Transcriptomic data in tumor-adjacent normal tissues harbor prognostic information on multiple cancer types.
Sign Up to like & getrecommendations! Published in 2023 at "Cancer medicine"
DOI: 10.1002/cam4.5864
Abstract: In identifying prognostic markers in cancer, the roles of tumor‐adjacent normal tissues are often confined to drawing expression differences between tumor and normal tissues rather than being treated as the main targets of investigations. Thus,… read more here.
Keywords: adjacent normal; tumor adjacent; normal tissues; data tumor ... See more keywords
Boolean analysis of the transcriptomic data to identify novel biomarkers of IVIG response.
Sign Up to like & getrecommendations! Published in 2021 at "Autoimmunity reviews"
DOI: 10.1016/j.autrev.2021.102850
Abstract: Intravenous immunoglobulin (IVIG) is used to treat several autoimmune and inflammatory diseases, but some patients are refractory to IVIG and require alternative treatments. Identifying a biomarker that could segregate IVIG responders from non-responders has been… read more here.
Keywords: biomarkers ivig; ivig response; analysis transcriptomic; transcriptomic data ... See more keywords
Glucocorticoids, genes and brain function
Sign Up to like & getrecommendations! Published in 2018 at "Progress in Neuro-Psychopharmacology and Biological Psychiatry"
DOI: 10.1016/j.pnpbp.2017.11.020
Abstract: &NA; The identification of key genes in transcriptomic data constitutes a huge challenge. Our review of microarray reports revealed 88 genes whose transcription is consistently regulated by glucocorticoids (GCs), such as cortisol, corticosterone and dexamethasone,… read more here.
Keywords: transcription; response; glucocorticoids genes; transcriptomic data ... See more keywords
A hybrid deep learning framework for gene regulatory network inference from single-cell transcriptomic data
Sign Up to like & getrecommendations! Published in 2022 at "Briefings in bioinformatics"
DOI: 10.1093/bib/bbab568
Abstract: Inferring gene regulatory networks (GRNs) based on gene expression profiles is able to provide an insight into a number of cellular phenotypes from the genomic level and reveal the essential laws underlying various life phenomena.… read more here.
Keywords: cell; network; cell transcriptomic; single cell ... See more keywords
Integrating DNA sequencing and transcriptomic data for association analyses of low-frequency variants and lipid traits.
Sign Up to like & getrecommendations! Published in 2020 at "Human molecular genetics"
DOI: 10.1093/hmg/ddz314
Abstract: Transcriptome-wide association studies (TWAS) integrate GWAS and transcriptomic data to showcase their improved statistical power of identifying gene-trait associations while, importantly, offering further biological insights. TWAS have thus far focused on common variants as available… read more here.
Keywords: common variants; association; transcriptomic data; frequency variants ... See more keywords
Custom methods to identify conserved genetic modules applied to novel transcriptomic data from Amborella trichopoda.
Sign Up to like & getrecommendations! Published in 2022 at "Journal of experimental botany"
DOI: 10.1093/jxb/erac044
Abstract: We have devised a procedure for the inter-species comparison of transcriptomic data and used this to reconstruct the expression dynamics of major genetic modules that were present at least 149 million years ago in the… read more here.
Keywords: genetic modules; novel transcriptomic; expression; amborella trichopoda ... See more keywords
Identification of MTHFD2 as a novel prognosis biomarker in esophageal carcinoma patients based on transcriptomic data and methylation profiling
Sign Up to like & getrecommendations! Published in 2020 at "Medicine"
DOI: 10.1097/md.0000000000022194
Abstract: Abstract DNA methylation is an important epigenetic regulatory mechanism in esophageal carcinoma (EC) and is associated with genomic instability and carcinogenesis. In the present study, we aimed to identify tumor biomarkers for predicting prognosis of… read more here.
Keywords: expression; esophageal carcinoma; prognosis; methylation ... See more keywords
Modulating innate immune activation states impacts the efficacy of specific Aβ immunotherapy
Sign Up to like & getrecommendations! Published in 2021 at "Molecular Neurodegeneration"
DOI: 10.1186/s13024-021-00453-4
Abstract: Introduction Passive immunotherapies targeting Aβ continue to be evaluated as Alzheimer’s disease (AD) therapeutics, but there remains debate over the mechanisms by which these immunotherapies work. Besides the amount of preexisting Aβ deposition and the… read more here.
Keywords: immune activation; immunotherapy; activation states; transcriptomic data ... See more keywords
A Unified Probabilistic Framework for Modeling and Inferring Spatial Transcriptomic Data
Sign Up to like & getrecommendations! Published in 2023 at "Current Bioinformatics"
DOI: 10.2174/1574893618666230529145130
Abstract: Spatial transcriptomics (ST) can provide vital insights into tissue function with the spatial organization of cell types. However, most technologies have limited spatial resolution, i.e., each measured location contains a mixture of cells, which only… read more here.
Keywords: probabilistic framework; inferring spatial; unified probabilistic; modeling inferring ... See more keywords
Transcriptomic Data Analyses Reveal That Sow Fertility-Related lincRNA NORFA Is Essential for the Normal States and Functions of Granulosa Cells
Sign Up to like & getrecommendations! Published in 2021 at "Frontiers in Cell and Developmental Biology"
DOI: 10.3389/fcell.2021.610553
Abstract: NORFA, the first lincRNA associated with sow fertility, has been shown to control granulosa cell (GC) functions and follicular atresia. However, the underlying mechanism is not fully understood. In this study, RNA-seq was performed and… read more here.
Keywords: data analyses; normal states; transcriptomic data; sow fertility ... See more keywords
A Computational Framework to Characterize the Cancer Drug Induced Effect on Aging Using Transcriptomic Data
Sign Up to like & getrecommendations! Published in 2022 at "Frontiers in Pharmacology"
DOI: 10.3389/fphar.2022.906429
Abstract: Cancer treatments such as chemotherapies may change or accelerate aging trajectories in cancer patients. Emerging evidence has shown that “omics” data can be used to study molecular changes of the aging process. Here, we integrated… read more here.
Keywords: drug induced; effect; cancer drug; transcriptomic data ... See more keywords