TENET: Tracing Enhancer Networks using Epigenetic Traits
TENET is developed to identify key transcriptional regulators such as transcription factors and enhancers linked to a specific cell type.
Please visit our github page, https://github.com/rhielab/TENET_2.0 and see Rhie et al (PMID: 27833659) and Mullen et al (PMID: 32925947) for its usage.
Citation
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Mullen DJ, Yan C, Kang DL, Zhou B, Borok Z, Marconett CN, Farnham PJ, Offringa IA, Rhie SK TENET 2.0: identification of key transcriptional regulators and enhancers in lung adenocarcinoma Plos Genetics 2020 Sep 14;16(9):e1009023. PMID: 32925947 Rhie SK, Guo Y, Tak YG, Yao L, Shen H, Coetzee GA, Laird PW, Farnham PJ Identification of activated enhancers and linked transcription factors in breast prostate and kidney tumors by Tracing Enhancer Networks using Epigenetic Traits Epigenetics Chromatin 2016 Nov 9;9:50 PMID: 27833659 |
3D Genome Project
In-house developed scripts to analyze Hi-C, Micro-C, and promoter capture Micro-C data are published.
Please visit our github page, https://github.com/rhielab/3Dgenome and see Lee et al (PMID: 36544209) for its usage.
Citation
Lee, B.H., Wu, Z. & Rhie, S.K. Characterizing chromatin interactions of regulatory elements and nucleosome positions, using Hi-C, Micro-C, and promoter capture Micro-C. Epigenetics & Chromatin 2022 Dec 21;15(1):41. https://doi.org/10.1186/s13072-022-00473-4 PMID: 36544209
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Lee, B.H., Wu, Z. & Rhie, S.K. Characterizing chromatin interactions of regulatory elements and nucleosome positions, using Hi-C, Micro-C, and promoter capture Micro-C. Epigenetics & Chromatin 2022 Dec 21;15(1):41. https://doi.org/10.1186/s13072-022-00473-4 PMID: 36544209 |