Journal: MethodsX

Article Title: Detection of key mRNAs in liver tissue of hepatocellular carcinoma patients based on machine learning and bioinformatics analysis

doi: 10.1016/j.mex.2023.102021

Figure Lengend Snippet: Three-step identification of HCC potential biomarkers. First, DEGs using non-fusion integrative method detected. Based on ComBat approach, the batch effect between data from two main microarray platforms (Affymetrix and Illumina), removed. Second, to deal with a more in-depth analysis of HCC expression datasets to identify potential diagnosis and prognosis biomarkers, classification methods and biomarker recognition conducted. Third, to evaluate the diagnostic performance in classifying HCC from normal, the risk score model was developed, and to assess the prognostic value of gene biomarkers, Kaplan–Meier (KM) survival analysis performed.

Article Snippet: In this investigation, which was based on the Illumina and Affymetrix platforms, seven microarray gene expression transcriptome datasets were considered.

Techniques: Microarray, Expressing, Biomarker Discovery, Diagnostic Assay

Journal: Stem Cell Research & Therapy

Article Title: HMGB1-modified mesenchymal stem cells attenuate radiation-induced vascular injury possibly via their high motility and facilitation of endothelial differentiation

doi: 10.1186/s13287-019-1197-x

Figure Lengend Snippet: Microarray analysis of differentially expressed genes in MSCs during endothelial differentiation. In EC-MSC coculture system, there MSC samples for each group were collected at days 0 and 7, respectively, and sent to microarray analysis of differentially expressed genes. The inclusion criteria for differentially expressed genes were the absolute fold change of RNA levels > 1.5 and P value < 0.05. The analysis yielded 2482 (999 upregulated and 1483 downregulated) genes in MSC-H cells and 1325 (671 upregulated and 654 downregulated) genes in MSC-C cells. These genes were enriched in GO terms ( a ) and KEGG pathways analysis ( b ). The enriched terms that were present in both MSC-C and MSC-H groups were marked by asterisks. The MSC-H cells yielded a cluster of the most enriched terms with high similarity to MSC-C cells. Approximately one-half of the most enriched GO terms and pathways were consistent between them. Nevertheless, multiple pathways were noteworthy of being exclusively enriched in MSC-H cells, including MAPK and p53 signaling. c The number of differentially expressed genes (significance genes) enriched in the shared GO terms was counted and compared between groups. MSC-H cells yielded 1.7-fold (ranged from 1.5 to 1.9-fold) greater number of significance genes than MSC-C cells on average. d The number of differentially expressed genes (significance genes) enriched in the shared signaling pathways was counted and compared between groups. Similarly, MSC-H cells had an average 1.4-fold (ranged from 1.3 to 1.8-fold) increase of significance gene counts than the MSC-H cells

Article Snippet: Microarray analysis of MSC gene expression profile was performed by GeneChem (Shanghai, China).

Techniques: Microarray, Protein-Protein interactions