Search bioRxiv⌕ Search
Home/Archive/bioRxiv

bioRxiv · 10.1101/116061

Pathway-Level Information ExtractoR (PLIER): a generative model for gene expression data

Mao, W.·Chikina, M.
View original source ↗Export metadata ↓

Abstract

A major challenge in gene expression analysis is to accurately infer relevant biological insight, such as regulation of cell type proportion or pathways, from global gene expression studies. We present a general solution for this problem that outperforms available cell proportion inference algorithms, and is more widely useful to automatically identify specific pathways that regulate gene expression. Our method improves replicability and biological insight when applied to trans-eQTL identification.

Source connections

Explore related subjects

genomicsPreprint

Keep this discovery

Explore connections, maps & timelines

BibTeXRIS

Mao, W., Chikina, M.. 2017-03-11. Pathway-Level Information ExtractoR (PLIER): a generative model for gene expression data. https://doi.org/10.1101/116061

Cite the original work for its findings. Save a collection to share your selection of sources.

KEEP EXPLORING

Related preprints

bioRxiv2026

Recurrent mitotic error and purifying selection shape chromosomal mosaicism across human tissues

Mosaic chromosomal alterations (mCAs) have been extensively studied in cancer and clonal hematopoiesis but less so in healthy solid tissues. Here, we characterized mCAs in 19 tissues across 25 donors (aged 42-89+ years) by analyzing >200x whole-genome sequencing data generated by the Somatic Mosaicism across Human Tissues (SMaHT) Network. Across 722 tissue samples, we identified 1,008 autosomal mCAs >1 Mb in length and ubiquitous losses of sex chromosomes. Surprisingly, the highest levels of Y chromosome loss in males (5-10% cell fraction in elderly donors) were observed in the lung, adrenal gland, and heart. These tissues also tended to experience more X loss in females, revealing a gradient of mitotic error burden across human tissues. Autosomal aneuploidies displayed distinct tissue-specific patterns indicative of negative selection against most events, except in the adrenal gland, in which low-level aneuploidy was pervasive. In contrast to the adrenal gland, testis rarely harbored aneuploidies but frequently experienced low-level copy-neutral loss of heterozygosity (CN-LOH), suggesting increased mitotic recombination in spermatogonial stem cells. Recurrent X chromosome losses within tissues of female donors exhibited allelic skews explained by a combination of genetic and epigenetic effects. Together, these results show that the chromosomal landscape of aging human tissues is shaped by genetics and recurrent mutations, most but not all of which are held in check by purifying selection.

genomics↗
bioRxiv2026

Multi-modal in situ profiling of human cells using the AVITI24 platform characterizes single-cell responses to acute stress

Cells begin to respond to stress within minutes, but how this early response depends on cell type, neighboring cells, or cell cycle phase has been difficult to determine, because bulk assays average across cells and synchronization can induce stress. We measured 338 transcripts, 48 proteins and phosphoproteins, and six cell paint stains in situ in 1.18 million single cells from four human cell lines exposed to H2O2, alone and in co-culture, and in A549 cells exposed to TNF-, cadmium, dithiothreitol or lipopolysaccharide. In A549 cells, five distinct stressors changed the same targets in the same direction within 15 min, differing mainly in magnitude, and modestly increased JNK phosphorylation. By 30 min of H2O2 treatment, immediate-early genes (FOS, JUN, DDIT3, DUSP1, NR4A1) were induced most strongly in HCT116 and A549 cells. These changes occurred across the whole cell population rather than in a responsive subset. Cell line-specific differences persisted in co-culture, and the response of MCF7 cells did not increase with the number of adjacent, strongly-responding A549 cells. Ordering cells along the cell cycle from the same measurements identified 106 cycle-associated transcripts, and the response varied more between cell lines than among cell cycle phases. Overall, the measured regulators respond to stress within 30 minutes through a largely shared program whose magnitude depends more on cell identity than on cell cycle state or neighboring cell type.

genomics↗
bioRxiv2026

A Chromosome Scale Genome Assembly for the Australian blue mussel Mytilus planulatus

Mussels belonging to the genus Mytilus are among the world's most ecologically and economically important bivalve molluscs. Although the genus most likely originated in the Northern Hemisphere, the evolutionary history of Southern Hemisphere lineages, including the timing and number of colonisation events leading to the extant Australian populations, remains debated. Limited genomic resources have hindered the reconstruction of these evolutionary histories. In Australia, distinguishing native Mytilus planulatus from invasive Mytilus galloprovincialis is critical for biosecurity and conservation, but previous molecular approaches lacked sufficient resolution to resolve species boundaries and hybridisation patterns. Here, we present the first chromosome-scale reference genome for M. planulatus. The assembly consists of 14 chromosomes and over 51,000 annotated protein-coding genes per haplotype. Comparative analysis revealed extensive structural variation and widespread hemizygosity despite a largely conserved chromosomal organisation relative to M. galloprovincialis. Population analyses using SNPs and gene presence-absence variation in resequenced individuals confirmed previously inferred patterns of population structure and establish this reference genome as a valuable resource for future studies of genome evolution, adaptation and population genomics in Mytilus.

genomics↗