Searching journal content for articles similar to Lee et al. 14 (6): 1085.

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  1. Research: Mapping multitissue regulatory variants reveals a liver-centric coexpression network associated with duck egg-laying performance
    • Yang Xi,
    • Jingjing Qi,
    • Zhao Yang,
    • Yutian Zeng,
    • Huicong Zhang,
    • Qiuyu Tao,
    • Mengru Xu,
    • Anqi Huang,
    • Shenqiang Hu,
    • Chunchun Han,
    • Lili Bai,
    • Jiwei Hu,
    • Jiwen Wang,
    • Liang Li,
    • Lingzhao Fang,
    • and Hehe Liu
    Genome Res. October 2025 35: 2211-2225; Published in Advance September 10, 2025, doi:10.1101/gr.280345.124
    ..., we performed weighted gene coexpression network analysis (WGCNA) across four tissues (Supplemental Fig. S8A). The analysis revealed that LOC101800576 and LOC101790890 were assigned to the shell gland ME3 module, GLP2R to the spleen ME7 module, and LOC119713219 to the ovary ME6 module (Supplemental...
  2. Method: Bayesian inference of sample-specific coexpression networks
    • Enakshi Saha,
    • Viola Fanfani,
    • Panagiotis Mandros,
    • Marouen Ben Guebila,
    • Jonas Fischer,
    • Katherine H. Shutta,
    • Dawn L. DeMeo,
    • Camila M. Lopes-Ramos,
    • and John Quackenbush
    Genome Res. September 2024 34: 1397-1410; Published in Advance August 12, 2024, doi:10.1101/gr.279117.124
    ...and so fail to fully capture population heterogeneity. Bayesian optimized networks obtained by assimilating omic data (BONOBO) is a scalable Bayesian model for deriving individual sample-specific coexpression matrices that recognizes variations in molecular interactions across individuals. For each...
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  3. Research: Transcriptional modulation unique to vulnerable motor neurons predicts ALS across species and SOD1 mutations
    • Irene Mei,
    • Susanne Nichterwitz,
    • Melanie Leboeuf,
    • Jik Nijssen,
    • Isadora Lenoel,
    • Dirk Repsilber,
    • Christian S. Lobsiger,
    • and Eva Hedlund
    Genome Res. September 2025 35: 1975-1991; Published in Advance July 17, 2025, doi:10.1101/gr.279501.124
    .../4 and spinal MNs). The initial analysis showed that only 17 DEGs were shared across all data sets (Supplemental Fig. S6A,B). RNA-seq data sets revealed a substantially larger number of DEGs between CN3/4 and spinal MNs compared with microarray analyses (Supplemental Fig. S6A), and we thus focused on the RNA...
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  4. Method: Characterizing the targets of transcription regulators by aggregating ChIP-seq and perturbation expression data sets
    • Alexander Morin,
    • Eric Ching-Pan Chu,
    • Aman Sharma,
    • Alex Adrian-Hamazaki,
    • and Paul Pavlidis
    Genome Res. May 2023 33: 763-778; Published in Advance June 12, 2023, doi:10.1101/gr.277273.122
    ...and mouse TR–target interactions.Here we outline a framework to identify and rank experimentally derived TR–target relationships by aggregating ChIP-seq and perturbation data sets from both mouse and human. We describe the degree of similarity across experiments and note characteristics of each data type...
  5. Research: Untangling the effects of cellular composition on coexpression analysis
    • Marjan Farahbod and
    • Paul Pavlidis
    Genome Res. June 2020 30: 849-859; Published in Advance June 24, 2020, doi:10.1101/gr.256735.119
    ...observed are likely dominated by differential expression across cell types, not coexpression within cell types (Aibar et al. 2017).Our study does have some limitations. First, our analysis of cell-type-level coexpression is based on a single (albeit large and unusually deeply sequenced) data set that used...
  6. Method: Multi–cell type gene coexpression network analysis reveals coordinated interferon response and cross–cell type correlations in systemic lupus erythematosus
    • Bharat Panwar,
    • Benjamin J. Schmiedel,
    • Shu Liang,
    • Brandie White,
    • Enrique Rodriguez,
    • Kenneth Kalunian,
    • Andrew J. McKnight,
    • Rachel Soloff,
    • Gregory Seumois,
    • Pandurangan Vijayanand,
    • and Ferhat Ay
    Genome Res. April 2021 31: 659-676; Published in Advance March 5, 2021, doi:10.1101/gr.265249.120
    ...-based stratification of SLE patients is relatively stable across their longitudinal samples and the relationship between changes in gene transcriptome-derived status and changes in the plasma levels of specific pro-inflammatory cytokines or chemokines is not one-to-one.Weighted gene coexpression network analysis...
  7. Research: Coexpression enrichment analysis at the single-cell level reveals convergent defects in neural progenitor cells and their cell-type transitions in neurodevelopmental disorders
    • Kaifang Pang,
    • Li Wang,
    • Wei Wang,
    • Jian Zhou,
    • Chao Cheng,
    • Kihoon Han,
    • Huda Y. Zoghbi,
    • and Zhandong Liu
    Genome Res. June 2020 30: 835-848; Published in Advance June 18, 2020, doi:10.1101/gr.254987.119
    ...Table S1A).We calculated coexpression fold enrichment scores for the eight NDD gene sets and four control gene sets across the six major cell types (Fig. 1A; Supplemental Fig. S2). In general, NDD gene sets showed significantly higher coexpression than control gene sets (Fig. 1A; Supplemental Figs. S2...
  8. Resource: An 11-point time course midgut transcriptome across 72 h after bloodfeeding provides detailed temporal resolution of transcript expression in the arbovirus vector, Aedes aegypti
    • Hitoshi Tsujimoto and
    • Zach N. Adelman
    Genome Res. September 2023 33: 1638-1648; Published in Advance October 6, 2023, doi:10.1101/gr.277808.123
    ...against viruses. Despite its importance, transcriptomic dynamics with fine temporal resolution across the entire digestion cycle have not yet been reported. To fill this gap, we conducted a transcriptomic analysis of A. aegypti female midguts across a 72-h bloodmeal digestion cycle for 11 time points...
  9. Method: Analysis of coding gene expression from small RNA sequencing
    • Aygun Azadova,
    • Anthonia Ekperuoh,
    • Greg N. Brooke,
    • and Antonio Marco
    Genome Res. March 2026 36: 611-618; Published in Advance February 10, 2026, doi:10.1101/gr.281364.125
    ...transcripts derived from sRNA-seq data sets are comparable to those from total RNA-seq experiments (R2 ranging from 0.33 to 0.76). Analyses across multiple tissues and species show similar correlations, indicating that the approach is applicable across organisms. We confirm that transcript half...
  10. Research: Global regulatory features of alternative splicing across tissues and within the nervous system of C. elegans
    • Bina Koterniak,
    • Pallavi P. Pilaka,
    • Xicotencatl Gracida,
    • Lisa-Marie Schneider,
    • Iva Pritišanac,
    • Yun Zhang,
    • and John A. Calarco
    Genome Res. December 2020 30: 1766-1780; Published in Advance October 30, 2020, doi:10.1101/gr.267328.120
    ...uniquely mapped reads were aligned across all data sets, with summed coverage for each tissue-enriched or cell type–enriched transcriptome ranging from over 100 million to over 300 million reads (Supplemental Fig. S1).View larger version: In this window In a new window Figure 1. TRAP-seq identifies tissue...
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