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Research: Coexpression patterns define epigenetic regulators associated with neurological dysfunction
- Leandros Boukas,
- James M. Havrilla,
- Peter F. Hickey,
- Aaron R. Quinlan,
- Hans T. Bjornsson,
- and Kasper D. Hansen
Genome Res. April 2019 29: 532-542; Published in Advance March 11, 2019, doi:10.1101/gr.239442.118
.... Therefore, we hypothesized that EM genes whose expression patterns display this coordinated behavior (coexpression) would differ in their mutational constraint from those who do not. To test this, we constructed tissue-specific coexpression networks and determined modules of coexpressed genes using Weighted...
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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
...motor-somatosensory cortex are a key point of ASD gene convergence (Willsey et al. 2013). Integrating gene coexpression with protein–protein interaction networks to identify modules that enrich for genes mutated in several NDDs revealed that different NDDs share a major point of gene convergence during...
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Method: Targeted single-cell RNA sequencing of transcription factors enhances the identification of cell types and trajectories
- Alexandra Pokhilko,
- Adam E. Handel,
- Fabiola Curion,
- Viola Volpato,
- Emma S. Whiteley,
- Sunniva Bøstrand,
- Sarah E. Newey,
- Colin J. Akerman,
- Caleb Webber,
- Michael B. Clark,
- Rory Bowden,
- and M. Zameel Cader
Genome Res. June 2021 31: 1069-1081; Published in Advance May 19, 2021, doi:10.1101/gr.273961.120
...into either excitatory cortical neurons or inhibitory interneurons. Furthermore, scCapture-seq revealed a role for of retinoic acid signaling in the developmental divergence between these different neuronal populations. Our results show that TF targeting improves the characterization of human cellular models...
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Research: The clustering of functionally related genes contributes to CNV-mediated disease
- Tallulah Andrews,
- Frantisek Honti,
- Rolph Pfundt,
- Nicole de Leeuw,
- Jayne Hehir-Kwa,
- Anneke Vulto-van Silfhout,
- Bert de Vries,
- and Caleb Webber
Genome Res. June 2015 25: 802-813; Published in Advance April 17, 2015, doi:10.1101/gr.184325.114
...genes is a frequent and significant characteristic of de novo CNVs in patients with developmental disorders ( P = 1 × 10 −3 ). Using three different functional networks, we identified unexpectedly large numbers of functionally related genes within de novo CNVs from two large independent cohorts...
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Research: Loss of transcriptional control over endogenous retroelements during reprogramming to pluripotency
- Marc Friedli,
- Priscilla Turelli,
- Adamandia Kapopoulou,
- Benjamin Rauwel,
- Nathaly Castro-Díaz,
- Helen M. Rowe,
- Gabriela Ecco,
- Carmen Unzu,
- Evarist Planet,
- Angelo Lombardo,
- Bastien Mangeat,
- Barbara E. Wildhaber,
- Luigi Naldini,
- and Didier Trono
Genome Res. August 2014 24: 1251-1259; Published in Advance May 30, 2014, doi:10.1101/gr.172809.114
...and transcriptional perturbators is suppressed by early embryonic epigenetic silencing. Here, we asked how ERE control is maintained during the generation of induced pluripotent stem cells (iPSCs), as this procedure involves profound epigenetic remodeling. We found that all EREs tested were markedly up...
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Research: Alternative transcription exceeds alternative splicing in generating the transcriptome diversity of cerebellar development
- Sharmistha Pal,
- Ravi Gupta,
- Hyunsoo Kim,
- Priyankara Wickramasinghe,
- Valérie Baubet,
- Louise C. Showe,
- Nadia Dahmane,
- and Ramana V. Davuluri
Genome Res. August 2011 21: 1260-1272; Published in Advance June 28, 2011, doi:10.1101/gr.120535.111
...an important aspect of biological networks. Therefore, acquiring the knowledge of all possible gene isoforms and their in vivo expression patterns in specific cell populations and tissues, as well as their developmental 4 These authors contributed equally to this work. 5Corresponding author. E-mail rdavuluri...
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Research: Autism spectrum disorder risk genes have convergent effects on transcription and neuronal firing patterns in primary neurons
- Alekh Paranjapye,
- Rili Ahmad,
- Steven Su,
- Abraham J. Waldman,
- Jennifer E. Phillips-Cremins,
- Shuo Zhang,
- and Erica Korb
Genome Res. November 2025 35: 2433-2444; Published in Advance October 20, 2025, doi:10.1101/gr.280698.125
...influenced by ASD-linked transcriptional regulatorsNext, we sought to expand these comparisons using more sensitive measures. We therefore used weighted gene coexpression network analysis (WGCNA) (Zhang and Horvath 2005) to capture system-level changes associated with the depletion of ASD...
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Research: Genome-wide, integrative analysis of circular RNA dysregulation and the corresponding circular RNA-microRNA-mRNA regulatory axes in autism
- Yen-Ju Chen,
- Chia-Ying Chen,
- Te-Lun Mai,
- Chih-Fan Chuang,
- Yu-Chen Chen,
- Sachin Kumar Gupta,
- Laising Yen,
- Yi-Da Wang,
- and Trees-Juen Chuang
Genome Res. March 2020 30: 375-391; Published in Advance March 3, 2020, doi:10.1101/gr.255463.119
...such as brain region, age, sex, RIN, brain bank, and PMI did not drive the similar clustering (Fig. 1I). Our result thus revealed a shared circRNA dysregulation signature among the majority of ASD samples.Construction of signed coexpression networks of circRNA dysregulation in ASDTo probe the correlation...
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Research: Human-specific features of spatial gene expression and regulation in eight brain regions
- Chuan Xu,
- Qian Li,
- Olga Efimova,
- Liu He,
- Shoji Tatsumoto,
- Vita Stepanova,
- Takao Oishi,
- Toshifumi Udono,
- Katsushi Yamaguchi,
- Shuji Shigenobu,
- Akiyoshi Kakita,
- Hiroyuki Nawa,
- Philipp Khaitovich,
- and Yasuhiro Go
Genome Res. August 2018 28: 1097-1110; Published in Advance June 13, 2018, doi:10.1101/gr.231357.117
...hippocampus. Furthermore, an analysis of the coexpression network revealed an additional module (module 16) closely linked to module 22 and showing human-specific hippocampal overexpression of a smaller magnitude (Fig. 6; Supplemental Fig. S9). This result is notable, because the hippocampus is central...
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