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. 2024 Feb 12;22(5):452–464. doi: 10.1158/1541-7786.MCR-23-0976

Figure 4.

Figure 4. Proteomic and transcriptomic data integration reveals dissonance of targetable proteins. A, The table shows the three main stratification levels of protein and mRNA expression agreements, concordant (C); discordant I (DC.I); discordant II (DC.II) and the total number of hyper-abundant proteins in AdCa (n = 361) and in NE (n = 337) including percent distribution of total, respectively. B, Protein and mRNA log2 fold change evaluating only the hyper-abundant protein in NE (337 proteins) and AdCa (361 proteins) and simultaneously evaluating the direction of the mRNA expression of those proteins that are stratified as concordant (C; mRNA and protein are upregulated and hyper-abundant), discordant I (DC.I; mRNA is not altered significantly and protein is hyper-abundant) and discordant II (DC.II; mRNA is significantly downregulated whereas the protein is hyper-abundant). C–D, AdCa and NE hyper-abundant proteins iBAQ (VSN normalized and ROTS P value adjusted <0.05 significances) mRNA FPKM (ROTS normalized and P value adjusted <0.05) log2 fold change highlighting proteins of interest. E, GO protein class analysis of the NE and AdCa concordant and non-concordant plus discordant proteins. Box plots of protein log2 fold change VSN normalized and mRNA log2 fold change of n = 33 AdCa and n = 14 NE evaluating the overall expression in (F) HIC-2 and (G) COL3A1. Data are represented as mean ± SEM; ∗∗, P < 0.01; ∗∗∗, P < 0.001, two-tailed Welch-corrected.

Proteomic and transcriptomic data integration reveals dissonance of targetable proteins. A, The table shows the three main stratification levels of protein and mRNA expression agreements, concordant (C); discordant I (DC.I); discordant II (DC.II) and the total number of hyper-abundant proteins in AdCa (n = 361) and in NE (n = 337) including percent distribution of total, respectively. B, Protein and mRNA log2 fold change evaluating only the hyper-abundant protein in NE (337 proteins) and AdCa (361 proteins) and simultaneously evaluating the direction of the mRNA expression of those proteins that are stratified as concordant (C; mRNA and protein are upregulated and hyper-abundant), discordant I (DC.I; mRNA is not altered significantly and protein is hyper-abundant) and discordant II (DC.II; mRNA is significantly downregulated whereas the protein is hyper-abundant). C–D, AdCa and NE hyper-abundant proteins iBAQ (VSN normalized and ROTS P value adjusted <0.05 significances) mRNA FPKM (ROTS normalized and P value adjusted <0.05) log2 fold change highlighting proteins of interest. E, GO protein class analysis of the NE and AdCa concordant and non-concordant plus discordant proteins. Box plots of protein log2 fold change VSN normalized and mRNA log2 fold change of n = 33 AdCa and n = 14 NE evaluating the overall expression in (F) HIC-2 and (G) COL3A1. Data are represented as mean ± SEM; ∗∗, P < 0.01; ∗∗∗, P < 0.001, two-tailed Welch-corrected.