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. 2024 Aug 6;13(16):1311. doi: 10.3390/cells13161311

Table 2.

Proteins (n = 91) with significant changes between groups (p-values < 0.05, cumulative FDR < 5%, FC ± 1.5). “p”: p-value; “change”: direction of the variation; “FC”: absolute fold change. Proteins are grouped based on the type and direction of the variation. When a short name of the protein is commonly used, it is reported. “ND”: failure to detect the protein. The 21 proteins selected by the Boruta method for the RF classification analysis are highlighted in gray. MW, Mann–Whitney test; KW, Kruskal–Wallis test. The GDA score from DisGeNET analysis is also indicated, as well as a previous reference (Ref.) associating the protein with CRC and the technique used for protein identification.

UniProt KB Code (Gene) Protein ND MW S vs. D
p Change FC		 MW S vs. H
p Change FC		 MW D vs. H
p Change FC		 KW
p 		GDA Score Ref. for CRC and Used Technique
Proteins changing in the comparison S–D and D–H
Q4V328 (GRIPAP1) GRASP-1 ND in S 0.00001 S<D >100 0.0001 D>H >100 0.00001
Q96RF0 (SNX18) Sorting nexin-18 ND in D 0.00001 S>D >100 0.0003 D<H >100 0.0001 LC–MS/MS [24]
Proteins changing in the comparison S–H with S↓
P15090 (FABP4) A-FABP ND in S 0.0007 S<H >100 0.0009 0.02 qPCR a, IF b [4]
P02511 (CRYAB) AlphaB-crystallin 0.0009 S<H >100 0.0016 0.04 qPCR, IHC c, WB d [25,26]
P50995 (ANXA11) Annexin A11 0.0011 S<H 2.8 0.01 MALDI–TOF MS e, IHC [27]
P00403 (MT–CO2) Cytochrome c oxidase subunit 2 ND in S 0.0007 S<H >100 0.5 Gene expression, WB, IHC [28]
P08294 (SOD3) EC–SOD 0.0001 S<H 4.1
Q13642 (FHL1) FHL-1 0.0002 S<H 10.1 0.0003 mRNA expression [29]
P21695 (GPD1) GPDH-C ND in S 0.0001 S<H >100 0.0004 MALDI–TOF [30]
P10915 (HAPLN1) HPLPN1 ND in S 0.0003 S<H >100 0.0004 0.5 Gene expression, qMSP f [31]
P51884 (LUM) Lumican 0.0001 S<H 7.2 0.0004 0.01 WB, IHC, PCR [32]
P20774 (OGN) Mimecan (osteoglycin) 0.0004 S<H 11.7 0.0004 0.03 IHC, WB, IF [33]
Q02218 (OGDH) OGDH-E1 0.0008 S<H >100 0.0002 0.01 LC–MS/MS, WB [5]
Q9UIQ6 (LNPEP) OTase ND in S 0.0000 S<H >100 0.00001
P11177 (PDHB) PDHE1-B 0.0002 S<H >100 0.0005
P36871 (PGM1) PGM-1 0.0009 S<H 3.2 0.3 qPCR, WB IHC [34]
Q5T013 (HYI) Putative Hyi ND in S 0.0007 S<H >100
Q9HD15 (SRA1) SRA1 ND in S 0.0007 S<H >100 WGCNA g [35]
Q9C0C2 (TNKS1BP1) TAB182 0.0009 S<H 1.6
P09936 (UCHL1) UCH-L1 0.0002 S<H >100 0.0004 0.04 WB, gene expression, qMSP [36]
P51452 (DUSP3) VHR ND in S 0.0007 S<H >100
Proteins changing in the comparison S–H with S↑
P13674 (P4HA1) 4-PH alpha-1 ND in H 0.0003 S>H >100 0.0006 LC–MS/MS [37]
P55957 (BID) BH3-interacting domain death agonist 0.0012 S>H >100 0.01 qPCR [38]
P02788 (LTF) Lactotransferrin 0.0001 S>H 6.0 0.0004 qPCR, IHC, WB [39]
P49321 (NASP) NASP 0.0012 S>H 4.3
P48681 (NES) Nestin ND in H 0.0007 S>H >100 0.01 IHC [40]
P02775 (PPBP) PBP 0.0004 S>H 2.2 0.03 mRNA analysis, WB, IF [41]
O15212 (PFDN6) Prefoldin subunit 6 0.0006 S>H 2.8
Q9Y2Z0 (SUGT1) Protein SGT1 homolog ND in H 0.0003 S>H >100 0.0008
P05109 (S100A8) S100-A8 0.0006 S>H 7.7 qPCR, WB, IHC [42]
P06702 (S100A9) S100-A9 0.0000 S>H 8.1 0.0001 0.08 qPCR, WB, IHC [42]
P61964 (WDR5) WDR5 ND in H 0.0003 S>H >100 0.0008 0.01 qPCR, WB [43]
Proteins changing in the comparison D–H with D↓
P15121 (AKR1B1) Aldo-keto reductase 1B1 0.0008 D<H 3.7 0.05 gene expression, qMSP [44]
P17050 (NAGA) Alpha-N-acetylgalactosaminidase 0.0009 D<H 5.1
P35613 (BSG) Basigin 0.0002 D<H 4.8 0.0011 0.06 WB [45]
P17174 (GOT1) cAspAT 0.0002 D<H 2.4 0.01 qPCR [46]
Q9Y5K6 (CD2AP) CD2-associated protein 0.0012 D<H 3.7 0.02 LC–MS/MS, IHC [47]
P10606 (COX5B) Cytochrome c oxidase sub. 5B 0.0012 D<H 4.5
Q13011 (ECH1) DI (mitochondrial) 0.0007 D<H 3.3
P36957 (DLST) DLST 0.0008 D<H 3.4 0.0011
O95571 (ETHE1) ETHE1 0.0000 D<H 4.0 0.0002 0.02 IHC, WB, LC–MS/MS [48]
Q05315 (CLC) Gal-10 0.0011 D<H 4.9 0.03 RNA analysis [49]
P00390 (GSR) GRase 0.0002 D<H 4.6 0.0012 0.01 Enzymatic assay [50]
P06870 (KLK1) Kallikrein-1 0.0006 D<H >100 0.0003
O00401 (WASL) N-WASP 0.0009 D<H >100 0.01 qPCR [51]
Q8IV08 (PLD3) PLD3 0.0005 D<H >100 0.0012
O95716 (RAB3D) Rab-3D 0.0010 D<H >100 IHC, WB, qPCR [52]
O43760 (SYNGR2) Synaptogyrin-2 ND in D 0.0007 D<H >100 0.0015 GSEA h [53]
Proteins changing in the comparison D–H with D↑
Q15121 (PEA15) 15 kDa phosphoprotein enriched in astrocytes 0.0009 D>H >100 0.0011 0.02 WB, cell assays [54]
O94875 (SORBS2) ArgBP2 0.0007 D>H >100
P53618 (COPB1) Beta-COP 0.0002 D>H 5.7 0.0001 0.01 WB, IHC, LC–TOF MS [55]
P08572 (COL4A2) Collagen alpha-2(IV) chain 0.0003 D>H >100 0.0005 0.1 LC–MS/MS [37]
P02751 (FN1) FN 0.0002 D>H 2.9 0.0004 0.4 RNA analysis, WB, IHC, GSEA [56]
P29279 (CCN2) CTGF ND in H 0.0003 D>H >100 0.0012 0.08 WB, qPCR [57]
P13639 (EEF2) EF-2 0.0002 D>H 10.7 0.01 MALDI–TOF, IHC, WB, ELISA [58]
P84243 (H3–3A) Histone H3.3 0.0012 D>H >100 0.01 RNA analysis [49]
O14979 (HNRNPDL) hnRNP D-like 0.0001 D>H 2.0 0.0009 0.03 LC–MS/MS [59]
P14174 (MIF) MIF 0.0007 D>H 2.4 0.03 IHC, WB, qPCR [60]
P14543 (NID1) NID-1 0.0002 D>H >100 0.000001 0.3 qPCR [61]
P42696 (RBM34) RNA-binding protein 34 0.0009 D>H >100 0.0013 qPCR, WB, IHC [62]
P50454 (SERPINH1) Serpin H1 0.0004 D>H 3.4 0.01 DEGs i, WGCNA [63]
Q8WUH6 (TMEM263) Transmembrane protein 263 ND in S/H 0.0003 D>H >100 0.000001 0.02 DEGs, ML j [64]
P18887 (XRCC1) XRCC1 ND in H 0.0001 D>H >100 0.00001 0.4 Gene expression, IHC [65]
Proteins changing in the comparison D–H and S–H with D↓ and S↓
P27348 (YWHAQ) 14-3-3 protein theta 0.0001 S<H 8.2 0.0003 D<H 8.3 0.0001
P00325 (ADH1B) ADH1B 0.0010 S<H 9.5 0.0013 D<H 8.3 0.0006 0.4 Gene expression [66]
P00326 (ADH1C) ADH1C 0.00001 S<H 22.3 0.00001 D<H 26.3 0.00001 0.06 DEGs, ML, IHC, WB, qPCR [67]
P48047 (ATP5PO) ATP synthase subunit O 0.0008 S<H 16.5 0.0013 D<H 3.5 0.0004 LC–MS/MS, qPCR, WB [68]
O75363 (BCAS1) Breast carcinoma-amplified sequence 1 0.0011 S<H 3.5 0.00001 D<H 7.4 0.0001 qPCR [69]
A8H7I4 (CLCA1) CaCC-1 0.00001 S<H 9.2 0.00001 D<H 22.1 0.00001 0.06 ELISA, IHC, WB [70]
P00918 (CA2) CA-II 0.00001 S<H 5.7 0.00001 D<H 8.0 0.00001 0.02 IHC [71]
O00748 (SULT2) CE-2 0.0006 S<H 9.2 0.0004 D<H 10.9 0.0004 0.03 WB [72]
P34913 (EPHX2) CEH 0.0002 S<H 4.8 0.00001 D<H >100 0.00001 IHC, qPCR, WB [73]
P10645 (CHGA) CgA, pro-protein 0.0001 S<H 8.7 0.00001 D<H 18.2 0.00001 0.03 ML of gene data, qPCR [74]
P07585 (DCN) Decorin 0.0002 S<H 9.7 0.0008 D<H 5.7 0.0001 0.08 IF [75]
P16422 (EPCAM) Ep-CAM 0.0001 S<H >100 0.0001 D<H >100 0.00001 0.1 IHC [76]
Q9UHB6 (LIMA1) EPLIN 0.0010 S<H 4.0 0.0000 D<H 5.6 0.0001 0.1 LC–MS/MS [59]
P17931 (LGALS3) Gal-3 0.0008 S<H 2.2 0.0007 D<H 2.5 0.0008 0.1 IHC [77]
Q9Y6R7 (FCGBP) IgGFc-binding protein 0.00001 S<H 9.8 0.00001 D<H 35.7 0.00001 DEGs and ML [78]
P10082 (PYY) PYY ND in D 0.0010 S<H >100 0.0000 D<H >100 0.000001 0.01 LC–MS/MS, qPCR, IHC [79]
Q15661 (TPSAB1) Tryptase-1 0.0003 S<H 10.1 0.0002 D<H 6.5 0.0003
O60701 (UGDH) UDP-GlcDH 0.0001 S<H 3.4 0.0000 D<H 5.0 0.0001 qPCR, WB [80]
Proteins changing in the comparison D–H and S–H with D↑ and S↑
Q15582 (TGFBI) Beta ig-h3 0.0008 S>H 3.1 0.0000 D>H 2.7 0.0001 0.02 LC–MSMS, GSEA [81]
P04899 (GNAI2) Galphai2 0.00001 S>H 6.3 0.0003 D>H 5.4 0.00001 IF, WB, qPCR [82]
Proteins changing in KW comparisons among all three groups but not in MW pairwise comparisons
Q9NZK5 (ADA2) Adenosine deaminase 2 N.D in D 0.0006
P35611 (ADD1) Alpha-adducin 0.0012 0.01 Gene expression [83]
P0C0L5 (C4B) Complement C4-B ND in S/H 0.0013
Q96S86 (HAPLN3) HPLPN3 ND in D 0.0009
C9JLW8 (MCRIP1) MCRIP1 ND in S 0.0001
P49821 (NDUFV1) NDUFV1 ND in S/D 0.0003 WB, enzyme assay [84]
Q96IQ7 (VSIG2) VSIG2 0.0015 WGCNA [85]
O75312 (ZPR1) Zinc finger protein ZPR1 (ZPR1) ND in S 0.0005

a qPCR, quantitative real-time polymerase chain reaction; b IF, immunofluorescence; c IHC, immunohistochemistry; d WB, Western blot; e MALDI–TOF MS, matrix-assisted laser desorption ionization time of flight MS; f qMSP, quantitative methylation analysis; g WGCNA, gene co-expression network analysis; h GSEA, gene set enrichment analysis; i DEGs, differentially expressed genes; j ML, machine-learning analysis.