دورية أكاديمية
A transcriptomic dataset used to derive biomarkers of chemically induced histone deacetylase inhibition (HDACi) in human TK6 cells
| العنوان: | A transcriptomic dataset used to derive biomarkers of chemically induced histone deacetylase inhibition (HDACi) in human TK6 cells |
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| المؤلفون: | Eunnara Cho, Andrew Williams, Carole L. Yauk |
| المصدر: | Data in Brief, Vol 36, Iss , Pp 107097- (2021) |
| بيانات النشر: | Elsevier, 2021. |
| سنة النشر: | 2021 |
| المجموعة: | LCC:Computer applications to medicine. Medical informatics LCC:Science (General) |
| مصطلحات موضوعية: | Transcriptomic biomarker, Toxicogenomics, Predictive toxicology, Histone deacetylase inhibition, TempO-Seq, Epigenetics, Computer applications to medicine. Medical informatics, R858-859.7, Science (General), Q1-390 |
| الوصف: | Transcriptomic biomarkers facilitate mode of action analysis of toxicants by detecting specific patterns of gene expression perturbations. We identified an 81-gene transcriptomic biomarker of histone deacetylase inhibitors (HDACi) using whole transcriptome data sets of TK6 human lymphoblastoid cells generated by Templated Oligo-Sequencing (TempO-Seq) after 4 h of exposure to 20 reference compounds (10 HDACi and 10 non-HDACi) [1]. The biomarker, named TGx-HDACi, was derived using the nearest shrunken centroid (NSC) method and can distinguish HDACi from non-HDACi compounds based on the expression pattern across the 81 genes. The classification capability of TGx-HDACi was evaluated by NSC probability analysis of 11 external validation compounds (4 HDACi and 7 non-HDACi) with a probability cut-off of 90%. Thus far, TGx-HDACi has demonstrated 100% accuracy in classifying the reference and validation compounds as HDACi or non-HDACi. Of the 81 TGx-HDACi genes, 19 genes are part of the S1500+ gene panel containing 2753 genes, developed for toxicological assessments [2]. Herein, we assessed the classification performance of the biomarker with this reduced gene set to determine if TGx-HDACi can be applied to analyze S1500+ gene expression profiles. The 20 reference compounds and 11 validation compounds were correctly classified as HDACi or non-HDACi by the NSC probability analysis, principal component analysis, and hierarchical clustering based on the expression of the 19 genes, demonstrating 100% accuracy. |
| نوع الوثيقة: | article |
| وصف الملف: | electronic resource |
| اللغة: | English |
| تدمد: | 2352-3409 |
| Relation: | http://www.sciencedirect.com/science/article/pii/S2352340921003814; https://doaj.org/toc/2352-3409 |
| DOI: | 10.1016/j.dib.2021.107097 |
| URL الوصول: | https://doaj.org/article/b268d15265e64edeb14a73dd5ce35bcf |
| رقم الأكسشن: | edsdoj.b268d15265e64edeb14a73dd5ce35bcf |
| قاعدة البيانات: | Directory of Open Access Journals |
Full Text Finder | تدمد: | 23523409 |
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| DOI: | 10.1016/j.dib.2021.107097 |