oncomine database  (Mendeley Ltd)

Journal: bioRxiv

Article Title: Thyroid Hormone Receptor Beta Signaling is a Targetable Driver of Prostate Cancer Growth

doi: 10.1101/2025.03.05.641137

Figure Lengend Snippet: (A) Waterfall plot the most frequently mutated genes derived from whole exome sequencing of 102 treatment-naïve patients who had undergone radical prostatectomy. (B) Bubble plot of signaling pathways in which the SNV-affected genes from the same PCa patient cohort are enriched. Each bubble represents a pathway; the size corresponds to the number of genes affected by SNVs within that pathway, and the color indicates the number of patients affected. The x-axis represents the combined score, representing the significance and impact of the pathway mutations. Mutation impact ratings (high, moderate, low) were determined according to the Ensembl Variant Effect Predictor (VEP) classification. (C) THRB transcript levels across different cancer types (BLCA – Bladder urothelial carcinoma, BRCA – Breast invasive carcinoma, COAD – Colon adenocarcinoma, GBM – Glioblastoma multiforme, HNSC – Head and neck squamous cell carcinoma, LIHC – Liver hepatocellular carcinoma, LUAD – Lung squamous cell carcinoma, OV – Ovarian serous cystadenocarcinoma, PAAD – Pancreatic adenocarcinoma, PRAD – Prostate adenocarcinoma, TGCT – Testicular germ cell tumors, THCA – Thyroid carcinoma), source: GEPIA. Patient numbers in each cohort are listed in the supplementary table. (D) THRB mRNA levels extracted using the Oncomine database from three different datasets: Grasso et al. (Normal n = 26, PCa n = 59), Luo et al. (Normal n = 15, PCa n = 15), Arredouani et al. (Normal n = 8, PCa n = 13). (E) Representative IHC staining of TRβ in normal prostate and PCa tissue, low expression depicts H-score 20, high expression depicts H-score 300, scale bar 100 µm. (F) Histological scoring of IHC staining of TRβ sowing significantly higher TRβ expression in PCa patients (n = 230 slides) compared to healthy control tissue (n = 142 slides).

Article Snippet: Gene expression data for THRB mRNA were extracted from various prostate cancer datasets (Grasso Prostate, Luo Prostate 2, Arredouani Prostate), including normal and tumor samples, using in the Oncomine Research Premium Edition database (Thermo Fisher, Ann Arbor, MI) (10.1016/s1476-5586(04)80047-2).

Techniques: Derivative Assay, Sequencing, Protein-Protein interactions, Mutagenesis, Variant Assay, Immunohistochemistry, Expressing, Control

Journal: bioRxiv

Article Title: Cell-autonomous GP130 activation suppresses prostate cancer development via STAT3/ARF/p53-driven senescence and confers an immune-active tumor microenvironment

doi: 10.1101/2024.02.11.579838

Figure Lengend Snippet: a) GP130 gene expression in adjacent (n=52) and PCa (n=497) tissue in TCGA-PRAD data set. Statistical analysis of the two risk groups was determined by using the Mann-Whitney test. b) Kaplan-Meier plot showing time of disease-free survival in months for GP130 low and GP130 high risk groups of the TCGA-PRAD data set. Groups were assessed based on the maximally selected rank statistics. blue: high GP130 expressing group, red: low GP130 expressing group. The blue and red numbers below horizontal axis represent the number of patients. c) Proportion of GP130 alterations in the TCGA-PRAD data set. Mutation types: deep deletion (n=21; red), truncating mutations (n=2; black) and multiple alterations (n=1; grey). One patient has simultaneous mutations. The data originate from cBioPortal. d) GP130 mRNA expression levels of four different data sets of PCa patient samples compared to healthy prostate sample control. Normalized data and statistical analyses were extracted from the Oncomine Platform. The respective prostate data set and n-numbers are indicated. Representation: boxes as interquartile range, horizontal line as the mean, whiskers as lower and upper limits. e) Spearman-correlation analysis of GP130 and STAT3 expression in TCGA-PRAD data set using cBioPortal analysis tool.

Article Snippet: Gene expression data for GP130 ( IL6ST ) were extracted from the following data sets using the Oncomine™ Research Premium Edition database (Thermo Fisher, Ann Arbor, MI) : Arredouani Prostate (reporter: 204863_s_at), Lapointe Prostate (reporter: IMAGE:2018581), Wallace Prostate (reporter: 204863_s_at), Varambally Prostate (reporter: 204863_s_at and 204864_s_at), Grasso Prostate (reporter: A_32_P140656), Holzbeierlein Prostate (reporter: 35842_at), Taylor Prostate 3 (reporter: 6733), Glinsky Prostate (reporter: 212196_at) and Best Prostate 2 (reporter: 212196_at).

Techniques: Expressing, MANN-WHITNEY, Mutagenesis