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Method: Whole-genome analysis of noncoding genetic variations identifies multiscale regulatory element perturbations associated with Hirschsprung disease
- Alexander Xi Fu,
- Kathy Nga-Chu Lui,
- Clara Sze-Man Tang,
- Ray Kit Ng,
- Frank Pui-Ling Lai,
- Sin-Ting Lau,
- Zhixin Li,
- Maria-Mercè Garcia-Barcelo,
- Pak-Chung Sham,
- Paul Kwong-Hang Tam,
- Elly Sau-Wai Ngan,
- and Kevin Y. Yip
Genome Res. November 2020 30: 1618-1632; Published in Advance September 18, 2020, doi:10.1101/gr.264473.120
...analysis, in which some of the 417 genes loosely associated with S-HSCR were grouped into functional clusters that are highly related to NC migration.Our analysis of upstream regulators has identified 48 recurrent TFs, and they form an extensive network through PPIs. Notably, some of these TFs also have...
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Research: Oncogenic ETS fusions deregulate E2F3 target genes in Ewing sarcoma and prostate cancer
- Sven Bilke,
- Raphaela Schwentner,
- Fan Yang,
- Maximilian Kauer,
- Gunhild Jug,
- Robert L. Walker,
- Sean Davis,
- Yuelin J. Zhu,
- Marbin Pineda,
- Paul S. Meltzer,
- and Heinrich Kovar
Genome Res. November 2013 23: 1797-1809; Published in Advance August 12, 2013, doi:10.1101/gr.151340.112
...that there is a binding event. Even though these two observations are related by Bayes’ theorem, they are mutually independent, as discussed in detail in the Supplemental Material. Bilke et al. 1802 Genome Research www..org Together, these results demonstrate that EWSR1/FLI1 regulates distinct sets of target genes...
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Method: Guide Positioning Sequencing identifies aberrant DNA methylation patterns that alter cell identity and tumor-immune surveillance networks
- Jin Li,
- Yan Li,
- Wei Li,
- Huaibing Luo,
- Yanping Xi,
- Shihua Dong,
- Ming Gao,
- Peng Xu,
- Baolong Zhang,
- Ying Liang,
- Qingping Zou,
- Xin Hu,
- Lina Peng,
- Dan Zou,
- Ting Wang,
- Hongbo Yang,
- Cizhong Jiang,
- Shaoliang Peng,
- Feizhen Wu,
- and Wenqiang Yu
Genome Res. February 2019 29: 270-280; Published in Advance January 22, 2019, doi:10.1101/gr.240606.118
...) in the promoter region modulates gene expression. (A) MBS in 97L cells displaying MBS extension to the upstream or downstream from TSS compared with Liver cells. Genes are arranged from top to bottom according to the length and direction of MBS. (B) H3K4me3 and H3K36me3 in 97L display a mutually exclusive...
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Method: Single-cell RNA-seq analysis identifies markers of resistance to targeted BRAF inhibitors in melanoma cell populations
- Yu-Jui Ho,
- Naishitha Anaparthy,
- David Molik,
- Grinu Mathew,
- Toby Aicher,
- Ami Patel,
- James Hicks,
- and Molly Gale Hammell
Genome Res. September 2018 28: 1353-1363; Published in Advance July 30, 2018, doi:10.1101/gr.234062.117
...served as the reference, and normalized mutual information (NMI, shown in Fig. 2C) or adjusted Rand Index (ARI, shown in Supplemental Fig. S1) was used to evaluate the performance of SAKE compared with a number of recently published algorithms with demonstrated performance for scRNA-seq analysis: SINCERA...
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Research: Delineation of key regulatory elements identifies points of vulnerability in the mitogen-activated signaling network
- Noor Jailkhani,
- Srikanth Ravichandran,
- Shubhada R. Hegde,
- Zaved Siddiqui,
- Shekhar C. Mande,
- and Kanury V.S. Rao
Genome Res. December 2011 21: 2067-2081; Published in Advance August 24, 2011, doi:10.1101/gr.116145.110
...against cancer are often hampered by the complex properties of signaling networks. Here we combined the results of an RNAi screen targeting the cellular signaling machinery, with graph theoretical analysis to extract the core modules that process both mitogenic and oncogenic signals to drive cell cycle...
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Method: Diffusion-based generation of gene regulatory networks from scRNA-seq data with DigNet
- Chuanyuan Wang and
- Zhi-Ping Liu
Genome Res. February 2025 35: 340-354; Published in Advance December 18, 2024, doi:10.1101/gr.279551.124
...and Li 2017), PIDC (Chan et al. 2017), SCENIC (Aibar et al. 2017), SCODE (Matsumoto et al. 2017), SINCERITIES (Papili Gao et al. 2018), and Tigress (Haury et al. 2012), along with mutual information (MI)– and Pearson correlation coefficient (PCC)–based methods as baselines (Supplemental Table S7...
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Resource: A temporal in vivo catalog of chromatin accessibility and expression profiles in pineoblastoma reveals a prevalent role for repressor elements
- Salam Idriss,
- Mohammad Hallal,
- Abdullah El-Kurdi,
- Hasan Zalzali,
- Inaam El-Rassi,
- Erik A. Ehli,
- Christel M. Davis,
- Philip E.D. Chung,
- Deena M.A. Gendoo,
- Eldad Zacksenhaus,
- Raya Saab,
- and Pierre Khoueiry
Genome Res. February 2023 33: 269-282; Published in Advance January 17, 2023, doi:10.1101/gr.277037.122
...in DROSHA, which acts upstream of DICER1 in the miRNA processing cascade, in a subset of human PB tumors (Snuderl et al. 2018). Recent molecular classification identified several PB subgroups with distinct survival and clinical features (Li et al. 2020). Although the oncogenic landscape of PB in each...
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Method: Marker-free characterization of full-length transcriptomes of single live circulating tumor cells
- Sarita Poonia,
- Anurag Goel,
- Smriti Chawla,
- Namrata Bhattacharya,
- Priyadarshini Rai,
- Yi Fang Lee,
- Yoon Sim Yap,
- Jay West,
- Ali Asgar Bhagat,
- Juhi Tayal,
- Anurag Mehta,
- Gaurav Ahuja,
- Angshul Majumdar,
- Naveen Ramalingam,
- and Debarka Sengupta
Genome Res. January 2023 33: 80-95; Published in Advance November 22, 2022, doi:10.1101/gr.276600.122
...). For objective assessment of cluster qualities, we evaluated three frequently used metrics, namely, adjusted Rand index (ARI), normalized mutual information (NMI), and cluster purity for clusters produced by different methods under comparison. unCTC clearly outperformed the existing methods (Supplemental Figs. S...
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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
...similarity using four different metrics: adjusted rand score (ARI), adjusted mutual info score (AMI), completeness, and Fowlkes–Mallows score. Greater values indicate that the clusters group samples grown in the same media. (C) Clustering performance on top1k networks using the same protocol as in B. Sparse...
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Perspective: Cancer cell states and emergent properties of the dynamic tumor system
- Dalia Barkley,
- Anjali Rao,
- Maayan Pour,
- Gustavo S. França,
- and Itai Yanai
Genome Res. October 2021 31: 1719-1727; doi:10.1101/gr.275308.121
...in particular contexts.Collectively, these approaches allow for the description of a cancer cell state according to the expression of one or more gene modules (Fig. 1B). Unlike the programs underlying cell types, which are more stably defined by mutually exclusive differentiation determinants, these modules can...

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