Pectively (B) The proteins from the perfusion-driven urine without oxygen supplementation were resolved. Lane p4, p5, p6, and p7 represents proteins acquired from the first, second, third, and fourth ten-minute intervals of the perfusion respectively. doi:10.1371/journal.pone.0066911.gIdentifying Kidney Origin Proteins in Urinecontain such information. An additional database, 122.R_norvegicus.orthologues, is found on the EBI website (http://www.ebi.ac. uk/). We used these five databases to search for human MedChemExpress AKT inhibitor 2 orthologs of identified proteins. From the 1,402 rat proteins, 1,055, 1,096, 1,150, 1,180, and 937 proteins were matched to human orthologs according to the InParanoid [17], OrthoMCL-DB [18], Homogene [19], Ensembl Compare [20], and 122.R_norvegicus.orthologues databases, respectively. Human orthologs that were identified from the same rat proteins by at least two databases were compiled, resulting in the pairing of 1,234 of the 1,402 rat proteins to 1,233 human orthologs, which account for 1,278 human orthologous genes. We analyzed the data for human orthologs, and we propose that in biomarker studies that use animal models, it is best to choose proteins that have human orthologs to facilitate the translation of the data into human applications.2.3 Comparison of human orthologs for proteins in the perfusion-driven urine 16985061 with kidney protein expression data, the normal human urine proteome, and the plasma proteome. While the human orthologs expressed in the kidneyare likely to be kidney origin proteins found in the normal human urine, the human orthologs not expressed in the kidney may be residual interstitial fluid proteins and/or may be plasma proteins that were absorbed by the kidney. To identify kidney origin proteins in urine, the human orthologs were compared with human kidney expression data. Data detailing the expression of human kidney proteins were acquired from the Human Protein Atlas Database [21], which was constructed to show the expression and localization of proteins in a variety of normal human tissues. Expression data from 12,260 human kidney genes were acquired from the Human Protein Atlas Database [21]. The human orthologs of rat perfusion-driven urine proteins were also compared with the normal human urine proteome (including the urinary exosome proteome) and the human plasma proteome to 94361-06-5 web determine which human orthologs have been identified in normal human urine and plasma, respectively. For the normal human urine proteome, three large-scale datasets from previous studies [22?4] and one large-scale dataset from another team at our institution (data not published) were collected. For the normal human urinary exosome proteome, three large-scale human urinary exosome datasets from previous studies were collected [25?7]. For the normal human plasma proteome, the largest human plasma proteome dataset was acquired from an online database, Healthy Human Individual’s Integrated Plasma Proteome (HIP2) [28]. For easier comparison, the protein identifiers in different datasets and the kidney expression genes were standardized. We used Ensembl BioMart (http://asia.ensembl.org/biomart/ martview) to transform all of the different protein identifiers to Ensembl Gene ID(s). We compared the different proteome datasets at the gene level. All of the human urine proteins, urinary exosome proteins, and plasma proteins from different datasets were pooled together. This process resulted in 5,225 nonredundant genes in human urine, 3,416 no.Pectively (B) The proteins from the perfusion-driven urine without oxygen supplementation were resolved. Lane p4, p5, p6, and p7 represents proteins acquired from the first, second, third, and fourth ten-minute intervals of the perfusion respectively. doi:10.1371/journal.pone.0066911.gIdentifying Kidney Origin Proteins in Urinecontain such information. An additional database, 122.R_norvegicus.orthologues, is found on the EBI website (http://www.ebi.ac. uk/). We used these five databases to search for human orthologs of identified proteins. From the 1,402 rat proteins, 1,055, 1,096, 1,150, 1,180, and 937 proteins were matched to human orthologs according to the InParanoid [17], OrthoMCL-DB [18], Homogene [19], Ensembl Compare [20], and 122.R_norvegicus.orthologues databases, respectively. Human orthologs that were identified from the same rat proteins by at least two databases were compiled, resulting in the pairing of 1,234 of the 1,402 rat proteins to 1,233 human orthologs, which account for 1,278 human orthologous genes. We analyzed the data for human orthologs, and we propose that in biomarker studies that use animal models, it is best to choose proteins that have human orthologs to facilitate the translation of the data into human applications.2.3 Comparison of human orthologs for proteins in the perfusion-driven urine 16985061 with kidney protein expression data, the normal human urine proteome, and the plasma proteome. While the human orthologs expressed in the kidneyare likely to be kidney origin proteins found in the normal human urine, the human orthologs not expressed in the kidney may be residual interstitial fluid proteins and/or may be plasma proteins that were absorbed by the kidney. To identify kidney origin proteins in urine, the human orthologs were compared with human kidney expression data. Data detailing the expression of human kidney proteins were acquired from the Human Protein Atlas Database [21], which was constructed to show the expression and localization of proteins in a variety of normal human tissues. Expression data from 12,260 human kidney genes were acquired from the Human Protein Atlas Database [21]. The human orthologs of rat perfusion-driven urine proteins were also compared with the normal human urine proteome (including the urinary exosome proteome) and the human plasma proteome to determine which human orthologs have been identified in normal human urine and plasma, respectively. For the normal human urine proteome, three large-scale datasets from previous studies [22?4] and one large-scale dataset from another team at our institution (data not published) were collected. For the normal human urinary exosome proteome, three large-scale human urinary exosome datasets from previous studies were collected [25?7]. For the normal human plasma proteome, the largest human plasma proteome dataset was acquired from an online database, Healthy Human Individual’s Integrated Plasma Proteome (HIP2) [28]. For easier comparison, the protein identifiers in different datasets and the kidney expression genes were standardized. We used Ensembl BioMart (http://asia.ensembl.org/biomart/ martview) to transform all of the different protein identifiers to Ensembl Gene ID(s). We compared the different proteome datasets at the gene level. All of the human urine proteins, urinary exosome proteins, and plasma proteins from different datasets were pooled together. This process resulted in 5,225 nonredundant genes in human urine, 3,416 no.
