Imputation for transcription factor binding predictions based on deep learning

PLoS Computational Biology
Qian Qin, Jianxing Feng

Abstract

Understanding the cell-specific binding patterns of transcription factors (TFs) is fundamental to studying gene regulatory networks in biological systems, for which ChIP-seq not only provides valuable data but is also considered as the gold standard. Despite tremendous efforts from the scientific community to conduct TF ChIP-seq experiments, the available data represent only a limited percentage of ChIP-seq experiments, considering all possible combinations of TFs and cell lines. In this study, we demonstrate a method for accurately predicting cell-specific TF binding for TF-cell line combinations based on only a small fraction (4%) of the combinations using available ChIP-seq data. The proposed model, termed TFImpute, is based on a deep neural network with a multi-task learning setting to borrow information across transcription factors and cell lines. Compared with existing methods, TFImpute achieves comparable accuracy on TF-cell line combinations with ChIP-seq data; moreover, TFImpute achieves better accuracy on TF-cell line combinations without ChIP-seq data. This approach can predict cell line specific enhancer activities in K562 and HepG2 cell lines, as measured by massively parallel reporter assays, and predicts the impa...Continue Reading

References

Jun 2, 2007·Science·David S JohnsonBarbara Wold
Mar 4, 2008·Nature Methods·Jason B WarnerMartha L Bulyk
Aug 31, 2011·Genome Research·Dongwon LeeMichael A Beer
Feb 7, 2012·Nature·Jacob F DegnerJonathan K Pritchard
Sep 8, 2012·Nature·ENCODE Project Consortium
Jan 29, 2013·Nature Biotechnology·Matthew T WeirauchTimothy R Hughes
Nov 19, 2013·Cell·Dan XieMichael Snyder
Nov 19, 2013·Nucleic Acids Research·Trevor Siggers, Raluca Gordân
Apr 20, 2014·Cell and Tissue Research·Simon Friedensohn, Ritwick Sawarkar
Jun 17, 2014·Bioinformatics·Michael K K LeungBrendan J Frey
Jul 18, 2014·PLoS Computational Biology·Mahmoud GhandiMichael A Beer
Jul 22, 2014·Cold Spring Harbor Symposia on Quantitative Biology·Gary D Stormo
Sep 30, 2014·Nature Genetics·Nils WeinholdWilliam Lee
Oct 15, 2014·Proceedings of the National Academy of Sciences of the United States of America·Ariel AfekDavid B Lukatsky
Dec 3, 2014·Neural Networks : the Official Journal of the International Neural Network Society·Jürgen Schmidhuber
Dec 4, 2014·Proceedings of the National Academy of Sciences of the United States of America·Peter H von Hippel
Feb 1, 2015·Trends in Genetics : TIG·Anthony MathelierWyeth W Wasserman
May 29, 2015·Nature·Yann LeCunGeoffrey Hinton
Jun 16, 2015·Nature Genetics·Dongwon LeeMichael A Beer
Jul 28, 2015·Nature Biotechnology·Babak AlipanahiBrendan J Frey
Apr 14, 2016·Nature Communications·Chongzhi ZangX Shirley Liu

Citations

Apr 27, 2018·Pharmacogenomics·Alexandr A KalininBrian D Athey
Jul 13, 2019·Bioinformatics·Jakub M BartoszewiczBernhard Y Renard
Sep 20, 2019·Molecules : a Journal of Synthetic Chemistry and Natural Product Chemistry·Qing YuanZhen Li
Apr 6, 2018·Journal of the Royal Society, Interface·Travers ChingCasey S Greene
Oct 17, 2018·Scientific Reports·Zhen ShenDe-Shuang Huang
May 5, 2020·Frontiers in Pharmacology·Rim ShayakhmetovDaniil Polykovskiy
Jun 6, 2018·BMC Genomics·Shu ZhangZhaoyuan Fang
Apr 13, 2018·Human Molecular Genetics·Amalio TelentiMark DePristo
Jan 12, 2019·Genome Biology·Jens KeilwagenJan Grau
Jan 1, 2021·Bioinformatics·Derrick BlakelyYanjun Qi
Nov 14, 2017·Emerging Topics in Life Sciences·William JonesLeopold Parts
Oct 15, 2020·Science China. Life Sciences·Jianxiao LiuJianbing Yan
Jan 28, 2020·Current Opinion in Plant Biology·Hai WangEdward Buckler
Apr 30, 2021·Frontiers in Genetics·Sijie YangPeiyao Zhao
May 6, 2021·Nucleic Acids Research·Fahad Ullah, Asa Ben-Hur

Methods Mentioned

BETA
ChIP-seq
PCA

Related Concepts

Related Feeds

CREs: Gene & Cell Therapy

Gene and cell therapy advances have shown promising outcomes for several diseases. The role of cis-regulatory elements (CREs) is crucial in the design of gene therapy vectors. Here is the latest research on CREs in gene and cell therapy.