In Table 9.6, KEGG Pathway analysis is performed on WDCG obtained from pair of Acute–Chronic gene expression data set (i.e., AC–CH–WDCG-KEGG PATHWAY label in the Table), Chronic–Nonprogressor gene expression data set (i.e., CH-NONPRO-WDCG-KEGG PATHWAY label in the Table) and ...
SCPA is a method for pathway analysis in single cell RNA-seq data. It’s a different approach to pathway analysis that defines pathway activity as a change in multivariate distribution of a given pathway across conditions, rather than enrichment or over representation of genes. ...
2018. Perturbation-response genes reveal signaling footprints in cancer gene expression. Nature Communications: 10.1038/s41467-017-02391-6 [2] Holland CH, Szalai B, Saez-Rodriguez J. Transfer of regulatory knowledge from human to mouse for functional genomics analysis. Biochim Biophys Acta Gene ...
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Reactome aims to provide bioinformatics tools for visualisation, interpretation and analysis of pathway knowledge to support basic research, genome analysis, modelling, systems biology and education. Pathway analysis methods have a broad range of applications in physiological and biomedical research; one of...
We examined the whole-brain connectivity group-level effects by computing a 2nd-level analysis in CONN. To examine the association of VS-to-VMPFC connectivity with a positive bias, we performed a 2nd-level multiple regression analysis in CONN. As in the brain activity analysis, we entered ...
How data was acquired Microarray analysis; data were done by Phalanx Biotech Group using Human OneArray (array version HOA 6.1) which contains 31,741 mRNA probes that can detect 20, 672 genes in human genome. Data format Analyzed Experimental factors Both MCF-7 and MDA-MB-231cells (~500×...
GO functional analysis of DEGs based on RNA-Seq data. The results can be separated into 3 main categories: “biological processes”, “cellular components”, and “molecular function” Full size image Highly expressed genes in horse skins The keratin-family gene latherin (LATH) was the most hi...
snRNA-seq analysis The sequencing files in FASTQ format of each sample were aligned against mouse mm10 genome v4.0.0 and converted to gene count matrices using Cellranger software v7.0.1. Quality control and downstream analysis was performed using Seurat R package v4.3.0. Doublets were detected...