Spectacle: fast chromatin state annotation using spectral learning

Genome Biology
Jimin Song, Kevin C Chen

Abstract

Epigenomic data from ENCODE can be used to associate specific combinations of chromatin marks with regulatory elements in the human genome. Hidden Markov models and the expectation-maximization (EM) algorithm are often used to analyze epigenomic data. However, the EM algorithm can have overfitting problems in data sets where the chromatin states show high class-imbalance and it is often slow to converge. Here we use spectral learning instead of EM and find that our software Spectacle overcame these problems. Furthermore, Spectacle is able to find enhancer subtypes not found by ChromHMM but strongly enriched in GWAS SNPs. Spectacle is available at https://github.com/jiminsong/Spectacle.

References

Aug 10, 2000·Neural Computation·H Jaeger
Oct 18, 2006·Proceedings of the National Academy of Sciences of the United States of America·Tae-Young RohKeji Zhao
Oct 31, 2006·Nature Genetics·Kevin Chen, Nikolaus Rajewsky
Nov 30, 2006·Nucleic Acids Research·Axel ViselLen A Pennacchio
Jul 2, 2008·Bioinformatics·Heng LianCharles E Lawrence
Nov 26, 2008·Best Practice & Research. Clinical Rheumatology·Eric Toussirot, Jean Roudier
May 29, 2009·Proceedings of the National Academy of Sciences of the United States of America·Lucia A HindorffTeri A Manolio
Oct 8, 2009·Human Molecular Genetics·Gary C HonBing Ren
Oct 28, 2009·Genome Research·Katherine S PollardAdam Siepel
May 4, 2010·Nature Biotechnology·Cory Y McLeanGill Bejerano
Oct 15, 2010·Nature Biotechnology·Bradley E BernsteinJames A Thomson
Oct 29, 2010·Nature·Gonçalo R AbecasisGil A McVean
Dec 1, 2010·Nature Reviews. Genetics·Vicky W ZhouBradley E Bernstein
Dec 17, 2010·Nature·Alvaro Rada-IglesiasJoanna Wysocka
Dec 24, 2010·Nature·Peter V KharchenkoPeter J Park
Mar 29, 2011·Nature·Jason ErnstBradley E Bernstein
Apr 29, 2011·PLoS Biology·UNKNOWN ENCODE Project Consortium
Mar 1, 2012·Nature Methods·Jason Ernst, Manolis Kellis
Mar 9, 2012·Nature Biotechnology·David AdamsSpike Willcocks
Mar 20, 2012·Nature Methods·Michael M HoffmanWilliam Stafford Noble
Jun 12, 2012·Cell·Shu XiaoSheng Zhong
Sep 8, 2012·Nature·UNKNOWN ENCODE Project Consortium
Sep 8, 2012·Nature·Sarah DjebaliThomas R Gingeras
Sep 8, 2012·Science·Matthew T MauranoJohn A Stamatoyannopoulos
Sep 8, 2012·Genome Research·Marc A SchaubMichael Snyder
Sep 20, 2012·Nucleic Acids Research·Jianrong WangI King Jordan
Nov 28, 2012·Genome Biology·David Kelley, John Rinn
Dec 12, 2012·Nucleic Acids Research·Michael M HoffmanWilliam Stafford Noble
Mar 14, 2013·Nucleic Acids Research·Kyoung-Jae WonWei Wang
Jun 14, 2013·BMC Bioinformatics·Jacob BiesingerXiaohui Xie
Jul 13, 2013·Genome Biology·Xin ZengSündüz Keleş
Oct 1, 2013·Cell·Chloe M Rivera, Bing Ren
Oct 19, 2013·Science·Maya KasowskiMichael Snyder

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Citations

Mar 17, 2016·Briefings in Bioinformatics·Ryuichiro Nakato, Katsuhiko Shirahige
Nov 12, 2016·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·Chandler ZuoSündüz Keleş
Feb 14, 2018·Bioinformatics·Selin Jessa, Claudia L Kleinman
Mar 29, 2016·F1000Research·Davide CittaroPaolo Provero
Nov 10, 2017·Nature Protocols·Jason Ernst, Manolis Kellis
Sep 5, 2018·BMC Bioinformatics·Hani Z GirgisZachary E Reyes
May 3, 2019·Nucleic Acids Research·Xinzhou GeJingyi Jessica Li
Nov 25, 2020·Bioinformatics·Peter Ebert, Marcel H Schulz
Oct 15, 2021·PLoS Computational Biology·Maxwell W LibbrechtMichael M Hoffman

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Datasets Mentioned

BETA
GM12878

Methods Mentioned

BETA
immunoprecipitation
ChIP-seq
RNA-seq

Software Mentioned

Cap Analysis of Gene Expression ( CAGE
Spectacle
Python
jMOSAiCS
GREAT
Scripture
BLUEPRINT
VISTA
ENCODE
TreeHMM

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