Incorporating pathway information into boosting estimation of high-dimensional risk prediction models.

BMC Bioinformatics
Harald Binder, Martin Schumacher

Abstract

There are several techniques for fitting risk prediction models to high-dimensional data, arising from microarrays. However, the biological knowledge about relations between genes is only rarely taken into account. One recent approach incorporates pathway information, available, e.g., from the KEGG database, by augmenting the penalty term in Lasso estimation for continuous response models. As an alternative, we extend componentwise likelihood-based boosting techniques for incorporating pathway information into a larger number of model classes, such as generalized linear models and the Cox proportional hazards model for time-to-event data. In contrast to Lasso-like approaches, no further assumptions for explicitly specifying the penalty structure are needed, as pathway information is incorporated by adapting the penalties for single microarray features in the course of the boosting steps. This is shown to result in improved prediction performance when the coefficients of connected genes have opposite sign. The properties of the fitted models resulting from this approach are then investigated in two application examples with microarray survival data. The proposed approach results not only in improved prediction performance but al...Continue Reading

References

Dec 11, 1999·Nucleic Acids Research·M Kanehisa, S Goto
Jun 21, 2002·The New England Journal of Medicine·Andreas RosenwaldUNKNOWN Lymphoma/Leukemia Molecular Profiling Project
May 9, 2007·Bioinformatics·Martin SchumacherThomas Gerds
May 22, 2007·Biostatistics·Yihui Luan, Hongzhe Li
Jul 27, 2007·Biometrics·Thomas A Gerds, Martin Schumacher
Jan 12, 2008·BMC Bioinformatics·Harald Binder, Martin Schumacher
Jan 22, 2008·Bioinformatics·Jelle J Goeman, Ulrich Mansmann
Apr 4, 2008·Statistical Applications in Genetics and Molecular Biology·Harald Binder, Martin Schumacher
Dec 6, 2011·Nucleic Acids Research·Michael Cariaso, Greg Lennon

❮ Previous
Next ❯

Citations

Mar 10, 2010·Nature Reviews. Genetics·Duncan Thomas
Jun 29, 2010·Bioinformatics·Monika JelizarowAnne-Laure Boulesteix
Dec 15, 2010·Bioinformatics·Vinicius BonatoKim-Anh Do
Jul 18, 2012·BMC Bioinformatics·David EdwardsPeter Sørensen
May 2, 2012·BMC Bioinformatics·Tiziana SanaviaBarbara Di Camillo
Jan 21, 2014·Bioinformatics·Yupeng Cun, Holger Fröhlich
Oct 9, 2014·TheScientificWorldJournal·Francisco Gómez-Vela, Norberto Díaz-Díaz
Aug 13, 2014·Methods of Information in Medicine·A MayrM Schmid
Feb 18, 2011·Biometrical Journal. Biometrische Zeitschrift·Harald BinderMartin Schumacher
Feb 18, 2011·Biometrical Journal. Biometrische Zeitschrift·Christine PorzeliusTim Beissbarth
Jan 17, 2014·Biometrical Journal. Biometrische Zeitschrift·Holger Fröhlich
Mar 21, 2012·IEEE/ACM Transactions on Computational Biology and Bioinformatics·Shuichi KawanoSatoru Miyano
Nov 9, 2014·Human Genetics·Donald GemanLaurent Younes
Aug 11, 2016·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·Xin TianZhenran Jiang
Jun 29, 2017·Bioinformatics·Moritz HessHarald Binder
Jan 1, 2012·Biology·Yupeng Cun, Holger Fröhlich
Jan 3, 2018·Biometrical Journal. Biometrische Zeitschrift·Georg HeinzeDaniela Dunkler
May 18, 2019·Biometrical Journal. Biometrische Zeitschrift·Simon KlauSabine Hoffmann
Mar 19, 2014·Statistical Applications in Genetics and Molecular Biology·Murat SariyarHarald Binder
Sep 18, 2020·International Journal of Molecular Sciences·Davide B GissiLucio Montebugnoli
Dec 10, 2016·Lifetime Data Analysis·Hyokyoung G HongYi Li

❮ Previous
Next ❯

Software Mentioned

PathBoost

Related Concepts

Trending Feeds

COVID-19

Coronaviruses encompass a large family of viruses that cause the common cold as well as more serious diseases, such as the ongoing outbreak of coronavirus disease 2019 (COVID-19; formally known as 2019-nCoV). Coronaviruses can spread from animals to humans; symptoms include fever, cough, shortness of breath, and breathing difficulties; in more severe cases, infection can lead to death. This feed covers recent research on COVID-19.

Blastomycosis

Blastomycosis fungal infections spread through inhaling Blastomyces dermatitidis spores. Discover the latest research on blastomycosis fungal infections here.

Nuclear Pore Complex in ALS/FTD

Alterations in nucleocytoplasmic transport, controlled by the nuclear pore complex, may be involved in the pathomechanism underlying multiple neurodegenerative diseases including Amyotrophic Lateral Sclerosis and Frontotemporal Dementia. Here is the latest research on the nuclear pore complex in ALS and FTD.

Applications of Molecular Barcoding

The concept of molecular barcoding is that each original DNA or RNA molecule is attached to a unique sequence barcode. Sequence reads having different barcodes represent different original molecules, while sequence reads having the same barcode are results of PCR duplication from one original molecule. Discover the latest research on molecular barcoding here.

Chronic Fatigue Syndrome

Chronic fatigue syndrome is a disease characterized by unexplained disabling fatigue; the pathology of which is incompletely understood. Discover the latest research on chronic fatigue syndrome here.

Evolution of Pluripotency

Pluripotency refers to the ability of a cell to develop into three primary germ cell layers of the embryo. This feed focuses on the mechanisms that underlie the evolution of pluripotency. Here is the latest research.

Position Effect Variegation

Position Effect Variagation occurs when a gene is inactivated due to its positioning near heterochromatic regions within a chromosome. Discover the latest research on Position Effect Variagation here.

STING Receptor Agonists

Stimulator of IFN genes (STING) are a group of transmembrane proteins that are involved in the induction of type I interferon that is important in the innate immune response. The stimulation of STING has been an active area of research in the treatment of cancer and infectious diseases. Here is the latest research on STING receptor agonists.

Microbicide

Microbicides are products that can be applied to vaginal or rectal mucosal surfaces with the goal of preventing, or at least significantly reducing, the transmission of sexually transmitted infections. Here is the latest research on microbicides.