[4]
1
[5]
12.43
[6]
4.33 × 10−3
[7]
1.57
[8]
BPH
[9]
PCa
[10]
PCa vs. BPH
[11]
4.89 × 10−2
[12]
0.6
[83] array · 13 items
[0]
P0CF74
[1]
Ig lambda-6 chain C region
[2]
IGLC6
[3]
3
[4]
3
[5]
28.38
[6]
7.00 × 10−4
[7]
1.97
[8]
BPH
[9]
Bc
[10]
PCa vs. BPH
[11]
2.30 × 10−2
[12]
0.5
[84] array · 13 items
[0]
P02788
[1]
Lactotransferrin
[2]
LTF
[3]
43
[4]
41
[5]
601.64
[6]
8.73 × 10−5
[7]
2.61
[8]
BPH
[9]
Rc
[10]
PCa vs. BPH
[11]
4.20 × 10−2
[12]
0.5
[85] array · 13 items
[0]
P10253
[1]
Lysosomal alpha-glucosidase
[2]
GAA
[3]
8
[4]
8
[5]
80.33
[6]
9.63 × 10−5
[7]
1.77
[8]
BPH
[9]
PCa
[10]
PCa vs. BPH
[11]
4.14 × 10−2
[12]
0.6
[86] array · 13 items
[0]
P05164
[1]
Myeloperoxidase
[2]
MPO
[3]
16
[4]
15
[5]
159.24
[6]
4.69 × 10−5
[7]
1.76
[8]
BPH
[9]
PCa
[10]
PCa vs. BPH
[11]
4.67 × 10−3
[12]
0.6
[87] array · 13 items
[0]
P32119
[1]
Peroxiredoxin-2
[2]
PRDX2
[3]
3
[4]
1
[5]
23.32
[6]
2.58 × 10−2
[7]
13.40
[8]
Bc
[9]
PCa
[10]
PCa vs. BPH
[11]
5.03 × 10−2
[12]
0.2
[88] array · 13 items
[0]
P05155
[1]
Plasma protease C1 inhibitor
[2]
SERPING1
[3]
4
[4]
4
[5]
35.56
[6]
4.75 × 10−3
[7]
1.71
[8]
BPH
[9]
PCa
[10]
PCa vs. BPH
[11]
4.99 × 10−2
[12]
0.6
[89] array · 13 items
[0]
Q6S8J3
[1]
POTE ankyrin domain family member E
[2]
POTEE
[3]
11
[4]
8
[5]
93.51
[6]
3.30 × 10−4
[7]
2.04
[8]
BPH
[9]
Rc
[10]
PCa vs. BPH
[11]
4.76 × 10−2
[12]
0.5
[90] array · 13 items
[0]
P43652
[1]
Afamin
[2]
AFM
[3]
6
[4]
5
[5]
48.31
[6]
8.56 × 10−4
[7]
1.65
[8]
PCa
[9]
Bc
[10]
PCa vs. BC
[11]
5.76 × 10−3
[12]
1.6
[91] array · 13 items
[0]
P02647
[1]
Apolipoprotein A-I
[2]
APOA1
[3]
12
[4]
12
[5]
145.00
[6]
4.72 × 10−4
[7]
1.86
[8]
BPH
[9]
Rc
[10]
PCa vs. BC
[11]
3.02 × 10−2
[12]
0.7
[92] array · 13 items
[0]
P05090
[1]
Apolipoprotein D
[2]
APOD
[3]
6
[4]
6
[5]
69.92
[6]
4.00 × 10−7
[7]
2.12
[8]
PCa
[9]
Bc
[10]
PCa vs. BC
[11]
1.19 × 10−3
[12]
2.1
[93] array · 13 items
[0]
P02749
[1]
Beta-2-glycoprotein 1
[2]
APOH
[3]
11
[4]
10
[5]
112.68
[6]
1.13 × 10−4
[7]
3.66
[8]
Bc
[9]
Rc
[10]
PCa vs. BC
[11]
7.15 × 10−4
[12]
0.3
[94] array · 13 items
[0]
P19835
[1]
Bile salt-activated lipase
[2]
CEL
[3]
3
[4]
3
[5]
20.03
[6]
1.76 × 10−6
[7]
2.04
[8]
Rc
[9]
Bc
[10]
PCa vs. BC
[11]
7.58 × 10−3
[12]
1.6
[95] array · 13 items
[0]
P07339
[1]
Cathepsin D
[2]
CTSD
[3]
6
[4]
6
[5]
54.69
[6]
1.61 × 10−3
[7]
1.85
[8]
PCa
[9]
Bc
[10]
PCa vs. BC
[11]
1.38 × 10−2
[12]
1.9
[96] array · 13 items
[0]
P13987
[1]
CD59 glycoprotein
[2]
CD59
[3]
5
[4]
5
[5]
85.01
[6]
1.42 × 10−6
[7]
4.38
[8]
Rc
[9]
Bc
[10]
PCa vs. BC
[11]
2.94 × 10−3
[12]
4.3
[97] array · 13 items
[0]
P0C0L4
[1]
Complement C4-A
[2]
C4A
[3]
3
[4]
3
[5]
21.19
[6]
1.16 × 10−2
[7]
1.85
[8]
Bc
[9]
PCa
[10]
PCa vs. BC
[11]
6.21 × 10−3
[12]
0.5
[98] array · 13 items
[0]
P08174
[1]
Complement decay-accelerating factor
[2]
CD55
[3]
5
[4]
5
[5]
40.67
[6]
2.66 × 10−5
[7]
2.37
[8]
Rc
[9]
Bc
[10]
PCa vs. BC
[11]
1.02 × 10−2
[12]
2.2
[99] array · 13 items
[0]
Q02487
[1]
Desmocollin-2
[2]
DSC2
[3]
4
[4]
3
[5]
24.44
[6]
4.00 × 10−6
[7]
2.62
[8]
Bc
[9]
BPH
[10]
PCa vs. BC
[11]
1.78 × 10−3
[12]
0.6
[100] array · 13 items
[0]
Q9UHL4
[1]
Dipeptidyl peptidase 2
[2]
DPP7
[3]
2
[4]
2
[5]
12.10
[6]
4.08 × 10−2
[7]
4.13
[8]
BPH
[9]
PCa
[10]
PCa vs. BC
[11]
2.84 × 10−2
[12]
0.6
[101] array · 13 items
[0]
Q9HCU0
[1]
Endosialin
[2]
CD248
[3]
6
[4]
6
[5]
43.09
[6]
2.31 × 10−6
[7]
2.20
[8]
PCa
[9]
Bc
[10]
PCa vs. BC
[11]
1.14 × 10−2
[12]
2.2
[102] array · 13 items
[0]
P01834
[1]
Ig kappa chain C region
[2]
IGKC
[3]
9
[4]
9
[5]
154.85
[6]
3.59 × 10−3
[7]
2.04
[8]
PCa
[9]
Bc
[10]
PCa vs. BC
[11]
1.11 × 10−3
[12]
2.0
[103] array · 13 items
[0]
P01617
[1]
Ig kappa chain V-II region TEW
[2]
IGKV2D-28
[3]
5
[4]
3
[5]
60.57
[6]
1.37 × 10−2
[7]
2.22
[8]
Rc
[9]
Bc
[10]
PCa vs. BC
[11]
7.15 × 10−4
[12]
1.6
[104] array · 13 items
[0]
P01625
[1]
Ig kappa chain V-IV region Len
[2]
IGKV4-1
[3]
2
[4]
1
[5]
17.70
[6]
1.49 × 10−3
[7]
1.62
[8]
Rc
[9]
Bc
[10]
PCa vs. BC
[11]
7.58 × 10−3
[12]
1.6
[105] array · 13 items
[0]
P80748
[1]
Ig lambda chain V-III region LOI
[2]
IGLV3-21
[3]
3
[4]
3
[5]
29.50
[6]
1.01 × 10−3
[7]
2.13
[8]
PCa
[9]
Bc
[10]
PCa vs. BC
[11]
1.00 × 10−4
[12]
2.1
[106] array · 13 items
[0]
P0CG04
[1]
Ig lambda-1 chain C regions
[2]
IGLC1
[3]
6
[4]
6
[5]
112.58
[6]
6.98 × 10−3
[7]
2.14
[8]
BPH
[9]
Bc
[10]
PCa vs. BC
[11]
2.40 × 10−3
[12]
1.8
[107] array · 13 items
[0]
P0CG05
[1]
Ig lambda-2 chain C regions
[2]
IGLC2
[3]
3
[4]
3
[5]
57.93
[6]
1.94 × 10−2
[7]
1.73
[8]
BPH
[9]
Bc
[10]
PCa vs. BC
[11]
3.90 × 10−3
[12]
1.7
[108] array · 13 items
[0]
P01042
[1]
Kininogen-1
[2]
KNG1
[3]
27
[4]
27
[5]
362.50
[6]
8.88 × 10−7
[7]
2.71
[8]
Rc
[9]
Bc
[10]
PCa vs. BC
[11]
8.22 × 10−3
[12]
1.7
[109] array · 13 items
[0]
P14543
[1]
Nidogen-1
[2]
NID1
[3]
9
[4]
8
[5]
84.01
[6]
5.13 × 10−5
[7]
3.95
[8]
BPH
[9]
Bc
[10]
PCa vs. BC
[11]
2.23 × 10−3
[12]
2.0
[110] array · 13 items
[0]
O75594
[1]
Peptidoglycan recognition protein 1
[2]
PGLYRP1
[3]
5
[4]
5
[5]
50.82
[6]
6.11 × 10−5
[7]
2.30
[8]
BPH
[9]
Bc
[10]
PCa vs. BC
[11]
3.28 × 10−3
[12]
1.9
[111] array · 13 items
[0]
P01833
[1]
Polymeric immunoglobulin receptor
[2]
PIGR
[3]
25
[4]
24
[5]
263.55
[6]
5.20 × 10−5
[7]
2.50
[8]
Rc
[9]
Bc
[10]
PCa vs. BC
[11]
6.21 × 10−3
[12]
1.6
[112] array · 13 items
[0]
P02760
[1]
Protein AMBP
[2]
AMBP
[3]
25
[4]
24
[5]
366.65
[6]
4.27 × 10−3
[7]
2.49
[8]
Rc
[9]
Bc
[10]
PCa vs. BC
[11]
1.02 × 10−2
[12]
1.9
[113] array · 13 items
[0]
P00734
[1]
Prothrombin
[2]
F2
[3]
16
[4]
14
[5]
176.60
[6]
3.60 × 10−5
[7]
5.38
[8]
Rc
[9]
Bc
[10]
PCa vs. BC
[11]
7.15 × 10−4
[12]
2.7
[114] array · 13 items
[0]
P07998
[1]
Ribonuclease pancreatic
[2]
RNASE1
[3]
4
[4]
4
[5]
39.91
[6]
7.99 × 10−15
[7]
4.42
[8]
Rc
[9]
Bc
[10]
PCa vs. BC
[11]
7.63 × 10−4
[12]
3.5
[115] array · 13 items
[0]
Q9UBC9
[1]
Small proline-rich protein 3
[2]
SPRR3
[3]
2
[4]
2
[5]
22.69
[6]
7.14 × 10−3
[7]
2.10
[8]
PCa
[9]
Bc
[10]
PCa vs. BC
[11]
1.25 × 10−2
[12]
2.1
[116] array · 13 items
[0]
Q9UGT4
[1]
Sushi domain-containing protein 2
[2]
SUSD2
[3]
2
[4]
2
[5]
13.45
[6]
5.40 × 10−5
[7]
32.32
[8]
PCa
[9]
Bc
[10]
PCa vs. BC
[11]
4.99 × 10−2
[12]
32.3
[117] array · 13 items
[0]
P07911
[1]
Uromodulin
[2]
UMOD
[3]
27
[4]
27
[5]
399.14
[6]
6.23 × 10−6
[7]
2.98
[8]
Rc
[9]
Bc
[10]
PCa vs. BC
[11]
4.00 × 10−2
[12]
1.7
[118] array · 13 items
[0]
P22891
[1]
Vitamin K-dependent protein Z
[2]
PROZ
[3]
4
[4]
3
[5]
42.25
[6]
1.29 × 10−2
[7]
2.21
[8]
PCa
[9]
Bc
[10]
PCa vs. BC
[11]
2.92 × 10−2
[12]
2.2
[119] array · 13 items
[0]
P25311
[1]
Zinc-alpha-2-glycoprotein
[2]
AZGP1
[3]
17
[4]
15
[5]
230.16
[6]
1.61 × 10−2
[7]
2.47
[8]
PCa
[9]
Bc
[10]
PCa vs. BC
[11]
1.25 × 10−2
[12]
2.5
[120] array · 13 items
[0]
P06870
[1]
Kallikrein-1
[2]
KLK1
[3]
6
[4]
6
[5]
64.59
[6]
4.90 × 10−4
[7]
2.36
[8]
BPH
[9]
Bc
[10]
PCa vs. RC
[11]
2.61 × 10−2
[12]
0.6
[121] array · 13 items
[0]
Q96PD5
[1]
N-acetylmuramoyl-L-alanine amidase
[2]
PGLYRP2
[3]
5
[4]
5
[5]
56.28
[6]
7.41 × 10−3
[7]
2.14
[8]
PCa
[9]
Rc
[10]
PCa vs. RC
[11]
2.56 × 10−3
[12]
2.1
row_count
122
column_count
13
numeric_cells
788
header_rows
1
locator
section[10]/table-wrap[1]#proteomes-06-00001-t002
gaps array · 2 items
[0]
asset:data:geo:PXD008407 not downloaded
[1]
asset:data:geo:PXD008407 licence not read
analysis object · 4 fields
state
complete
methods array · 1 item
[0] object · 10 fields
id
method-1
family
group_comparison
specific
anova
label
Group comparison
dsl_operations array · 4 items
[0]
group_summary
[1]
welch_t
[2]
bootstrap_mean_difference
[3]
group_comparison_anova
missing_operations array · 0 items
expressible
true
parameters object · 0 fields
data_shapes array · 1 item
[0]
two_or_more_groups_continuous
evidence object · 3 fields
score
1
band
reordered
quote
“Proteins with differential abundance among the four groups were considered with fold change ≥ 1.5 and Anova ≤ 0.05. p-values between groups were calculated using t-test (independent, 2-tailed, unequal variance) and subsequently false discovery rate (FDR) correction for multiple testing [21] was applied.” “The mass spectrometry proteomics data have been deposited in the ProteomeXchange Consortium (http://proteomecentral.proteomexchange.org) via the PRIDE partner repository [20] with data set identifier PXD008407 and 10.6019/PXD008407.”
targets array · 0 items
gaps array · 0 items
capability object · 3 fields
state
complete
requirements array · 1 item
[0] object · 6 fields
capability_id
capability:computational_analysis
label
Computational analysis platform
assay_families array · 9 items
[0]
meta_analysis
[1]
machine_learning
[2]
survival_analysis
[3]
statistical_regression
[4]
pca
[5]
molecular_docking
[6]
network_analysis
[7]
differential_expression
[8]
gwas
availability_state
owned
tier_unlocked
R1
candidate
Automated Assays Laravel application and simulated adapters
gaps array · 0 items
readiness object · 8 fields
state
complete
tier
R1
blocking_axis
none
blocked_on
nothing:replicable_now
axes object · 3 fields
method object · 5 fields
tier
R1
expressible
true
required_operations array · 4 items
[0]
group_summary
[1]
welch_t
[2]
bootstrap_mean_difference
[3]
group_comparison_anova
missing_operations array · 0 items
basis
The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: anova.
capability object · 4 fields
tier
R1
capability_id
capability:computational_analysis
availability_state
owned
basis
The computational analysis is owned. The physical bench the paper used is not, so a physical validation cannot be run here.
data object · 6 fields
tier
R1
reachable
true
accessions array · 1 item
[0]
PXD008407
resolved_accessions array · 1 item
[0]
PXD008407
statements array · 1 item
[0]
The mass spectrometry proteomics data have been deposited in the ProteomeXchange Consortium (http://proteomecentral.proteomexchange.org) via the PRIDE partner repository [20] with data set identifier PXD008407 and 10.6019/PXD008407.
basis
The paper names PXD008407 in ProteomeXchange Consortium via the PRIDE partner repository and the accession resolves in the repository. No dataset was downloaded and no licence was read.
can_run object · 3 fields
dsl_operations array · 4 items
[0]
group_summary
[1]
welch_t
[2]
bootstrap_mean_difference
[3]
group_comparison_anova
assets array · 4 items
[0]
source:pmid:29286311
[1]
data:geo:PXD008407
[2]
asset:table:pmid:29286311:1
[3]
asset:table:pmid:29286311:2
steps array · 1 item
[0]
run_analysis
must_build object · 5 fields
dsl_operations array · 0 items
converters array · 0 items
readers array · 0 items
capabilities array · 0 items
data_gaps array · 1 item
[0]
data:geo:PXD008407
gaps array · 0 items
review object · 5 fields
state
partial
machine_critique object · 5 fields
kind
extraction_review
reader object · 5 fields
model
MiniMax-M3.1-Flash
provider
minimax
provider_family
minimax
read_at
2026-10-31T18:33:19Z
independence
same_provider
evidence_check object · 2 fields
method
reordered
availability
verbatim
calls
8
usage object · 3 fields
prompt_tokens
129568
completion_tokens
4647
cached_tokens
2088
human_critique
null
stages array · 1 item
[0] object · 4 fields
id
extraction
state
complete
reader
MiniMax-M3.1-Flash
provider
minimax
gaps array · 3 items
[0]
review.independent_reader
[1]
review.machine_critique
[2]
review.human_critique
execution object · 5 fields
state
absent
status
not_run
mode
null
runs array · 0 items
gaps array · 1 item
[0]
execution.not_run
provenance object · 7 fields
entities array · 3 items
[0] object · 3 fields
id
pmid:29286311
type
paper
label
pmid:29286311
[1] object · 3 fields
id
source:pmid:29286311
type
manuscript
label
PMID 29286311 full text
[2] object · 3 fields
id
data:geo:PXD008407
type
dataset
label
GEO PXD008407
activities array · 3 items
[0] object · 4 fields
id
activity-reading-sci-2026-11-01
type
classification
used array · 3 items
[0] object · 3 fields
id
pmid:29286311
type
paper
label
pmid:29286311
[1] object · 3 fields
id
source:pmid:29286311
type
manuscript
label
PMID 29286311 full text
[2] object · 3 fields
id
data:geo:PXD008407
type
dataset
label
GEO PXD008407
agent
agent:corpus-assay-engine
[1] object · 4 fields
id
activity-read-29286311
type
extraction
used array · 1 item
[0]
source:pmid:29286311
agent
agent:minimax-reader
[2] object · 4 fields
id
activity-resolve-PXD008407
type
accession_resolution
used array · 1 item
[0]
data:geo:PXD008407
agent
agent:corpus-assay-engine
agents array · 2 items
[0] object · 3 fields
id
agent:corpus-assay-engine
type
software
label
Corpus assay engine
[1] object · 3 fields
id
agent:minimax-reader
type
software
label
MiniMax literature reader
source_run_id
reading-sci-2026-11-01
dsl_catalogue_fingerprint
343fb30756ba6ec3
capability_table_fingerprint
2cb3e42f047d2ecf
snapshot_id
ba34b49490d9bfaf
lineage object · 4 fields
parent_id
pmid:29286311
parent_hash
sha256:595fb876549167132f97b1aa0c28d12281575c997a41347cac6ef88aed8eeaa7
fork_of
null
generation
7
gaps array · 6 items
[0]
asset:data:geo:PXD008407 licence not read
[1]
asset:data:geo:PXD008407 not downloaded
[2]
execution.not_run
[3]
review.human_critique
[4]
review.independent_reader
[5]
review.machine_critique
assays array · 4 items
[0] object · 11 fields
role
data_generation
definition_id
mass_spectrometry
definition_version
99e1195c7d6f
definition_digest
null
required_operations array · 0 items
support_state
partial
source_hashes object · 1 field
assay_lexicon
99e1195c7d6f
confidence
0.99
evidence array · 4 items
[0]
Comparative Proteomics Analysis of Urine Reveals Down-Regulation of
[1]
detect PCa in the early stages. Comparative proteomics profiling of urine from patients with PCa, b
[2]
a, Buchs, Switzerland). 2.5. Analysis of the Proteomics Data Proteins with differential abundance am
[3]
5 proteins in the 2-D DIGE/MS and label-free LC-MS/MS experiments, respectively. In silico analysi
order_basis
paper_text_order:0
id
assay:1
[1] object · 11 fields
role
data_generation
definition_id
ihc
definition_version
99e1195c7d6f
definition_digest
null
required_operations array · 0 items
support_state
partial
source_hashes object · 1 field
assay_lexicon
99e1195c7d6f
confidence
0.93
evidence array · 1 item
[0]
on is determined based on antibody staining (immunohistochemistry, Western blot) and protein arrays. Supplemen
order_basis
paper_text_order:7593
id
assay:2
[2] object · 11 fields
role
data_generation
definition_id
western_blot
definition_version
99e1195c7d6f
definition_digest
null
required_operations array · 0 items
support_state
partial
source_hashes object · 1 field
assay_lexicon
99e1195c7d6f
confidence
0.93
evidence array · 1 item
[0]
on antibody staining (immunohistochemistry, Western blot) and protein arrays. Supplementary Materials
order_basis
paper_text_order:7616
id
assay:3
[3] object · 11 fields
role
analysis
definition_id
group_comparison
definition_version
f2132e96ae6c7a4e
definition_digest
null
required_operations array · 4 items
[0]
group_summary
[1]
welch_t
[2]
bootstrap_mean_difference
[3]
group_comparison_anova
support_state
supported
source_hashes object · 1 field
dsl_catalogue
f2132e96ae6c7a4e
confidence
1
evidence array · 1 item
[0]
“Proteins with differential abundance among the four groups were considered with fold change ≥ 1.5 and Anova ≤ 0.05. p-values between groups were calculated using t-test (independent, 2-tailed, unequal variance) and subsequently false discovery rate (FDR) correction for multiple testing [21] was applied.” “The mass spectrometry proteomics data have been deposited in the ProteomeXchange Consortium (http://proteomecentral.proteomexchange.org) via the PRIDE partner repository [20] with data set identifier PXD008407 and 10.6019/PXD008407.”
order_basis
consumes_earlier_output
id
assay:4
Complete file 
{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:29286311", "kind": "science-record", "revision": 8, "content_hash": "sha256:ea5d6158fec3495be96785d653dcb44002e230222db32c04c79f7c3fb19e2592", "created_at": "2026-11-01T15:40:30Z", "updated_at": "2026-11-01T22:43:13Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Comparative Proteomics Analysis of Urine Reveals Down-Regulation of Acute Phase Response Signaling and LXR/RXR Activation Pathways in Prostate Cancer.", "doi": "10.3390/proteomes6010001", "pmid": "29286311", "authors": ["Katarina Davalieva", "Sanja Kiprijanovska", "Ivana Maleva Kostovska", "Sotir Stavridis", "Oliver Stankov", "Selim Komina", "Gordana Petrusevska", "Momir Polenakovic"], "journal": "Proteomes", "year": 2017, "abstract": "Detecting prostate cancer (PCa) using non-invasive diagnostic markers still remains a challenge. The aim of this study was the identification of urine proteins that are sufficiently sensitive and specific to detect PCa in the early stages. Comparative proteomics profiling of urine from patients with PCa, benign prostate hyperplasia, bladder cancer, and renal cancer, coupled with bioinformatics analysis, were performed. Statistically significant difference in abundance showed 20 and 85 proteins in the 2-D DIGE/MS and label-free LC-MS/MS experiments, respectively. In silico analysis indicated activation, binding, and cell movement of subset of immune cells as the top affected cellular functions in PCa, together with the down-regulation of Acute Phase Response Signaling and Liver X Receptor/ Retinoid X Receptor (LXR/RXR) activation pathways. The most promising biomarkers were 35, altered in PCa when compared to more than one group. Half of these have confirmed localization in normal or PCa tissues. Twenty proteins (CD14, AHSG, ENO1, ANXA1, CLU, COL6A1, C3, FGA, FGG, HPX, PTGDS, S100A9, LMAN2, ITIH4, ACTA2, GRN, HBB, PEBP1, CTSB, SPP1) are oncogenes, tumor suppressors, and multifunctional proteins with highly confirmed involvement in PCa, while 9 (AZU1, IGHG1, RNASE2, PZP, REG1A, AMY1A, AMY2A, ACTG2, COL18A1) have been associated with different cancers, but not with PCa so far, and may represent novel findings. LC-MS/MS data are available via ProteomeXchange with identifier PXD008407.", "claims": [{"id": "claim-data-access", "statement": "The mass spectrometry proteomics data have been deposited in the ProteomeXchange Consortium (http://proteomecentral.proteomexchange.org) via the PRIDE partner repository [20] with data set identifier PXD008407 and 10.6019/PXD008407.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:29286311", "locator": "sections[6] \"2.4. 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Analysis of the Proteomics Data\" paragraph 2", "quote": "Proteins with differential abundance among the four groups were considered with fold change ≥ 1.5 and Anova ≤ 0.05. p-values between groups were calculated using t-test (independent, 2-tailed, unequal variance) and subsequently false discovery rate (FDR) correction for multiple testing [21] was applied."}, {"asset": "source:pmid:29286311", "locator": "sections[6] \"2.4. 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Spot No.", "PCa/BPH", "PCa/BC", "PCa/RC", "Protein Name", "Gene Name", "Mw (kDa) b", "pl", "Mascot Protein Score", "p Value", "RMS Error (ppm)", "Matched Peptides/Total", "% of Sequence Coverage"], ["t-Test", "Fold Change", "t-Test", "Fold Change", "t-Test", "Fold Change"], ["1", "", "", "4.0 × 10−2", "−3.8", "", "", "Serotransferrin", "TF", "79.3", "6.81", "205", "6.4 × 10−17", "35", "20/23", "35"], ["2", "", "", "8.5 × 10−3", "−3.6", "", "", "Serotransferrin", "TF", "79.3", "6.81", "203", "1.0 × 10−16", "33", "21/27", "31"], ["3", "", "", "2.7 × 10−2", "−3.6", "", "", "Serotransferrin", "TF", "79.3", "6.81", "190", "2.0 × 10−15", "46", "23/37", "37"], ["4", "", "", "3.7 × 10−2", "−3.0", "", "", "Serotransferrin", "TF", "79.3", "6.81", "287", "4.0 × 10−25", "39", "29/36", "41"], ["5", "", "", "4.5 × 10−2", "−3.6", "", "", "Serotransferrin", "TF", "79.3", "6.81", "148", "3.2 × 10−11", "44", "17/34", "23"], ["6", "", "", "3.1 × 10−3", "−6.5", "", "", "Serotransferrin", "TF", "79.3", "6.81", "70", "1.8 × 10−3", "99", "8/11", "13"], ["7", "2.3 × 10−2", "3.5", "", "", "", "", "Kininogen-1", "KNG1", "73.0", "6.34", "94", "7.9 × 10−6", "88", "9/13", "18"], ["8", "4.3 × 10−2", "2.6", "6.2 × 10−5", "3.0", "", "", "Kininogen-1", "KNG1", "73.0", "6.34", "156", "5.1 × 10−12", "43", "17/24", "24"], ["9", "", "", "2.2 × 10−2", "2.4", "", "", "Kininogen-1", "KNG1", "73.0", "6.34", "139", "2.5 × 10−10", "56", "14/20", "24"], ["10", "", "", "3.4 × 10−2", "2.6", "", "", "Kininogen-1", "KNG1", "73.0", "6.34", "131", "1.6 × 10−9", "101", "11/12", "18"], ["11", "4.5 × 10−2", "2.5", "6.9 × 10−3", "4.4", "", "", "Kininogen-1", "KNG1", "73.0", "6.34", "111", "1.6 × 10−7", "35", "10/14", "19"], ["12", "", "", "5.5 × 10−3", "3.1", "", "", "Kininogen-1", "KNG1", "73.0", "6.34", "90", "5.6 × 10−6", "58", "9/14", "18"], ["13", "1.3 × 10−2", "−2.8", "3.7 × 10−2", "−2.6", "", "", "mix (Ig alpha-1 chain C region/Ig alpha-2 chain C region)", "IGHA1/ IGHA2", "38.5/ 37.3", "6.08/ 5.71", "65/81", "2.4 × 10−3/ 1.1 × 10−4", "48/45", "6/6/8", "14/20"], ["14", "3.9 × 10−2", "−2.4", "1.9 × 10−2", "−2.7", "", "", "mix (Ig alpha-1 chain C region/Ig alpha-2 chain C region)", "IGHA1/ IGHA2", "38.5/ 37.3", "6.08/ 5.71", "59/82", "2.4 × 10−2/ 1.3 × 10−4", "48/45", "5/6/8", "13/20"], ["15", "2.2 × 10−2", "−2.9", "1.3 × 10−2", "−2.5", "", "", "Ig alpha-1 chain C region", "IGHA1", "38.5", "6.08", "84", "8.8 × 10−5", "13", "7/13", "31"], ["16", "", "", "8.3 × 10−3", "−2.1", "", "", "mix (Ig alpha-1 chain C region/Ig alpha-2 chain C region)", "IGHA1/ IGHA2", "38.5/ 37.3", "6.08/ 5.71", "111/84", "1.6 × 10−7/ 7.7 × 10−5", "59/63", "10/8/19", "38/27"], ["17", "2.1 × 10−2", "−2.7", "3.5 × 10−2", "−2.5", "", "", "mix (Ig alpha-1 chain C region/Ig alpha-2 chain C region)", "IGHA1/ IGHA2", "38.5/ 37.3", "6.08/ 5.71", "102/84", "1.3 × 10−6/ 7.7 × 10−5", "89/93", "9/8/19", "33/27"], ["18", "3.1 × 10−2", "−2.2", "1.2 × 10−2", "−2.1", "5.1 × 10−3", "−1.6", "mix (Ig alpha-1 chain C region/Ig alpha-2 chain C region)", "IGHA1", "38.5/ 37.3", "6.08/ 5.71", "92/56", "1.2 × 10−5/ 5.0 × 10−2", "23/28", "7/6/20", "28/26"], ["19", "1.4 × 10−2", "−2.4", "", "", "5.6 × 10−2", "−1.6", "mix (Ig alpha-1 chain C region/Ig alpha-2 chain C region)", "IGHA1/ IGHA2", "38.5/ 37.3", "6.08/ 5.71", "97/69", "3.8 × 10−6/ 2.4 × 10−3", "37/37", "10/8/38", "38/27"], ["20", "2.9 × 10−2", "−2.0", "6.4 × 10−3", "−2.0", "6.7 × 10−2", "−1.7", "mix (Ig alpha-1 chain C region/Ig alpha-2 chain C region)", "IGHA1/ IGHA2", "38.5/ 37.3", "6.08/ 5.71", "122/82", "1.3 × 10−8/ 1.4 × 10−4", "11/12", "9/8/12", "26/21"], ["21 a", "", "", "2.0 × 10−2", "−3.2", "", "", "Arginyl-tRNA-protein transferase 1", "ATE1", "60.0", "8.17", "98", "3.6 × 10−6", "67", "9/16", "28"], ["22", "", "", "1.8 × 10−2", "−2.0", "", "", "Fibrinogen gamma chain", "FGG", "52.1", "5.37", "121", "1.6 × 10−8", "43", "12/23", "38"], ["23", "", "", "2.1 × 10−2", "−5.3", "", "", "Fibrinogen gamma chain", "FGG", "52.1", "5.37", "174", "8.0 × 10−14", "39", "14/18", "42"], ["24", "", "", "3.4 × 10−2", "−5.7", "", "", "Fibrinogen gamma chain", "FGG", "52.1", "5.37", "117", "4.0 × 10−8", "83", "12/19", "31"], ["25", "", "", "3.5 × 10−2", "−7.1", "", "", "Fibrinogen gamma chain", "FGG", "52.1", "5.37", "107", "4.0 × 10−7", "35", "12/26", "32"], ["26", "", "", "4.1 × 10−2", "−5.8", "", "", "Fibrinogen gamma chain", "FGG", "52.1", "5.37", "139", "2.5 × 10−10", "39", "13/25", "37"], ["27", "", "", "2.0 × 10−3", "2.1", "", "", "Zinc-alpha-2-glycoprotein", "AZGP1", "34.5", "5.71", "102", "1.3 × 10−6", "45", "13/27", "30"], ["28", "", "", "2.0 × 10−2", "−4.7", "", "", "Haptoglobin", "HP", "45.9", "6.13", "87", "3.8 × 10−5", "104", "8/17", "18"], ["29", "", "", "1.9 × 10−2", "−6.7", "", "", "Haptoglobin", "HP", "45.9", "6.13", "108", "3.2 × 10−7", "11", "13/25", "27"], ["30", "", "", "2.2 × 10−2", "−6.3", "", "", "Haptoglobin", "HP", "45.9", "6.13", "107", "4.0 × 10−7", "53", "16/37", "28"], ["31", "", "", "2.6 × 10−2", "−7.5", "", "", "Haptoglobin", "HP", "45.9", "6.13", "98", "3.1 × 10−6", "47", "12/27", "27"], ["32", "", "", "2.6 × 10−2", "−8.1", "", "", "Haptoglobin", "HP", "45.9", "6.13", "86", "5.0 × 10−5", "55", "13/30", "28"], ["33", "", "", "2.1 × 10−2", "−7.7", "", "", "Haptoglobin", "HP", "45.9", "6.13", "129", "2.5 × 10−9", "44", "12/16", "30"], ["34", "", "", "1.8 × 10−3", "3.4", "", "", "Fibrinogen alpha chain (fragment)", "FGA", "95.7 (45)", "5.7", "125", "6.4 × 10−9", "72", "12/16", "15"], ["35", "", "", "2.6 × 10−3", "5.3", "", "", "Inter-alpha-trypsin inhibitor heavy chain H4 (fragment)", "ITIH4", "103.5 (45)", "6.57", "69", "2.5 × 10−3", "47", "9/26", "12"], ["36", "2.2 × 10−2", "2.5", "", "", "", "", "Hemoglobin subunit beta", "HBB", "16.1", "6.75", "141", "1.6 × 10−10", "88", "11/22", "69"], ["37", "8.4 × 10−3", "2.5", "5.0 × 10−4", "4.3", "", "", "Inter-alpha-trypsin inhibitor heavy chain H4 (fragment)", "ITIH4", "103.5 (45)", "6.57", "90", "2.1 × 10−5", "59", "13/23", "15"], ["38", "", "", "1.6 × 10−2", "4.8", "", "", "Protein AMBP", "AMBP", "39.9", "5.95", "94", "8.0 × 10−6", "66", "11/30", "24"], ["39", "", "", "1.5 × 10−2", "5.0", "", "", "Protein AMBP", "AMBP", "39.9", "5.95", "135", "6.4 × 10−10", "37", "13/18", "32"], ["40", "", "", "1.4 × 10−2", "5.2", "", "", "Protein AMBP", "AMBP", "39.9", "5.95", "108", "3.2 × 10−7", "91", "10/19", "18"], ["41", "5.3 × 10−3", "2.0", "", "", "", "", "Protein AMBP", "AMBP", "39.9", "5.95", "74", "7.3 × 10−4", "12", "9/17", "26"], ["42", "", "", "3.3 × 10−3", "4.0", "", "", "Prostaglandin-H2 D-isomerase", "PTGDS", "21.2", "7.66", "64", "7.3 × 10−3", "63", "7/15", "33"], ["43", "", "", "6.2 × 10−3", "4.0", "", "", "Prostaglandin-H2 D-isomerase", "PTGDS", "21.2", "7.66", "70", "2.3 × 10−3", "72", "8/25", "27"], ["44", "", "", "8.9 × 10−3", "3.3", "", "", "Prostaglandin-H2 D-isomerase", "PTGDS", "21.2", "7.66", "60", "1.9 × 10−2", "93", "7/26", "26"], ["45 a", "", "", "4.6 × 10−2", "1.9", "", "", "Ig kappa chain C region", "IGKC", "11.8", 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identified proteins with differential abundance in PCa when compared to the three groups (BPH, BC, and RC) by LC-MS/MS.", "structure": {"pmcid": "PMC5874760", "section_index": 10, "section_title": "3.2. LC-MS/MS Analysis", "row_count": 122, "column_count": 13}, "table": {"label": "Table 2", "caption": "List of identified proteins with differential abundance in PCa when compared to the three groups (BPH, BC, and RC) by LC-MS/MS.", "rows": [["Uniprot Accession No.", "Protein Name", "Gene Name", "Peptide Count", "Unique Peptides", "Confidence Score", "ANOVA", "Max Fold Change", "Highest Mean Condition", "Lowest Mean Condition", "Group Comparison", "p-Value a", "Ratio"], ["P08571", "Monocyte differentiation antigen", "CD14", "8", "7", "75.64", "8.87 × 10−10", "2.70", "PCa", "Bc", "PCa vs. BC", "2.71 × 10−4", "2.7"], ["", "CD14", "", "", "", "", "", "", "", "", "PCa vs. BPH", "4.67 × 10−3", "1.8"], ["", "", "", "", "", "", "", "", "", "", "PCa vs. RC", "2.61 × 10−2", "1.6"], ["P62736", "Actin_ aortic smooth muscle", "ACTA2", "3", "3", "24.21", "1.75 × 10−9", "5.89", "Bc", "PCa", "PCa vs. BC", "3.40 × 10−4", "0.2"], ["", "", "", "", "", "", "", "", "", "", "PCa vs. BPH", "1.75 × 10−2", "0.4"], ["P02765", "Alpha-2-HS-glycoprotein", "AHSG", "9", "9", "94.63", "5.73 × 10−4", "2.70", "PCa", "Bc", "PCa vs. BC", "9.03 × 10−3", "2.7"], ["", "", "", "", "", "", "", "", "", "", "PCa vs. BPH", "4.14 × 10−2", "2.1"], ["P04745", "Alpha-amylase 1", "AMY1A", "9", "5", "101.49", "1.42 × 10−7", "3.46", "PCa", "Bc", "PCa vs. BC", "3.40 × 10−4", "3.5"], ["", "", "", "", "", "", "", "", "", "", "PCa vs. BPH", "4.14 × 10−2", "1.7"], ["P19961", "Alpha-amylase 2B", "AMY2B", "3", "1", "21.24", "3.52 × 10−6", "12.86", "Rc", "Bc", "PCa vs. BC", "1.25 × 10−2", "11.9"], ["", "", "", "", "", "", "", "", "", "", "PCa vs. BPH", "4.32 × 10−2", "4.1"], ["P06733", "Alpha-enolase", "ENO1", "2", "2", "14.73", "3.64 × 10−5", "1.78", "BPH", "PCa", "PCa vs. BC", "1.54 × 10−2", "0.7"], ["", "", "", "", "", "", "", "", "", "", "PCa vs. BPH", "7.97 × 10−3", "0.6"], ["P04083", "Annexin A1", "ANXA1", "5", "5", "41.02", "5.95 × 10−12", "5.45", "Rc", "Bc", "PCa vs. BC", "1.08 × 10−3", "3.8"], ["", "", "", "", "", "", "", "", "", "", "PCa vs. BPH", "1.20 × 10−2", "2.2"], ["P20160", "Azurocidin", "AZU1", "2", "2", "13.76", "7.34 × 10−5", "2.80", "BPH", "PCa", "PCa vs. BC", "3.35 × 10−2", "0.6"], ["", "", "", "", "", "", "", "", "", "", "PCa vs. BPH", "8.89 × 10−3", "0.4"], ["P10909", "Clusterin", "CLU", "10", "10", "99.24", "6.33 × 10−6", "2.26", "BPH", "PCa", "PCa vs. BC", "5.24 × 10−3", "0.6"], ["", "", "", "", "", "", "", "", "", "", "PCa vs. BPH", "2.55 × 10−2", "0.4"], ["P12109", "Collagen alpha-1(VI)", "COL6A1", "6", "4", "46.91", "2.05 × 10−7", "3.44", "BPH", "PCa", "PCa vs. BC", "7.15 × 10−4", "0.4"], ["", "chain", "", "", "", "", "", "", "", "", "PCa vs. BPH", "8.66 × 10−3", "0.3"], ["P39060", "Collagen alpha-1(XVIII)", "COL18A1", "2", "2", "14.39", "2.92 × 10−9", "14.26", "Rc", "Bc", "PCa vs. BC", "6.21 × 10−3", "7.1"], ["", "chain", "", "", "", "", "", "", "", "", "PCa vs. BPH", "2.30 × 10−2", "4.2"], ["P01024", "Complement C3", "C3", "57", "57", "545.51", "2.30 × 10−7", "3.43", "Rc", "Bc", "PCa vs. BC", "6.30 × 10−3", "2.9"], ["", "", "", "", "", "", "", "", "", "", "PCa vs. BPH", "2.77 × 10−2", "2.2"], ["P24855", "Deoxyribonuclease-1", "DNASE1", "3", "3", "23.62", "1.84 × 10−10", "4.85", "Rc", "Bc", "PCa vs. BC", "6.30 × 10−3", "3.6"], ["", "", "", "", "", "", "", "", "", "", "PCa vs. BPH", "3.55 × 10−2", "2.3"], ["O94919", "Endonuclease domain-containing 1", "ENDOD1", "3", "3", "24.51", "1.64 × 10−7", "2.97", "PCa", "Bc", "PCa vs. BC", "1.01 × 10−3", "3.0"], ["", "protein", "", "", "", "", "", "", "", "", "PCa vs. BPH", "4.67 × 10−3", "2.8"], ["P02671", "Fibrinogen alpha chain", "FGA", "24", "24", "293.54", "7.67 × 10−6", "2.72", "BPH", "Rc", "PCa vs. BC", "2.94 × 10−3", "0.6"], ["", "", "", "", "", "", "", "", "", "", "PCa vs. BPH", "3.15 × 10−2", "0.4"], ["P02679", "Fibrinogen gamma chain", "FGG", "20", "20", "251.65", "1.07 × 10−4", "2.32", "BPH", "Rc", "PCa vs. BC", "2.48 × 10−2", "0.5"], ["", "", "", "", "", "", "", "", "", "", "PCa vs. BPH", "4.25 × 10−2", "0.5"], ["P28799", "Granulins", "GRN", "2", "2", "18.13", "2.87 × 10−8", "3.92", "BPH", "PCa", "PCa vs. BC", "2.32 × 10−3", "0.5"], ["", "", "", "", "", "", "", "", "", "", "PCa vs. BPH", "8.89 × 10−3", "0.3"], ["P68871", "Hemoglobin subunit beta", "HBB", "10", "10", "138.23", "1.54 × 10−5", "4.62", "Bc", "PCa", "PCa vs. BC", "2.96 × 10−2", "0.2"], ["", "", "", "", "", "", "", "", "", "", "PCa vs. BPH", "1.75 × 10−2", "0.3"], ["P02790", "Hemopexin", "HPX", "16", "16", "164.63", "4.66 × 10−6", "2.44", "BPH", "PCa", "PCa vs. BC", "6.60 × 10−3", "0.6"], ["", "", "", "", "", "", "", "", "", "", "PCa vs. BPH", "1.30 × 10−2", "0.4"], ["P01857", "Ig gamma-1 chain C region", "IGHG1", "6", "6", "76.08", "6.40 × 10−4", "3.29", "BPH", "PCa", "PCa vs. BC", "6.71 × 10−3", "0.5"], ["", "", "", "", "", "", "", "", "", "", "PCa vs. BPH", "4.14 × 10−2", "0.3"], ["P05451", "Lithostathine-1-alpha", "REG1A", "5", "4", "35.95", "3.83 × 10−4", "3.96", "PCa", "BPH", "PCa vs. BC", "6.30 × 10−3", "3.8"], ["", "", "", "", "", "", "", "", "", "", "PCa vs. BPH", "1.50 × 10−2", "4.0"], ["P11117", "Lysosomal acid", "ACP2", "5", "4", "45.84", "5.59 × 10−6", "2.11", "BPH", "PCa", "PCa vs. BC", "7.15 × 10−4", "0.6"], ["", "phosphatase", "", "", "", "", "", "", "", "", "PCa vs. BPH", "6.07 × 10−3", "0.5"], ["P08246", "Neutrophil elastase", "ELANE", "3", "3", "39.04", "6.45 × 10−3", "3.25", "BPH", "PCa", "PCa vs. BC", "2.74 × 10−2", "0.5"], ["", "", "", "", "", "", "", "", "", "", "PCa vs. BPH", "4.99 × 10−2", "0.3"], ["P10153", "Non-secretory", "RNASE2", "4", "3", "51.80", "3.38 × 10−8", "5.21", "PCa", "Bc", "PCa vs. BC", "8.08 × 10−3", "5.2"], ["", "ribonuclease", "", "", "", "", "", "", "", "", "PCa vs. BPH", "2.55 × 10−2", "3.9"], ["P10451", "Osteopontin", "SPP1", "12", "11", "164.02", "1.10 × 10−11", "15.72", "Rc", "Bc", "PCa vs. BC", "2.32 × 10−3", "8.4"], ["", "", "", "", "", "", "", "", "", "", "PCa vs. BPH", "2.55 × 10−2", "2.6"], ["P04746", "Pancreatic alpha-amylase", "AMY2A", "3", "1", "27.44", "3.66 × 10−6", "5.06", "PCa", "Bc", "PCa vs. BC", "4.27 × 10−3", "5.1"], ["", "", "", "", "", "", "", "", "", "", "PCa vs. BPH", "4.32 × 10−2", "2.3"], ["P30086", "Phosphatidylethanolamine-", "PEBP1", "3", "3", "27.16", "2.93 × 10−5", "3.38", "BPH", "PCa", "PCa vs. BC", "7.15 × 10−4", "0.5"], ["", "binding protein 1", "", "", "", "", "", "", "", "", "PCa vs. BPH", "1.75 × 10−2", "0.3"], ["P20742", "Pregnancy zone protein", "PZP", "7", "7", "82.62", "4.09 × 10−8", "2.27", "Bc", "Rc", "PCa vs. BC", "2.32 × 10−3", "0.5"], ["", "", "", "", "", "", "", "", "", "", "PCa vs. BPH", "4.76 × 10−2", "0.7"], ["P41222", "Prostaglandin-H2", "PTGDS", "9", "7", "140.59", "4.51 × 10−11", "5.56", "PCa", "Bc", "PCa vs. BC", "3.40 × 10−4", "5.6"], ["", "D-isomerase", "", "", "", "", "", "", "", "", "PCa vs. BPH", "1.75 × 10−2", "1.8"], ["P06702", "Protein S100-A9", "S100A9", "3", "3", "26.61", "1.49 × 10−6", "6.46", "BPH", "PCa", "PCa vs. BC", "1.22 × 10−3", "0.5"], ["", "", "", "", "", "", "", "", "", "", "PCa vs. BPH", "5.03 × 10−2", "0.2"], ["Q8WZ75", "Roundabout homolog 4", "ROBO4", "7", "7", "55.71", "3.32 × 10−3", "2.27", "BPH", "PCa", "PCa vs. BC", "1.47 × 10−2", "0.6"], ["", "", "", "", "", "", "", "", "", "", "PCa vs. BPH", "2.96 × 10−2", "0.4"], ["Q12907", "Vesicular integral-membrane", "LMAN2", "9", "8", "94.66", "1.64 × 10−6", "2.48", "Rc", "Bc", "PCa vs. BC", "2.32 × 10−3", "2.4"], ["", "protein VIP36", "", "", "", "", "", "", "", "", "PCa vs. BPH", "2.55 × 10−2", "1.7"], ["Q14624", "Inter-alpha-trypsin inhibitor heavy", "ITIH4", "9", "9", "94.01", "3.21 × 10−13", "5.55", "Rc", "Bc", "PCa vs. BC", "5.07 × 10−5", "3.5"], ["", "chain H4", "", "", "", "", "", "", "", "", "PCa vs. BPH", "4.67 × 10−3", "1.6"], ["P63267", "Actin_ gamma-enteric", "ACTG2", "3", "3", "19.63", "4.29 × 10−2", "1.79", "PCa", "Rc", "PCa vs. BC", "1.08 × 10−3", "1.7"], ["", "smooth muscle", "", "", "", "", "", "", "", "", "PCa vs. RC", "2.56 × 10−3", "1.8"], ["P07858", "Cathepsin B", "CTSB", "3", "2", "19.04", "5.87 × 10−3", "3.16", "Bc", "PCa", "PCa vs. BC", "3.10 × 10−2", "0.3"], ["", "", "", "", "", "", "", "", "", "", "PCa vs. RC", "3.14 × 10−2", "0.4"], ["P01023", "Alpha-2-macroglobulin", "A2M", "38", "38", "491.82", "1.42 × 10−4", "2.29", "BPH", "PCa", "PCa vs. BPH", "6.07 × 10−3", "0.4"], ["P15144", "Aminopeptidase N", "ANPEP", "2", "2", "14.55", "3.31 × 10−4", "1.70", "BPH", "PCa", "PCa vs. BPH", "4.20 × 10−2", "0.6"], ["P07355", "Annexin A2", "ANXA2", "2", "2", "16.06", "9.99 × 10−5", "4.27", "Rc", "BPH", "PCa vs. BPH", "4.76 × 10−2", "4.1"], ["P06727", "Apolipoprotein A-IV", "APOA4", "3", "3", "31.32", "3.77 × 10−3", "2.28", "BPH", "PCa", "PCa vs. BPH", "5.03 × 10−2", "0.4"], ["Q8NFZ8", "Cell adhesion molecule 4", "CADM4", "8", "7", "60.30", "1.09 × 10−3", "2.26", "BPH", "PCa", "PCa vs. BPH", "3.15 × 10−2", "0.4"], ["P17900", "Ganglioside GM2 activator", "GM2A", "4", "3", "40.41", "4.80 × 10−2", "1.81", "BPH", "PCa", "PCa vs. BPH", "4.97 × 10−2", "0.6"], ["P69905", "Hemoglobin subunit alpha", "HBA1", "5", "5", "56.91", "9.41 × 10−3", "4.36", "Bc", "PCa", "PCa vs. BPH", "4.67 × 10−3", "0.6"], ["P02042", "Hemoglobin subunit delta", "HBD", "3", "3", "29.39", "1.38 × 10−5", "13.11", "Bc", "Rc", "PCa vs. BPH", "4.20 × 10−2", "0.5"], ["P01859", "Ig gamma-2 chain C region", "IGHG2", "7", "7", "67.03", "6.75 × 10−5", "2.18", "BPH", "Bc", "PCa vs. BPH", "6.07 × 10−3", "0.5"], ["P01861", "Ig gamma-4 chain C region", "IGHG4", "6", "6", "72.40", "9.74 × 10−4", "2.05", "BPH", "Rc", "PCa vs. BPH", "4.32 × 10−2", "0.6"], ["P01772", "Ig heavy chain V-III region KOL", "IGHV3-33", "2", "1", "12.43", "4.33 × 10−3", "1.57", "BPH", "PCa", "PCa vs. BPH", "4.89 × 10−2", "0.6"], ["P0CF74", "Ig lambda-6 chain C region", "IGLC6", "3", "3", "28.38", "7.00 × 10−4", "1.97", "BPH", "Bc", "PCa vs. BPH", "2.30 × 10−2", "0.5"], ["P02788", "Lactotransferrin", "LTF", "43", "41", "601.64", "8.73 × 10−5", "2.61", "BPH", "Rc", "PCa vs. BPH", "4.20 × 10−2", "0.5"], ["P10253", "Lysosomal alpha-glucosidase", "GAA", "8", "8", "80.33", "9.63 × 10−5", "1.77", "BPH", "PCa", "PCa vs. BPH", "4.14 × 10−2", "0.6"], ["P05164", "Myeloperoxidase", "MPO", "16", "15", "159.24", "4.69 × 10−5", "1.76", "BPH", "PCa", "PCa vs. BPH", "4.67 × 10−3", "0.6"], ["P32119", "Peroxiredoxin-2", "PRDX2", "3", "1", "23.32", "2.58 × 10−2", "13.40", "Bc", "PCa", "PCa vs. BPH", "5.03 × 10−2", "0.2"], ["P05155", "Plasma protease C1 inhibitor", "SERPING1", "4", "4", "35.56", "4.75 × 10−3", "1.71", "BPH", "PCa", "PCa vs. BPH", "4.99 × 10−2", "0.6"], ["Q6S8J3", "POTE ankyrin domain family member E", "POTEE", "11", "8", "93.51", "3.30 × 10−4", "2.04", "BPH", "Rc", "PCa vs. BPH", "4.76 × 10−2", "0.5"], ["P43652", "Afamin", "AFM", "6", "5", "48.31", "8.56 × 10−4", "1.65", "PCa", "Bc", "PCa vs. BC", "5.76 × 10−3", "1.6"], ["P02647", "Apolipoprotein A-I", "APOA1", "12", "12", "145.00", "4.72 × 10−4", "1.86", "BPH", "Rc", "PCa vs. BC", "3.02 × 10−2", "0.7"], ["P05090", "Apolipoprotein D", "APOD", "6", "6", "69.92", "4.00 × 10−7", "2.12", "PCa", "Bc", "PCa vs. BC", "1.19 × 10−3", "2.1"], ["P02749", "Beta-2-glycoprotein 1", "APOH", "11", "10", "112.68", "1.13 × 10−4", "3.66", "Bc", "Rc", "PCa vs. BC", "7.15 × 10−4", "0.3"], ["P19835", "Bile salt-activated lipase", "CEL", "3", "3", "20.03", "1.76 × 10−6", "2.04", "Rc", "Bc", "PCa vs. BC", "7.58 × 10−3", "1.6"], ["P07339", "Cathepsin D", "CTSD", "6", "6", "54.69", "1.61 × 10−3", "1.85", "PCa", "Bc", "PCa vs. BC", "1.38 × 10−2", "1.9"], ["P13987", "CD59 glycoprotein", "CD59", "5", "5", "85.01", "1.42 × 10−6", "4.38", "Rc", "Bc", "PCa vs. BC", "2.94 × 10−3", "4.3"], ["P0C0L4", "Complement C4-A", "C4A", "3", "3", "21.19", "1.16 × 10−2", "1.85", "Bc", "PCa", "PCa vs. BC", "6.21 × 10−3", "0.5"], ["P08174", "Complement decay-accelerating factor", "CD55", "5", "5", "40.67", "2.66 × 10−5", "2.37", "Rc", "Bc", "PCa vs. BC", "1.02 × 10−2", "2.2"], ["Q02487", "Desmocollin-2", "DSC2", "4", "3", "24.44", "4.00 × 10−6", "2.62", "Bc", "BPH", "PCa vs. BC", "1.78 × 10−3", "0.6"], ["Q9UHL4", "Dipeptidyl peptidase 2", "DPP7", "2", "2", "12.10", "4.08 × 10−2", "4.13", "BPH", "PCa", "PCa vs. BC", "2.84 × 10−2", "0.6"], ["Q9HCU0", "Endosialin", "CD248", "6", "6", "43.09", "2.31 × 10−6", "2.20", "PCa", "Bc", "PCa vs. BC", "1.14 × 10−2", "2.2"], ["P01834", "Ig kappa chain C region", "IGKC", "9", "9", "154.85", "3.59 × 10−3", "2.04", "PCa", "Bc", "PCa vs. BC", "1.11 × 10−3", "2.0"], ["P01617", "Ig kappa chain V-II region TEW", "IGKV2D-28", "5", "3", "60.57", "1.37 × 10−2", "2.22", "Rc", "Bc", "PCa vs. BC", "7.15 × 10−4", "1.6"], ["P01625", "Ig kappa chain V-IV region Len", "IGKV4-1", "2", "1", "17.70", "1.49 × 10−3", "1.62", "Rc", "Bc", "PCa vs. BC", "7.58 × 10−3", "1.6"], ["P80748", "Ig lambda chain V-III region LOI", "IGLV3-21", "3", "3", "29.50", "1.01 × 10−3", "2.13", "PCa", "Bc", "PCa vs. BC", "1.00 × 10−4", "2.1"], ["P0CG04", "Ig lambda-1 chain C regions", "IGLC1", "6", "6", "112.58", "6.98 × 10−3", "2.14", "BPH", "Bc", "PCa vs. BC", "2.40 × 10−3", "1.8"], ["P0CG05", "Ig lambda-2 chain C regions", "IGLC2", "3", "3", "57.93", "1.94 × 10−2", "1.73", "BPH", "Bc", "PCa vs. BC", "3.90 × 10−3", "1.7"], ["P01042", "Kininogen-1", "KNG1", "27", "27", "362.50", "8.88 × 10−7", "2.71", "Rc", "Bc", "PCa vs. BC", "8.22 × 10−3", "1.7"], ["P14543", "Nidogen-1", "NID1", "9", "8", "84.01", "5.13 × 10−5", "3.95", "BPH", "Bc", "PCa vs. BC", "2.23 × 10−3", "2.0"], ["O75594", "Peptidoglycan recognition protein 1", "PGLYRP1", "5", "5", "50.82", "6.11 × 10−5", "2.30", "BPH", "Bc", "PCa vs. BC", "3.28 × 10−3", "1.9"], ["P01833", "Polymeric immunoglobulin receptor", "PIGR", "25", "24", "263.55", "5.20 × 10−5", "2.50", "Rc", "Bc", "PCa vs. BC", "6.21 × 10−3", "1.6"], ["P02760", "Protein AMBP", "AMBP", "25", "24", "366.65", "4.27 × 10−3", "2.49", "Rc", "Bc", "PCa vs. BC", "1.02 × 10−2", "1.9"], ["P00734", "Prothrombin", "F2", "16", "14", "176.60", "3.60 × 10−5", "5.38", "Rc", "Bc", "PCa vs. BC", "7.15 × 10−4", "2.7"], ["P07998", "Ribonuclease pancreatic", "RNASE1", "4", "4", "39.91", "7.99 × 10−15", "4.42", "Rc", "Bc", "PCa vs. BC", "7.63 × 10−4", "3.5"], ["Q9UBC9", "Small proline-rich protein 3", "SPRR3", "2", "2", "22.69", "7.14 × 10−3", "2.10", "PCa", "Bc", "PCa vs. BC", "1.25 × 10−2", "2.1"], ["Q9UGT4", "Sushi domain-containing protein 2", "SUSD2", "2", "2", "13.45", "5.40 × 10−5", "32.32", "PCa", "Bc", "PCa vs. BC", "4.99 × 10−2", "32.3"], ["P07911", "Uromodulin", "UMOD", "27", "27", "399.14", "6.23 × 10−6", "2.98", "Rc", "Bc", "PCa vs. BC", "4.00 × 10−2", "1.7"], ["P22891", "Vitamin K-dependent protein Z", "PROZ", "4", "3", "42.25", "1.29 × 10−2", "2.21", "PCa", "Bc", "PCa vs. BC", "2.92 × 10−2", "2.2"], ["P25311", "Zinc-alpha-2-glycoprotein", "AZGP1", "17", "15", "230.16", "1.61 × 10−2", "2.47", "PCa", "Bc", "PCa vs. BC", "1.25 × 10−2", "2.5"], ["P06870", "Kallikrein-1", "KLK1", "6", "6", "64.59", "4.90 × 10−4", "2.36", "BPH", "Bc", "PCa vs. RC", "2.61 × 10−2", "0.6"], ["Q96PD5", "N-acetylmuramoyl-L-alanine amidase", "PGLYRP2", "5", "5", "56.28", "7.41 × 10−3", "2.14", "PCa", "Rc", "PCa vs. RC", "2.56 × 10−3", "2.1"]], "row_count": 122, "column_count": 13, "numeric_cells": 788, "header_rows": 1, "locator": "section[10]/table-wrap[1]#proteomes-06-00001-t002"}}], "gaps": ["asset:data:geo:PXD008407 not downloaded", "asset:data:geo:PXD008407 licence not read"]}, "analysis": {"state": "complete", "methods": [{"id": "method-1", "family": "group_comparison", "specific": "anova", "label": "Group comparison", "dsl_operations": ["group_summary", "welch_t", "bootstrap_mean_difference", "group_comparison_anova"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["two_or_more_groups_continuous"], "evidence": {"score": 1.0, "band": "reordered", "quote": "“Proteins with differential abundance among the four groups were considered with fold change ≥ 1.5 and Anova ≤ 0.05. p-values between groups were calculated using t-test (independent, 2-tailed, unequal variance) and subsequently false discovery rate (FDR) correction for multiple testing [21] was applied.” “The mass spectrometry proteomics data have been deposited in the ProteomeXchange Consortium (http://proteomecentral.proteomexchange.org) via the PRIDE partner repository [20] with data set identifier PXD008407 and 10.6019/PXD008407.”"}}], "targets": [], "gaps": []}, "capability": {"state": "complete", "requirements": [{"capability_id": "capability:computational_analysis", "label": "Computational analysis platform", "assay_families": ["meta_analysis", "machine_learning", "survival_analysis", "statistical_regression", "pca", "molecular_docking", "network_analysis", "differential_expression", "gwas"], "availability_state": "owned", "tier_unlocked": "R1", "candidate": "Automated Assays Laravel application and simulated adapters"}], "gaps": []}, "readiness": {"state": "complete", "tier": "R1", "blocking_axis": "none", "blocked_on": "nothing:replicable_now", "axes": {"method": 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