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Peer-reviewedCC BY 4.0Genetics

Estimating cis and trans contributions to differences in gene regulation

  • Ingileif B. Hallgrímsdóttir1
  • Maria Carilli1
  • Lior S. Pachter2,1
  1. 1Division of Biology and Biological Engineering, California Institute of Technology , Pasadena, CA 91125 ,
  2. 2Department of Computing and Mathematical Sciences, California Institute of Technology , Pasadena, CA 91125 ,
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Abstract

We describe a coordinate system and associated hypothesis testing framework for determining whether cis or trans regulation is responsible for differences in gene expression between two homozygous strains or species. We apply our framework to data from single replicate studies on yeast strains and human-chimpanzee hybrid cells, as well as to data from a mouse study with replicates, showing marked differences between our gene regulatory assignments and those previously reported. We also show how our multi-sample framework can determine the context dependency of cis and trans effects as well as explicitly model different hypotheses regarding the underlying mechanism of trans regulation.

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Cite

BibTeXRIS
BibTeX
@article{hallgrimsdottir2026estimating,
  title = {{Estimating cis and trans contributions to differences in gene regulation}},
  author = {Ingileif B. Hallgrímsdóttir and Maria Carilli and Lior S. Pachter},
  journal = {Genetics},
  year = {2026},
  month = sep,
  doi = {10.1093/genetics/iyag228},
  url = {https://doi.org/10.1093/genetics/iyag228},
  note = {CC BY 4.0},
}
RIS
TY  - JOUR
TI  - Estimating cis and trans contributions to differences in gene regulation
AU  - Ingileif B. Hallgrímsdóttir
AU  - Maria Carilli
AU  - Lior S. Pachter
PY  - 2026
DA  - 2026/09/11
JO  - Genetics
DO  - 10.1093/genetics/iyag228
UR  - https://doi.org/10.1093/genetics/iyag228
AB  - We describe a coordinate system and associated hypothesis testing framework for determining whether cis or trans regulation is responsible for differences in gene expression between two homozygous strains or species. We apply our framework to data from single replicate studies on yeast strains and human-chimpanzee hybrid cells, as well as to data from a mouse study with replicates, showing marked differences between our gene regulatory assignments and those previously reported. We also show how our multi-sample framework can determine the context dependency of cis and trans effects as well as explicitly model different hypotheses regarding the underlying mechanism of trans regulation.
SN  - 0016-6731
SN  - 1943-2631
ER  -