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X-ORIGINAL-URL:https://www.ibs.re.kr/bimag
X-WR-CALDESC:Events for Biomedical Mathematics Group
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TZID:Asia/Seoul
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TZOFFSETFROM:+0900
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DTSTART:20230101T000000
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DTSTART;TZID=Asia/Seoul:20240117T110000
DTEND;TZID=Asia/Seoul:20240117T120000
DTSTAMP:20260505T110304
CREATED:20240111T072709Z
LAST-MODIFIED:20240111T073014Z
UID:9084-1705489200-1705492800@www.ibs.re.kr
SUMMARY:Junil Kim\, TENET+: a tool for reconstructing gene networks by integrating single cell expression and chromatin accessibility data
DESCRIPTION:Abstract: Reconstruction of gene regulatory networks (GRNs) is a powerful approach to capture a prioritized gene set controlling cellular processes. In our previous study\, we developed TENET a GRN reconstructor from single cell RNA sequencing (scRNAseq). TENET has a superior capability to identify key regulators compared with other algorithms. However\, accurate inference of gene regulation is still challenging. Here\, we suggest an integrative strategy called TENET+ by combining single cell transcriptome and chromatin accessibility data. TENET+ predicts target genes and open chromatin regions associated with transcription factors (TFs) and links the target regions to their corresponding target gene. As a result\, TENET+ can infer regulatory triplets of TF\, target gene\, and enhancer. By applying TENET+ to a paired scRNAseq and scATACseq dataset of human peripheral blood mononuclear cells\, we found critical regulators and their epigenetic regulations for the differentiations of CD4 T cells\, CD8 T cells\, B cells and monocytes. Interestingly\, not only did TENET+ predict several top regulators of each cell type which were not predicted by the motif-based tool SCENIC\, but we also found that TENET+ outperformed SCENIC in prioritizing critical regulators by using a cell type associated gene list. Furthermore\, utilizing and modeling regulatory triplets\, we can infer a comprehensive epigenetic GRN. In sum\, TENET+ is a tool predicting epigenetic gene regulatory programs for various types of datasets in an unbiased way\, suggesting that novel epigenetic regulations can be identified by TENET+. \nGithub page: https://github.com/hg0426/TENETPLUS.
URL:https://www.ibs.re.kr/bimag/event/junil-kim-tenet-a-tool-for-reconstructing-gene-networks-by-integrating-single-cell-expression-and-chromatin-accessibility-data/
LOCATION:B232 Seminar Room\, IBS\, 55 Expo-ro Yuseong-gu\, Daejeon\, Daejeon\, 34126\, Korea\, Republic of
CATEGORIES:Biomedical Mathematics Seminar
ATTACH;FMTTYPE=image/jpeg:https://www.ibs.re.kr/bimag/cms/wp-content/uploads/2024/01/프로필사진-e1704958090187.jpg
ORGANIZER;CN="Jae Kyoung Kim":MAILTO:jaekkim@kaist.ac.kr
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