Table 5.
Methodologies using bioinformatics for the prediction of biomarkers for different types of cancer. TCGA: The Cancer Genome Atlas, GEO: Gene Expression Omnibus, LIMMA: Linear Models for Microarray Data, STRING: Search Tool for the Retrieval of Interacting Genes/Proteins, GO: Gene Ontology, KEGG: Kyoto Encyclopedia of Genes and Genomes, FUNRICH: Functional Enrichment Analysis Tool, DAVID: Database for Annotation, Visualization, and Integrated Discovery, GEPIA: Gene Expression Profiling Interactive Analysis, Affy: Affymetrix, HMDD: Human MicroRNA Disease Database, BLAST: Basic Local Alignment Search Tool, miRDB: MicroRNA Target Prediction Database.
| Author | Type of Cancer | Type of Data | Database | Data Preprocessing and Differentially Expressed Genes (DEGs) | MicroRNA Target Prediction | Protein–Protein Interaction (PPI) | Functional Enrichment Analysis | Validation |
|---|---|---|---|---|---|---|---|---|
| Zhang et al., 2020 [103] | Bladder | Gene | TCGA-BLCA, GEO | R software | Not Realized | CytoHubba, STRING | GO, KEGG, FUNRICH, DAVID | Oncomine database, GEPIA |
| Sarafidis et al., 2022 [95] | Bladder | Gene | GEO (metanalysis) | Affy, LIMMA R packages, outlier removal quality control | Not Realized | STRING, Cytoscape | GO, KEGG, Disease Ontology (DO), Reactome | GEPIA2, TCGA, Human Protein Atlas (proteomics, RNA-Seq), survival analysis |
| Pandi et al., 2022 [96] |
Breast | Gene | GEO | R LIMMA package, GEO2R | Not Realized | STRING, Cytoscape | Enrichr, KEGG | TCGA-BRCA, GEPIA, survival analysis |
| Xu et al., 2022 [104] | Breast | Gene | GEO | R LIMMA package | Not Realized | STRING | GO, KEGG | GEPIA, survival analysis |
| Wu et al., 2022 [105] | Breast | Gene | TCGA | R LIMMA package | Not Realized | STRING | GO, clusterProfiler R package | Breast Cancer Gene-Expression Miner v4.8 (bc-GenExMiner v4.8), survival analysis |
| Fadaka et al., 2019 [106] | Colon | microRNA | miRBase (https://www.mirbase.org/ accessed on 20 March 2023), miR2Disease (http://www.mir2disease.org/ accessed on 20 March 2023), HMDD (http://www.cuilab.cn/hmdd accessed on 20 March 2023), y miRCancer (http://mircancer.ecu.edu/ accessed on 20 March 2023), BLAST | R software | miRDB (http://www.mirdb.org/index.html accessed on 20 March 2023), TargetScan (https://www.targetscan.org/vert_72/ accessed on 20 March 2023) y mirDIP (http://ophid.utoronto.ca/mirDIP/index.jsp accessed on 20 March 2023) | STRING, Cytoscape | DAVID, GO, KEGG | Gene correlation (gbCRC) at http://gbcrc.bioinfo-minzhao.org/ accessed on 20 March 2023 |
| Dai et al., 2019 [107] | Colon | Gene | GEO (systematic review) | R software, BRB array tools | Not Realized | STRING, Cytoscape | FunRich (http://www.funrich.org/ accessed on 20 March 2023), KEGG, DAVID | The Human Protein Atlas (HPA), The Cancer Genome Atlas (TCGA), survival analysis |
| Li et al., 2021 [108] | Colon | Gene | GEO | R limma package | Not Realized | STRING, Cytoscape | KEGG, DAVID | TCGA, GEPIA, survival analysis |
| Hammad et al., 2021 [77] | Colon | Gene | GEO | R software | Not Realized | STRING, Cytoscape | KEGG, DAVID | GEPIA, survival analysis (PROGgene) |
| Paksoy and Hilal, 2022 [109] | Colon | Gene | https://figshare.com/articles/dataset/The_microarray_dataset_of_colon_cancer_in_csv_format_/13658790/1 accessed on 20 March 2023 | Synthetic Minority Oversampling Technique, or SMOTE method | Not Realized | Not Realized | Not Realized | Not Realized |
| Wang et al., 2021 [110] | Gastric | Gene | TCGA | R limma package | Not Realized | Cytoscape | GO, KEGG | GEPIA, survival analysis, Jiangsu Province Yixing People’s Hospital |
| Liu et al., 2022 [111] | Gastric | Gene | GEO, TCGA | R limma package, clustering analysis (Bioconductor) | Not Realized | STRING, Cytoscape | KEGG, DAVID | TCGA, survival analysis |
| Lvu et al., 2020 [97] | Glioma | mRNAsi | TCGA | EdgeR method | Not Realized | Not Realized | GO, KEGG | Survival analysis, Chinese Glioma Genome Atlas (CGGA) (http://www.cgga.org.cn/ accessed on 20 March 2023) |
| Liao et al., 2020 [112] | Lung | mRNAsi | TCGA | R LIMMA package | Not Realized | STRING, Cytoscape | GO, KEGG, DAVID | GEPIA, survival analysis |
| Gong et al., 2021 [49] | NSCLC | Gene | GEO | GEO2R | Not Realized | STRING, Cytoscape | KEGG, DAVID | GEPIA, survival analysis, Oncomine database |
| Wu et al., 2019 [100] | Ovarian | microRNA | GEO (Systematic review and Metanalysis) | edgeR package of R | Not Realized | GO, KEGG, DAVID | Survival analysis | |
| Chen et al., 2020 [99] | Ovarian | Gene | GEO | R software | Not Realized | GeneMANIA (https://genemania.org/ accessed on 20 March 2023) | KEGG, DAVID | Survival analysis, Dataset GSE9891 |
| Zahra et al., 2022 [113] | Ovarian | Gene | TCGA, UK BioBank, cBioPortal | R software | Not Realized | Not Realized | Not Realized | Not Realized |
| Shi et al., 2022 [114] | Pancreas | Gene | GEO | GEO2R | STRING, Cytoscape | GO, KEGG, DAVID | GEPIA, Survival analysis | |
| Yuan et al., 2017 [98] | Prostate | Gene | GEO | Affy, LIMMA R packages | STRING, Cytoscape | GO, DAVID | Protein Atlas Database, Oncomine database | |
| Lombe et al., 2022 [94] | Prostate | microRNA | GEO | GENT2 (http://gent2.appex.kr/gent2/ accessed on 20 March 2023) | TargetScan Human, miRDB, DIANA microT | STRING, Cytoscape | GO, KEGG, DAVID | GEPIA, survival analysis |
| Author | Prediction of drug-gene interaction | Evaluation of pronostic biomarkers | Protein acquisition, 3D modeling and protein visualizer | In vitro Validation | ||||
| Zhang et al., 2020 [103] | Not Realized | Not Realized | Not Realized | Not Realized | ||||
| Sarafidis et al., 2022 [95] | Not Realized | Least Absolute Shrinkage and Selection Operator (LASSO) regression | Not Realized | Not Realized | ||||
| Pandi et al., 2022 [96] | Not Realized | Not Realized | Not Realized | Not Realized | ||||
| Xu et al., 2022 [104] | Not Realized | Not Realized | Not Realized | Not Realized | ||||
| Wu et al., 2022 [105] | DrugBank, Cytoscape | Not Realized | Not Realized | Not Realized | ||||
| Fadaka et al., 2019 [106] | Not Realized | PrognoScan (http://dna00.bio.kyutech.ac.jp/PrognoScan/ accessed on 20 March 2023) | Not Realized | Not Realized | ||||
| Dai et al., 2020 [107] | Not Realized | Not Realized | Not Realized | Not Realized | ||||
| Li et al., 2021 [108] | Not Realized | Not Realized | Not Realized | Not Realized | ||||
| Hammad et al., 2021 [77] | Not Realized | Prediction model with Support Vector Machine (SVM classifier) | Not Realized | Not Realized | ||||
| Paksoy and Hilal, 2022 [109] | Not Realized | Random Forest, Desicion Trees, Gaussian Bayes | Not Realized | Not Realized | ||||
| Wang et al., 2021 [110] | Not Realized | Not Realized | Not Realized | Gastric cell lines (AGS, HGC27 and MKN45) and normal gastric mucosa cells, FISH, RNA extraction, qRT-PCR |
||||
| Liu et al., 2022 [111] | Drug-Gene Interaction database (DGIdb), Cytoscape | Not Realized | Not Realized | Not Realized | ||||
| Lvu et al., 2020 [97] | Not Realized | Estimation of mRNAsi using one-class logistic regressionmachine learning (OCLR), Least Absolute Shrinkage and Selection Operator (LASSO) regression | Not Realized | Not Realized | ||||
| Liao et al., 2020 [112] | Not Realized | Estimation of mRNAsi using one-class logistic regressionmachine learning (OCLR) | Not Realized | Not Realized | ||||
| Gong et al., 2021 [49] | Not Realized | Not Realized | Not Realized | A549 and HBE normall cells, via qPCR | ||||
| Wu et al., 2019 [100] | Not Realized | Not Realized | Not Realized | Not Realized | ||||
| Chen et al., 2020 [99] | Not Realized | Not Realized | Not Realized | Not Realized | ||||
| Zahra et al., 2022 [113] | Not Realized | Not Realized | Uniprot, RSCB PDB (Protein Data Bank),Phyre2, Swissmodel, Alpha fold, Missense3D tool, YASARA, PYMOL, PROVEAN | Not Realized | ||||
| Shi et al., 2022 [114] | Not Realized | Not Realized | Not Realized | Four PDA cell lines (AsPC-1, SW1990, PANC-1, and BxPC-3) and a normal human pancreatic ductal epithelial cell line (HPDE), qRT-CPR | ||||
| Yuan et al., 2017 [98] | Not Realized | Not Realized | Not Realized | Not Realized | ||||
| Lombe et al., 2022 [94] | Not Realized | Not Realized | Not Realized | MicroRNAs via qPCR | ||||