title: Genome-wide targets identification of "core" pluripotency transcription factors with integrated features in human embryonic stem cells.
abstract: 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.
authors.affiliation: College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China. liaomingzhi83@163.com jialianghui@nwsuaf.edu.cn.
authors.forename: Leijie
authors.initials: L
authors.lastname: Li
authors.forename: Zhaobin
authors.initials: Z
authors.lastname: Chen
authors.forename: Liangcai
authors.initials: L
authors.lastname: Zhang
authors.forename: Guiyou
authors.initials: G
authors.lastname: Liu
authors.forename: Jinlian
authors.initials: J
authors.lastname: Hua
authors.forename: Lianghui
authors.initials: L
authors.lastname: Jia
authors.forename: Mingzhi
authors.initials: M
authors.lastname: Liao
mesh_terms: D000066673:Cell Self Renewal / Q000235:genetics; D019295:Computational Biology / Q000379:methods; D030541:Databases, Genetic; D005786:Gene Expression Regulation; D055106:Genome-Wide Association Study; D000066449:Human Embryonic Stem Cells / Q000166:cytology / Q000378:metabolism*; D006801:Humans; D008954:Models, Biological; D015233:Models, Statistical; D025941:Protein Interaction Mapping; D012323:RNA Processing, Post-Transcriptional; D012372:ROC Curve; D015203:Reproducibility of Results; D014157:Transcription Factors / Q000235:genetics* / Q000378:metabolism
chemical_list: D014157:Transcription Factors