Supplementary Material for: Validation of a urine- based proteomics test to predict clinically significant prostate cancer: complementing mpMRI pathway by Frantzi M. (20149656)

“…A major clinical need is to accurately predict clinically significant PCa (csPCa). A proteomics-based 19-biomarker model (19-BM) was previously developed using capillary electrophoresis-mass spectrometry (CE-MS) and validated in 1000 patients at risk for PCa. …”

Data Sheet 2_A structure-based tool to interpret the significance of kinase mutations in clinical next generation sequencing in cancer.pdf by Amith Rangarajan (21978383)

“…With the explosion of clinical NGS data and the concurrent availability of protein structures through the Protein Data Bank and protein models through programs such as AlphaFold, there exists an unprecedented opportunity to use structural information to help standardize NGS analysis with the overall goal of advancing personalized cancer therapy.</p>Methods<p>Using the Catalogue of Somatic Mutations in Cancer (COSMIC), the largest curated database of clinical cancer mutations, we mapped thousands of missense mutations in the kinase and juxtamembrane (JM) domains of 48 receptor tyrosine kinases (RTKs) onto structurally aligned kinase structures, then clustered known activating mutations along with VUSs based on proximity in three-dimensional structure. …”

Image_1_Significance of monocyte infiltration in patients with gastric cancer: A combined study based on single cell sequencing and TCGA.jpeg by Wei Xu (28953)

“…Despite some improvements, the prognosis of patients with gastric cancer is still not accurately predicted.</p>Methods<p>Based on single cell sequencing data, we conducted a detailed analysis of gastric cancer patients and normal tissues to determine the role of monocytes in the progression of gastric cancer. …”

Data Sheet 1_A structure-based tool to interpret the significance of kinase mutations in clinical next generation sequencing in cancer.pdf by Amith Rangarajan (21978383)

“…With the explosion of clinical NGS data and the concurrent availability of protein structures through the Protein Data Bank and protein models through programs such as AlphaFold, there exists an unprecedented opportunity to use structural information to help standardize NGS analysis with the overall goal of advancing personalized cancer therapy.</p>Methods<p>Using the Catalogue of Somatic Mutations in Cancer (COSMIC), the largest curated database of clinical cancer mutations, we mapped thousands of missense mutations in the kinase and juxtamembrane (JM) domains of 48 receptor tyrosine kinases (RTKs) onto structurally aligned kinase structures, then clustered known activating mutations along with VUSs based on proximity in three-dimensional structure. …”

Data Sheet 1_Construction of a clinically significant prostate cancer risk prediction model based on traditional diagnostic methods.docx by Wen-Tong Ji (20457248)

“…Objectives<p>to construct a prediction model for clinically significant prostate cancer (csPCa) based on prostate-specific antigen (PSA) levels, digital rectal examination (DRE), and transrectal ultrasonography (TRUS).…”

Data Sheet 2_Construction of a clinically significant prostate cancer risk prediction model based on traditional diagnostic methods.docx by Wen-Tong Ji (20457248)

“…Objectives<p>to construct a prediction model for clinically significant prostate cancer (csPCa) based on prostate-specific antigen (PSA) levels, digital rectal examination (DRE), and transrectal ultrasonography (TRUS).…”

Analysis of Collagen type X alpha 1 (COL10A1) expression and prognostic significance in gastric cancer based on bioinformatics by Shuai Chen (506142)

Table_3_Significance of monocyte infiltration in patients with gastric cancer: A combined study based on single cell sequencing and TCGA.xlsx by Wei Xu (28953)

“…Despite some improvements, the prognosis of patients with gastric cancer is still not accurately predicted.</p>Methods<p>Based on single cell sequencing data, we conducted a detailed analysis of gastric cancer patients and normal tissues to determine the role of monocytes in the progression of gastric cancer. …”

Table_1_Significance of monocyte infiltration in patients with gastric cancer: A combined study based on single cell sequencing and TCGA.xlsx by Wei Xu (28953)

“…Despite some improvements, the prognosis of patients with gastric cancer is still not accurately predicted.</p>Methods<p>Based on single cell sequencing data, we conducted a detailed analysis of gastric cancer patients and normal tissues to determine the role of monocytes in the progression of gastric cancer. …”

Table_2_Significance of monocyte infiltration in patients with gastric cancer: A combined study based on single cell sequencing and TCGA.xlsx by Wei Xu (28953)

“…Despite some improvements, the prognosis of patients with gastric cancer is still not accurately predicted.</p>Methods<p>Based on single cell sequencing data, we conducted a detailed analysis of gastric cancer patients and normal tissues to determine the role of monocytes in the progression of gastric cancer. …”

Ribosomal protein subunit large (Rpl) and small (Rps) transcripts are expressed at decreased levels at the site of <i>L</i>. <i>major</i> infection. by Gopinath Venugopal (638444)

IFNγ+LPS up-regulated DEGs identified by RRA and fold-change analysis. by Giorgia Colombo (6337118)

Significant genes identified in the gene-based test with GWAS summary data. by Samantha Gonzales (8798435)

Protein domains with significant mutations. by Meng Wang (124646)

Subjects:

Scoring system based on significant independent factors of multiple logistic regression analyses. by Tetsushi Oyama (13236918)

Table_1_A novel defined m7G regulator signature to investigate the association between molecular characterization and clinical significance in lung adenocarcinoma.xlsx by Yi Dong (440404)

“…Background<p>About170 chemical modifications to RNAs have been identified, which significantly affect gene expression. Dysregulation of RNA modifications induced by abnormal expression or mutations in RNA modifiers might result in cancer. …”

Changes in TEER and permeability of EA.hy926 cells exposed to EVs or pellets from infected or uninfected macrophages. by Myriam Lucia Velandia-Romero (8259726)

“…Interestingly, TEER increased significantly (up to 15 Ω/cm²) when EA.hy926 cells were exposed to EVs obtained from infected U937 macrophages (<i>EV (+)</i>_<i>4G2</i> or <i>P(+))</i> (B). …”

Expression Significance and Prognostic Value of GPR27 in Ovarian Cancer by Xiulan Peng (640576)

“…<p>This study explored the prognostic role of GPR27 and its predictive value to platinum-based therapy in ovarian cancer.</p> <p>A survival analysis of GPR27, and the therapeutic response to platinum in ovarian cancer was investigated using data from the cancer genome atlas (TCGA) and Gene Expression Omnibus (GEO) databases. …”

miRNAs that may have prognostic significance based on both TCGA-BC and METABRIC datasets. by Murat Kaya (578380)

Significant differences in collagen composition of equine wounds based on picrosirius red staining. by Lena Partusch (22574484)