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xcore: an R package for inference of gene expression regulators.
BMC Bioinformatics
January 2023
RIKEN Center for Integrative Medical Sciences, Yokohama, 230-0045, Japan.
Article Synopsis
- Researchers often need to identify which transcription factors (TFs) influence gene expression changes, but traditional methods depend on predicted binding sites and may not apply across all cell types.
- The xcore R package allows users to model TF activity directly using available ChIP-seq data, bypassing the need for motif finding and TFBS prediction, with a companion package called xcoredata providing preprocessed signatures.
- xcore has been shown to produce biologically relevant predictions in various experiments, offering an accessible way to analyze gene expression that can be integrated into existing analysis workflows.
Investigating the role of Ebp1 in Chandipura virus infection.
J Biosci
June 2019
Department of Biotechnology, University of Calcutta, Calcutta, India.
ErbB-3 binding protein 1 (Ebp1) is a host protein which binds ErbB-3 receptor to induce signalling events for cell growth regulation. In addition, Ebp1 also interacts with ribonucleoprotein complexes. In recent times, Ebp1 was found to play an antagonistic role in viral infections caused by Influenza and Rinderpest viruses.
View Article and Find Full Text PDFScreening of peste des petits ruminants virus in a population of district Khairpur, Pakistan.
Genet Mol Res
September 2017
Pest and Disease Research Laboratory, Department of Agriculture and Agribusiness, , , Pakistan
Goats are the Pakistan's fastest growing ruminants, and Pakistan is the third largest goat producer in the world after India and China. Goat meat preference is the main reason for its increased demand. In the country, there are 25 goat breeds and two wild relatives such as Mark and Goats.
View Article and Find Full Text PDFUse of SLAM and PVRL4 and identification of pro-HB-EGF as cell entry receptors for wild type phocine distemper virus.
PLoS One
November 2015
Centre for Infection and Immunity, School of Medicine, Dentistry and Biomedical Sciences, Queen's University Belfast, Belfast, United Kingdom.
Signalling lymphocyte activation molecule (SLAM) has been identified as an immune cell receptor for the morbilliviruses, measles (MV), canine distemper (CDV), rinderpest and peste des petits ruminants (PPRV) viruses, while CD46 is a receptor for vaccine strains of MV. More recently poliovirus like receptor 4 (PVRL4), also known as nectin 4, has been identified as a receptor for MV, CDV and PPRV on the basolateral surface of polarised epithelial cells. PVRL4 is also up-regulated by MV in human brain endothelial cells.
View Article and Find Full Text PDFThe risk of rinderpest re-introduction in post-eradication era.
Prev Vet Med
February 2014
Veterinary Epidemiology, Economics and Public Health Group, Department of Production and Population Health, Royal Veterinary College, Hawkshead Lane, North Mymms, AL9 7TA Hatfield, United Kingdom.
In 2011, ten years after the last reported outbreak, the eradication of rinderpest was declared. However, as rinderpest virus stocks still exist, there remains a risk of rinderpest re-introduction. A semi-quantitative risk assessment was conducted to assess this risk, which was defined as the probability of at least one host becoming infected and infectious outside a laboratory anywhere in the world within a one-year period.
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