.png){kind=icon}
返回
Transfer String Kernel for Cross-Context DNA-Protein Binding Prediction
.png){kind=icon}
OA
AI
DOI：10.1109/TCBB.2016.2609918.png)
.png){kind=icon}
.png){kind=icon}
分享.png){kind=icon}
收藏
摘要
En 中文
Through sequence-based classification, this paper tries to accurately predict the DNA binding sites of transcription factors (TFs) in an unannotated cellular context. Related methods in the literature fail to perform such predictions accurately, since they do not consider sample distribution shift of sequence segments from an annotated (source) context to an unannotated (target) context. We, therefore, propose a method called Transfer String Kernel (TSK) that achieves improved prediction of transcription factor binding site (TFBS) using knowledge transfer via cross-context sample adaptation. TSK maps sequence segments to a high-dimensional feature space using a discriminative mismatch string kernel framework. In this high-dimensional space, labeled examples of the source context are re-weighted so that the revised sample distribution matches the target context more closely. We have experimentally verified TSK for TFBS identifications on 14 different TFs under a cross-organism setting. We find that TSK consistently outperforms the state-of-the-art TFBS tools, especially when working with TFs whose binding sequences are not conserved across contexts. We also demonstrate the generalizability of TSK by showing its cutting-edge performance on a different set of cross-context tasks for the MHC peptide binding predictions.
Keyword:
Context
Kernel
Genomics
DNA
Proteins
Support vector machines
Bioinformatics
Machine learning
bioinformatics
support vector machines
domain adaptation
string classification
string kernel
AI总结
对已上传原文的论文进行重点信息的提取，主要内容包括：简要概述、研究摘要、背景介绍、关键亮点、图文解析、展望与总结。
期刊
I
IF:
3.4
论文数:
3.3K
被引数:
6.4K
机构
引用论文
Evolution of transcription factor binding sites in mammalian gene regulatory regions: Conservation and turnover哺乳动物基因调控区转录因子结合位点的进化: 保守和转换OAAI
.png){kind=icon}
OAAI分享收藏Cation ordering and structural variations with temperature in MgAl2O4spinel: An X-ray single-crystal studyMgAl2O4 尖晶石中阳离子有序性和结构随温度的变化: x射线单晶研究
PREAI
分享收藏
查看更多内容