Journal: bioRxiv

Article Title: Identification Drug Targets for Oxaliplatin-Induced Cardiotoxicity without Affecting Cancer Treatment through Inter Variability Cross-Correlation Analysis (IVCCA)

doi: 10.1101/2024.02.11.579390

Figure Lengend Snippet: Data is processed through a traditional pipeline of RNA-seq data preprocessing and differential expression genes (DEGs) extraction using specific filter parameters such as False Discovery Rate (FDR) <0.05 and fold change (FC) >1.5. The data are utilized to construct a correlation matrix, its correlation heatmap is generated to visualize DEGs’ correlation distribution. For further analysis, the absolute values of the correlations are ordered. The sorted heatmap aids in the visualization of the top genes. Clustering is performed using Dendrogram, Principal Component Analysis (PCA), and t-distributed Stochastic Neighbor Embedding (t-SNE) methods, followed by distance thresholding (for the Dendrogram results) or K-means (for the PCA and t-SNE results) for finer clustering. Clusters were analyzed via STRING or network analysis to identify potential target genes. All pathways, including generated and existing ones from databases like GO and KEGG, are quantitatively compared using novel indices and ranked for relevance.

Article Snippet: Our implemented t-distributed Stochastic Neighbor Embedding (t-SNE) toolbox that performs t-SNE calculations ( ) uses the results from the correlation matrix and presents the genes based on their correlation values in 3D using a built-in ‘ tsne ’ function implemented in MATLAB.

Techniques: RNA Sequencing Assay, Expressing, Extraction, Construct, Generated

Journal: JCI Insight

Article Title: T cell developmental arrest in former premature infants increases risk of respiratory morbidity later in infancy

doi: 10.1172/jci.insight.96724

Figure Lengend Snippet: A subset of 16 study samples was stained to explore the relationship between CD31 and cytokine function in umbilical cord blood. t-SNE was performed within the Flowjo package. (A) Event distribution based on nearest-neighbor analysis and walk through of the IL-8+/TNF-α neighborhood are shown within the circle. (B) Progression of CD31, IL-2, IL-8, and TNF-α (C) and 2-dimensional plots demonstrating a phenotypic continuum associated with age cohort while moving through local structure. t-SNE, t-stochastic neighbor embedding. This figure is available as a Supplemental Video.

Article Snippet: To validate findings based on manual gating, an unsupervised, nonlinear dimensionality reduction of flow cytometry data (staining panel 3, Supplemental Table 2 ) was performed using the t-distributed stochastic neighbor embedding (t-SNE) dimensionality reduction algorithm (FlowJo v.10.2) ( 24 ). t-SNE measures the similarity between pairwise points (single cells) in high dimensional space and embeds them into a reduced, visually rich two-dimensional scatter plot in such a way that the local, high dimensional structure of the single-cell data is maintained.

Techniques: Staining