Journal: OncoTargets and therapy

Article Title: Integrated Analysis To Identify Molecular Biomarkers Of High-Grade Serous Ovarian Cancer

doi: 10.2147/OTT.S228678

Figure Lengend Snippet: Heat map of the 103 DEGs identified in the integrated microarray analysis. Each column represents one dataset, and each row represents one gene. The number in each rectangle is the log 2 FC value. The color gradient from blue to red represents the progression from down- to upregulation. Abbreviations: DEGs, differentially expressed genes; FC, fold change.

Article Snippet: Gene expression microarray data (GSE14001, GSE18520, GSE26712, GSE27651, GSE40595, and GSE54388) were downloaded from the National Center for Biotechnology Information Gene Expression Omnibus (GEO) database ( http://www.ncbi.nlm.nih.gov/geo/ ).

Techniques: Microarray

Journal: Cytotechnology

Article Title: Optimization and evaluation of electroporation delivery of siRNA in the human leukemic CEM cell line

doi: 10.1007/s10616-010-9309-6

Figure Lengend Snippet: Whole-genome microarray data on electroporated cells

Article Snippet: RNA exonuclease 1 homolog BC130374 1.7 Up GAGE13 G antigen 13 Open in a separate window A whole-genome microarray was performed on RNA from untreated CEM cells, electroporated cells, and cells transfected with negative control siRNA or dCK siRNA transfected cells (dCK) 48 h after electroporation/transfection.

Techniques: Microarray, Control, Negative Control

Journal: BMC Bioinformatics

Article Title: AMEND: active module identification using experimental data and network diffusion

doi: 10.1186/s12859-023-05376-z

Figure Lengend Snippet: GLUT4 data module statistics

Article Snippet: The GLUT4 microarray gene expression data was obtained from the National Center for Biotechnology Information-Gene Expression Omnibus (NCBI-GEO) database (AC NO: GSE35378) and derives from an adipose tissue GLUT4 KO-OX experiment in mice by Herman et al. [ – ].

Techniques:

Journal: BMC Bioinformatics

Article Title: AMEND: active module identification using experimental data and network diffusion

doi: 10.1186/s12859-023-05376-z

Figure Lengend Snippet: Module-level empirical-to-hypergeometric ratio (mEHR) for selected modules, where each point is a pathway returned from ORA. Pathways below the red line are EV pathways. A AMEND GLUT4, B DOMINO GLUT4 module 2, C NetCore GLUT4 module 1, D AMEND Antidepressant, E DOMINO Antidepressant module 1, F NetCore Antidepressant module 1

Article Snippet: The GLUT4 microarray gene expression data was obtained from the National Center for Biotechnology Information-Gene Expression Omnibus (NCBI-GEO) database (AC NO: GSE35378) and derives from an adipose tissue GLUT4 KO-OX experiment in mice by Herman et al. [ – ].

Techniques:

Journal: BMC Bioinformatics

Article Title: AMEND: active module identification using experimental data and network diffusion

doi: 10.1186/s12859-023-05376-z

Figure Lengend Snippet: AMEND module for GLUT4 data. Darker shade of red signifies more extreme ECI

Article Snippet: The GLUT4 microarray gene expression data was obtained from the National Center for Biotechnology Information-Gene Expression Omnibus (NCBI-GEO) database (AC NO: GSE35378) and derives from an adipose tissue GLUT4 KO-OX experiment in mice by Herman et al. [ – ].

Techniques:

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