20 February 2022: Database Analysis
The Obesity-Related Metabolic Gene HSD17B8 Protects Against Breast Cancer: High RNA/Protein Expression Means a Better Prognosis
Yunmeng Nie ABEF , Fang Huang B , Lihua Lou B , Junbin Yan ABCDEF*DOI: 10.12659/MSM.934424
Med Sci Monit 2022; 28:e934424
Table 1 Databases and software used in the study.
| Obesity/breast cancer patients related database | |||
|---|---|---|---|
| Database | Number of subjects | Application | Ref |
| Kyoto Encyclopedia of Genes and Genomes (KEGG) | Null | Select MRGs | |
| GSE151839 dataset | 10 obese and 10 normal weight subjects | Select DEGs of overweight females | []15 |
| The Cancer Genome Atlas (TCGA) | 112 normal paracancerous and 1096 breast cancer samples | Download data of BRCA patients | |
| Kaplan Meier plotter | 1879 breast cancer samples | Verify the accuracy of results | []16 |
| Gene Expression Profiling Interactive Analysis (GEPIA) | 963 breast cancer samples with ABCA1 expression; 960 samples with LPIN1 expression; 964 samples with HSD17B8 expression | Verify the accuracy of results | []17 |
| Gene Expression database of Normal and Tumor tissues 2 (GENT2) | 475 normal and 5574 breast cancer samples (1484 breast cancer samples with subtype information) | Verify the relationship of breast cancer subtypes from RNA level | []18 |
| The Clinical Proteomic Tumor Analysis Consortium (CPTAC) | 18 normal paracancerous and 133 breast cancer samples | Verify the relationship of breast cancer from protein level | []19 |
| The Human Protein Atlas project (HLA) | NULL | Verify the protein expression | []20 |
| R software (4.1.0) | Data analysis and visualization | ||
| limma package | Data processing and DEGs screening | []21 | |
| ClusterProfiler package | GO/KEGG enrichment analysis | []22 | |
| Survival package | Survival analysis and univariate COX regression analysis | ||
| pROC package | DeLong’s test and ROC curve | []23 | |
| ggplot2 package | Data visualization | ||