Identification of genetic variants that impact gene co-expression relationships using large-scale single-cell data

S Li, KT Schmid, DH de Vries, M Korshevniuk, C Losert… - Genome Biology, 2023 - Springer
Background Expression quantitative trait loci (eQTL) studies show how genetic variants
affect downstream gene expression. Single-cell data allows reconstruction of personalized …

Differential co-expression analyses allow the identification of critical signalling pathways altered during tumour transformation and progression

A Savino, P Provero, V Poli - International journal of molecular sciences, 2020 - mdpi.com
Biological systems respond to perturbations through the rewiring of molecular interactions,
organised in gene regulatory networks (GRNs). Among these, the increasingly high …

[HTML][HTML] Analysis of candidate genes for cleft lip±cleft palate using murine single-cell expression data

A Siewert, B Reiz, C Krug, J Heggemann… - Frontiers in Cell and …, 2023 - frontiersin.org
Cleft lip+/-cleft palate (CL/P) is one of the most common birth defects. Although research has
identified multiple genetic risk loci for different types of CL/P (ie, syndromic or non-syndromic …

Alveolar macrophage transcriptomic profiling in COPD shows major lipid metabolism changes

W Fujii, TS Kapellos, K Baßler, K Händler… - ERJ Open …, 2021 - Eur Respiratory Soc
Background Immune cells play a major role in the pathogenesis of COPD. Changes in the
distribution and cellular functions of major immune cells, such as alveolar macrophages …

Integration of meta-analysis, machine learning and systems biology approach for investigating the transcriptomic response to drought stress in Populus species

A Tahmasebi, A Niazi, S Akrami - Scientific Reports, 2023 - nature.com
In Populus, drought is a major problem affecting plant growth and development which can
be closely reflected by corresponding transcriptomic changes. Nevertheless, how these …

Genetic architecture and molecular neuropathology of human cocaine addiction

SB Huggett, MC Stallings - Journal of Neuroscience, 2020 - Soc Neuroscience
We integrated genomic and bioinformatic analyses, using data from the largest genome-
wide association study of cocaine dependence (CD; n= 6546; 82.37% with CD; 57.39 …

Identification of key pathways and genes related to the development of hair follicle cycle in cashmere goats

J Wang, J Sui, C Mao, X Li, X Chen, C Liang, X Wang… - Genes, 2021 - mdpi.com
The development of hair follicle in cashmere goats shows significant periodic change, as
with mice and humans. However, for cashmere goat with double-coat, the periodic change …

Translational reprogramming as a driver of antimony-drug resistance in Leishmania

SA Gutierrez Guarnizo, EB Tikhonova… - Nature …, 2023 - nature.com
Leishmania is a unicellular protozoan that has a limited transcriptional control and mostly
uses post-transcriptional regulation of gene expression, although the molecular …

Co-expression analysis reveals interpretable gene modules controlled by trans-acting genetic variants

L Kolberg, N Kerimov, H Peterson, K Alasoo - Elife, 2020 - elifesciences.org
Understanding the causal processes that contribute to disease onset and progression is
essential for developing novel therapies. Although trans-acting expression quantitative trait …

GWENA: gene co-expression networks analysis and extended modules characterization in a single Bioconductor package

GG Lemoine, MP Scott-Boyer, B Ambroise, O Périn… - BMC …, 2021 - Springer
Background Network-based analysis of gene expression through co-expression networks
can be used to investigate modular relationships occurring between genes performing …