Biology subjects

Dong, D.

Publications and source records attributed to Dong, D..

3 recordsLinked to original sources

bioRxiv2018

ebayGSEA: An improved Gene Set Enrichment Analysis method for Epigenome-Wide-Association Studies

MotivationThe biological interpretation of differentially methylated sites derived from Epigenome-Wide-Association Studies remains a significant challenge. Gene Set Enrichment Analysis (GSEA) is a general tool to help aid biological interpretation, yet its correct and unbiased implementation in the EWAS context is difficult due to the differential probe representation of Illumina Infinium DNA methylation beadchips.\n\nResultsWe present a novel GSEA method, called ebayGSEA, which ranks genes, not CpGs, according to the overall level of differential methylation, as assessed using all the probes mapping to the given gene. Applied on simulated and real EWAS data, we show how ebayGSEA may exhibit higher sensitivity and specificity than the current state-of-the-art, whilst also avoiding differential probe representation bias. Thus, ebayGSEA will be a useful additional tool to aid the interpretation of EWAS data.\n\nAvailability and implementationebayGSEA is available from https://github.com/aet21/ebayGSEA, and has been incorporated into the ChAMP Bioconductor package (https://www.bioconductor.org).

bioinformatics↗

bioRxiv2018

Oxytocin modulates the intrinsic dynamics between attention-related large scale networks

Attention and salience processing have been linked to the intrinsic between- and within-network dynamics of large scale networks engaged in internal (default mode network, DN) and external attention allocation (dorsal attention, DAN, salience network, SN). The central oxytocin (OXT) system appears ideally organized to modulate widely distributed neural systems and to regulate the switch between internal attention and salient stimuli in the environment. The current randomized placebo (PLC) controlled between-subject pharmacological resting-state fMRI study in N = 187 (OXT, n = 94; n = 93; single-dose intranasal administration) healthy male and female participants employed an independent component analysis (ICA) approach to determine the modulatory effects of OXT on the within- and between-network dynamics of the DAN-SN-DN triple network system. OXT increased the functional integration between subsystems within SN and DN and increased functional segregation of the DN with the SN and DAN engaged in attentional control. Whereas no sex differences were observed, OXT effects on the DN-SN interaction were modulated by autism traits. Together, the findings suggest that OXT may facilitate efficient attentional allocation towards social cues by modulating the intrinsic functional dynamics between DN components engaged in social processing and large-scale networks involved in external attentional demands (SN, DAN).

neuroscience↗

bioRxiv2017

Diverse functions of closely homologous actin isoforms are defined by their nucleotide, rather than their amino acid sequence.

{beta}- and {gamma}-cytoplasmic-actin are nearly indistinguishable in their amino acid sequence, but are encoded by different genes that play non-redundant biological roles. The key determinants that drive their functional distinction are unknown. Here we tested the hypothesis that {beta}- and {gamma}-actin functions are defined by their nucleotide, rather than their amino acid sequence, using targeted editing of the mouse genome. Although previous studies have shown that disruption of {beta}-actin gene critically impacts cell migration and mouse embryogenesis, we demonstrate here that generation of a mouse lacking {beta}-actin protein by editing {beta}-actin gene to encode {gamma}-actin protein, and vice versa, does not affect cell migration and/or organism survival. Our data suggest that the essential in vivo function of {beta}-actin is provided by the gene sequence independent of the encoded protein isoform. We propose that this regulation constitutes a global \"silent code\" mechanism that controls the functional diversity of protein isoforms.

cell biology↗