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Method: Identification of phenotype-specific networks from paired gene expression–cell shape imaging data
- Charlie George Barker,
- Eirini Petsalaki,
- Girolamo Giudice,
- Julia Sero,
- Emmanuel Nsa Ekpenyong,
- Chris Bakal,
- and Evangelia Petsalaki
Genome Res. April 2022 32: 750-765; Published in Advance February 23, 2022, doi:10.1101/gr.276059.121
.... However, the exact regulatory systems that define these changes remain poorly characterized. In this study, we used a network-systems approach to integrate imaging data and RNA-seq expression data. Our workflow allowed the discovery of unbiased and context-specific gene expression signatures and cell...
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Resource: Quantitative RNA-seq meta-analysis of alternative exon usage in C. elegans
- Nicolas J. Tourasse,
- Jonathan R.M. Millet,
- and Denis Dupuy
Genome Res. December 2017 27: 2120-2128; Published in Advance October 31, 2017, doi:10.1101/gr.224626.117
...splicing is tolerated is still heavily debated. Here we gathered a compendium of 1682 publicly available C. elegans RNA-seq data sets to increase the dynamic range of detection of RNA isoforms, and obtained robust measurements of the relative abundance of each splicing event. While most of the splicing...
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Research: Integrative analysis of C. elegans modENCODE ChIP-seq data sets to infer gene regulatory interactions
- Eric L. Van Nostrand and
- Stuart K. Kim
Genome Res. June 2013 23: 941-953; Published in Advance March 26, 2013, doi:10.1101/gr.152876.112
...Integrative analysis of C. elegans modENCODE ChIP-seq data sets to infer gene regulatory interactions Eric L. Van Nostrand 1 and Stuart K. Kim 2 Department of Genetics and Department of Developmental Biology, Stanford University Medical Center, Stanford...
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Research: Transcription factor redundancy and tissue-specific regulation: Evidence from functional and physical network connectivity
- Steven G. Kuntz,
- Brian A. Williams,
- Paul W. Sternberg,
- and Barbara J. Wold
Genome Res. October 2012 22: 1907-1919; Published in Advance June 22, 2012, doi:10.1101/gr.133306.111
...cells expressing only HLH-1, 16 NSM cells expressing only hlh-8, and twononmuscle coelomocytes (Sulston and Horvitz 1977). Themolecular and regulatory relationship of BWM and NSM networks is a second focus of this work, based on our findings of crosstalk between them. Here, we construct a C. elegans BWM...
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Research: Dynamic landscape of tandem 3′ UTRs during zebrafish development
- Yuxin Li,
- Yu Sun,
- Yonggui Fu,
- Mengzhen Li,
- Guangrui Huang,
- Chenxu Zhang,
- Jiahui Liang,
- Shengfeng Huang,
- Gaoyang Shen,
- Shaochun Yuan,
- Liangfu Chen,
- Shangwu Chen,
- and Anlong Xu
Genome Res. October 2012 22: 1899-1906; Published in Advance September 5, 2012, doi:10.1101/gr.128488.111
....] Embryonic development involves a series of complex but ordered cellular processes including cell proliferation, differentiation, and migration under robust and precise management by gene regulatory networks (Gilbert 2003). As a major regulatory region terminating a transcribedmRNA, the 39UTRplays important...
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Research: Combinatorial microRNA activity is essential for the transition of pluripotent cells from proliferation into dormancy
- Dhanur P. Iyer,
- Lambert Moyon,
- Lars Wittler,
- Chieh-Yu Cheng,
- Francisca R. Ringeling,
- Stefan Canzar,
- Annalisa Marsico,
- and Aydan Bulut-Karslioğlu
Genome Res. April 2024 34: 572-589; Published in Advance May 6, 2024, doi:10.1101/gr.278662.123
...the top 25 highest scoring connections. Notably, miR-92, which is an insulin-dependent regulator of L1 diapause in C. elegans (Kasuga et al. 2013), was found up-regulated in paused ESCs and is part of the ESC network (Supplemental Fig. S7), suggesting a prominent role in pluripotent cells.In summary, we...
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Resource: GenomeMUSter mouse genetic variation service enables multitrait, multipopulation data integration and analysis
- Robyn L. Ball,
- Molly A. Bogue,
- Hongping Liang,
- Anuj Srivastava,
- David G. Ashbrook,
- Anna Lamoureux,
- Matthew W. Gerring,
- Alexander S. Hatoum,
- Matthew J. Kim,
- Hao He,
- Jake Emerson,
- Alexander K. Berger,
- David O. Walton,
- Keith Sheppard,
- Baha El Kassaby,
- Francisco Castellanos,
- Govindarajan Kunde-Ramamoorthy,
- Lu Lu,
- John Bluis,
- Sejal Desai,
- Beth A. Sundberg,
- Gary Peltz,
- Zhuoqing Fang,
- Gary A. Churchill,
- Robert W. Williams,
- Arpana Agrawal,
- Carol J. Bult,
- Vivek M. Philip,
- and Elissa J. Chesler
Genome Res. January 2024 34: 145-159; Published in Advance January 30, 2024, doi:10.1101/gr.278157.123
...to perform robust and integrative genetic analyses, such as meta-analysis of -wide association studies (GWAS), with adequate power and density. Therefore, an integrated data resource is needed.Prior efforts to harmonize variant data sets and address the sparsity of data incorporated known or inferred...
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Research: Characterization of transcript enrichment and detection bias in single-nucleus RNA-seq for mapping of distinct human adipocyte lineages
- Anushka Gupta,
- Farnaz Shamsi,
- Nicolas Altemose,
- Gabriel F. Dorlhiac,
- Aaron M. Cypess,
- Andrew P. White,
- Nir Yosef,
- Mary Elizabeth Patti,
- Yu-Hua Tseng,
- and Aaron Streets
Genome Res. February 2022 32: 242-257; Published in Advance January 18, 2022, doi:10.1101/gr.275509.121
..., right panel). Indeed, top marker genes for each cluster recovered previously reported expression trends such as enrichment of ECM components in day-0 preadipocytes (Weiner et al. 1989), enrichment of insulin-binding proteins in day-20 preadipocytes (Gleason et al. 2010), and enrichment of adipogenic...
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Research: Circadian gene variants and the skeletal muscle circadian clock contribute to the evolutionary divergence in longevity across Drosophila populations
- Liam C. Hunt,
- Jianqin Jiao,
- Yong-Dong Wang,
- David Finkelstein,
- Deepti Rao,
- Michelle Curley,
- Maricela Robles-Murguia,
- Abbas Shirinifard,
- Vishwajeeth R. Pagala,
- Junmin Peng,
- Yiping Fan,
- and Fabio Demontis
Genome Res. August 2019 29: 1262-1276; Published in Advance June 27, 2019, doi:10.1101/gr.246884.118
...) and Caenorhabditis elegans (Herndon et al. 2002), suggesting that skeletal muscle aging precedes and influences the aging of other tissues. Moreover, epidemiological studies in humans have established that age-related skeletal muscle weakness is the best predictor of mortality and morbidity (Metter et al. 2002; Ruiz...
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Method: End Sequence Analysis Toolkit (ESAT) expands the extractable information from single-cell RNA-seq data
- Alan Derr,
- Chaoxing Yang,
- Rapolas Zilionis,
- Alexey Sergushichev,
- David M. Blodgett,
- Sambra Redick,
- Rita Bortell,
- Jeremy Luban,
- David M. Harlan,
- Sebastian Kadener,
- Dale L. Greiner,
- Allon Klein,
- Maxim N. Artyomov,
- and Manuel Garber
Genome Res. October 2016 26: 1397-1410; Published in Advance July 28, 2016, doi:10.1101/gr.207902.116
...by providing a search step in which it identifies possible unannotated ends de novo. It provides a robust handling of multimapped reads, which is critical in 3′ DGE analysis. ESAT provides a module specifically designed for alternative start or 3′ UTR (untranslated region) differential isoform expression...
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