@article{Alasoo2018,
abstract = {Regulatory variants are often context specific, modulating gene expression in a subset of possible cellular states. Although these genetic effects can play important roles in disease, the molecular mechanisms underlying context specificity are poorly understood. Here, we identified shared quantitative trait loci (QTLs) for chromatin accessibility and gene expression in human macrophages exposed to IFN$\gamma$, Salmonella and IFN$\gamma$ plus Salmonella. We observed that {\~{}}60{\%} of stimulus-specific expression QTLs with a detectable effect on chromatin altered the chromatin accessibility in naive cells, thus suggesting that they perturb enhancer priming. Such variants probably influence binding of cell-type-specific transcription factors, such as PU.1, which can then indirectly alter the binding of stimulus-specific transcription factors, such as NF-$\kappa$B or STAT2. Thus, although chromatin accessibility assays are powerful for fine-mapping causal regulatory variants, detecting their downstream effects on gene expression will be challenging, requiring profiling of large numbers of stimulated cellular states and time points.},
author = {Alasoo, Kaur and Rodrigues, Julia and Mukhopadhyay, Subhankar and Knights, Andrew J. and Mann, Alice L. and Kundu, Kousik and Hale, Christine and Dougan, Gordon and Gaffney, Daniel J.},
doi = {10.1038/s41588-018-0046-7},
file = {:Users/fede/Library/Containers/com.apple.Preview/Data/Downloads/s41588-018-0046-7.pdf:pdf},
issn = {15461718},
journal = {Nature Genetics},
mendeley-groups = {ideal{\_}manuscript,GeneTonic{\_}manuscript},
number = {3},
pages = {424--431},
publisher = {Springer US},
title = {{Shared genetic effects on chromatin and gene expression indicate a role for enhancer priming in immune response}},
url = {http://dx.doi.org/10.1038/s41588-018-0046-7},
volume = {50},
year = {2018}
}

@article{Khatri2012,
  title = {Ten Years of Pathway Analysis: Current Approaches and Outstanding Challenges},
  volume = {8},
  ISSN = {1553-7358},
  url = {http://dx.doi.org/10.1371/journal.pcbi.1002375},
  DOI = {10.1371/journal.pcbi.1002375},
  number = {2},
  journal = {PLoS Computational Biology},
  publisher = {Public Library of Science (PLoS)},
  author = {Khatri,  Purvesh and Sirota,  Marina and Butte,  Atul J.},
  editor = {Ouzounis,  Christos A.},
  year = {2012},
  month = Feb,
  pages = {e1002375}
}

@article{Subramanian2005,
  title = {Gene set enrichment analysis: A knowledge-based approach for interpreting genome-wide expression profiles},
  volume = {102},
  ISSN = {1091-6490},
  url = {http://dx.doi.org/10.1073/pnas.0506580102},
  DOI = {10.1073/pnas.0506580102},
  number = {43},
  journal = {Proceedings of the National Academy of Sciences},
  publisher = {Proceedings of the National Academy of Sciences},
  author = {Subramanian,  Aravind and Tamayo,  Pablo and Mootha,  Vamsi K. and Mukherjee,  Sayan and Ebert,  Benjamin L. and Gillette,  Michael A. and Paulovich,  Amanda and Pomeroy,  Scott L. and Golub,  Todd R. and Lander,  Eric S. and Mesirov,  Jill P.},
  year = {2005},
  month = Sept,
  pages = {15545–15550}
}

@article{Wijesooriya2022,
  title = {Urgent need for consistent standards in functional enrichment analysis},
  volume = {18},
  ISSN = {1553-7358},
  url = {http://dx.doi.org/10.1371/journal.pcbi.1009935},
  DOI = {10.1371/journal.pcbi.1009935},
  number = {3},
  journal = {PLOS Computational Biology},
  publisher = {Public Library of Science (PLoS)},
  author = {Wijesooriya,  Kaumadi and Jadaan,  Sameer A. and Perera,  Kaushalya L. and Kaur,  Tanuveer and Ziemann,  Mark},
  editor = {Kemp,  Melissa L.},
  year = {2022},
  month = Mar,
  pages = {e1009935}
}

@article{Brazma2001,
  title = {Minimum information about a microarray experiment (MIAME)—toward standards for microarray data},
  volume = {29},
  ISSN = {1546-1718},
  url = {http://dx.doi.org/10.1038/ng1201-365},
  DOI = {10.1038/ng1201-365},
  number = {4},
  journal = {Nature Genetics},
  publisher = {Springer Science and Business Media LLC},
  author = {Brazma,  Alvis and Hingamp,  Pascal and Quackenbush,  John and Sherlock,  Gavin and Spellman,  Paul and Stoeckert,  Chris and Aach,  John and Ansorge,  Wilhelm and Ball,  Catherine A. and Causton,  Helen C. and Gaasterland,  Terry and Glenisson,  Patrick and Holstege,  Frank C.P. and Kim,  Irene F. and Markowitz,  Victor and Matese,  John C. and Parkinson,  Helen and Robinson,  Alan and Sarkans,  Ugis and Schulze-Kremer,  Steffen and Stewart,  Jason and Taylor,  Ronald and Vilo,  Jaak and Vingron,  Martin},
  year = {2001},
  month = Dec,
  pages = {365–371}
}

@article{Abassi2026,
  title = {DeeDeeExperiment: building an infrastructure for integrating and managing omics data analysis results in R/Bioconductor},
  volume = {42},
  ISSN = {1367-4811},
  url = {http://dx.doi.org/10.1093/bioinformatics/btag157},
  DOI = {10.1093/bioinformatics/btag157},
  number = {4},
  journal = {Bioinformatics},
  publisher = {Oxford University Press (OUP)},
  author = {Abassi,  Najla and Schwarz,  Lea and Filippi,  Edoardo and Marini,  Federico},
  editor = {Schwartz,  Russell},
  year = {2026},
  month = Mar
}














