Genome-wide targets identification of "core'' pluripotency transcription factors with integrated features in human embryonic stem cells
文献类型：期刊论文
| 作者 | Li, Leijie1; Chen, Zhaobin1; Zhang, Liangcai2; Liu, Guiyou3; Hua, Jinlian4; Jia, Lianghui1; Liao, Mingzhi1 |
| 刊名 | MOLECULAR BIOSYSTEMS
 |
| 出版日期 | 2016 |
| 卷号 | 12期号:4页码:1324-1332 |
| 英文摘要 | Embryonic stem cells (ESCs) play an important role in developmental biology which is still lacking clear molecular mechanisms. The "core'' transcription factors (TFs) including OCT4, SOX2 and NANOG are essential for maintaining the stemness of ESCs. But the downstream targets of these "core'' TFs are still ambiguous. Based on support vector machine (SVM) technology, this study develops a label method algorithm (LMA) for genome-wide target identification of "core'' TFs in humans, which eliminates the need for negative training samples. This method integrates histone modifications and TF binding motifs as identification features. Compared with a previous mapping-convergence (M-C) algorithm, the LMA can provide more stable and reliable predictions. 4796, 3166 and 4384 target genes of OCT4, SOX2 and NANOG, respectively, were identified with the LMA model. Then verifications of the predicted targets were carried out based on their functional consistency and their connection degree in networks from a computational system biology perspective. The results showed that the targets of "core'' TFs present higher gene functional similarity and closer connection distance than background levels. |
| WOS标题词 | Science & Technology ; Life Sciences & Biomedicine |
| 类目[WOS] | Biochemistry & Molecular Biology |
| 研究领域[WOS] | Biochemistry & Molecular Biology |
| 关键词[WOS] | BIOLOGICAL NETWORKS ; MOUSE DEVELOPMENT ; BINDING-SITES ; CANCER ; EXPRESSION ; OCT3/4 ; GENES ; VISUALIZATION ; EPIGENOMICS ; UPDATE |
| 收录类别 | SCI |
| 语种 | 英语 |
| WOS记录号 | WOS:000372612600026 |
| 源URL | [http://124.16.173.210/handle/834782/1532]  |
| 专题 | 天津工业生物技术研究所_基因组分析实验室 陈祖耕_期刊论文 |
| 作者单位 | 1.Northwest A&F Univ, Coll Life Sci, Yangling 712100, Shaanxi, Peoples R China 2.Rice Univ, Dept Stat, 6100 Main St, Houston, TX 77005 USA 3.Chinese Acad Sci, Tianjin Inst Ind Biotechnol, Genome Anal Lab, Tianjin, Peoples R China 4.Northwest A&F Univ, Shaanxi Ctr Stem Cells Engn & Technol, Coll Vet Med, Yangling 712100, Shaanxi, Peoples R China |
| 推荐引用方式 GB/T 7714 | Li, Leijie,Chen, Zhaobin,Zhang, Liangcai,et al. Genome-wide targets identification of "core'' pluripotency transcription factors with integrated features in human embryonic stem cells[J]. MOLECULAR BIOSYSTEMS,2016,12(4):1324-1332. |
| APA | Li, Leijie.,Chen, Zhaobin.,Zhang, Liangcai.,Liu, Guiyou.,Hua, Jinlian.,...&Liao, Mingzhi.(2016).Genome-wide targets identification of "core'' pluripotency transcription factors with integrated features in human embryonic stem cells.MOLECULAR BIOSYSTEMS,12(4),1324-1332. |
| MLA | Li, Leijie,et al."Genome-wide targets identification of "core'' pluripotency transcription factors with integrated features in human embryonic stem cells".MOLECULAR BIOSYSTEMS 12.4(2016):1324-1332. |
入库方式： OAI收割
来源：天津工业生物技术研究所
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