Inter-functional analysis of high-throughput phenotype data by non-parametric clustering and its application to photosynthesis

Bioinformatics
Qiaozi GaoJin Chen

Abstract

Phenomics is the study of the properties and behaviors of organisms (i.e. their phenotypes) on a high-throughput scale. New computational tools are needed to analyze complex phenomics data, which consists of multiple traits/behaviors that interact with each other and are dependent on external factors, such as genotype and environmental conditions, in a way that has not been well studied. We deployed an efficient framework for partitioning complex and high dimensional phenotype data into distinct functional groups. To achieve this, we represented measured phenotype data from each genotype as a cloud-of-points, and developed a novel non-parametric clustering algorithm to cluster all the genotypes. When compared with conventional clustering approaches, the new method is advantageous in that it makes no assumption about the parametric form of the underlying data distribution and is thus particularly suitable for phenotype data analysis. We demonstrated the utility of the new clustering technique by distinguishing novel phenotypic patterns in both synthetic data and a high-throughput plant photosynthetic phenotype dataset. We biologically verified the clustering results using four Arabidopsis chloroplast mutant lines. Software is av...Continue Reading

References

Nov 25, 1988·Nucleic Acids Research·F Corpet
Jan 1, 1986·Clinical and Experimental Dermatology·D S Jolliffe
Apr 7, 1985·Journal of Theoretical Biology·C E Lawrence, A A Reilly
Sep 1, 1967·Psychometrika·S C Johnson
Dec 9, 1998·Proceedings of the National Academy of Sciences of the United States of America·M B EisenD Botstein
Mar 17, 1999·Proceedings of the National Academy of Sciences of the United States of America·P TamayoT R Golub
Nov 24, 1999·Genome Research·R HerwigJ O'Brien
Dec 3, 1999·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·A Ben-DorZ Yakhini
Jun 28, 2000·Bioinformatics·A J Enright, C A Ouzounis
Jun 26, 2002·Proceedings of the National Academy of Sciences of the United States of America·Marco F RamoniIsaac S Kohane
Sep 12, 2002·Annual Review of Plant Biology·Bruce A Diner, Fabrice Rappaport
Jul 12, 2003·Bioinformatics·Alexander SchliepChristine Steinhoff
Aug 26, 2003·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·Ziv Bar-JosephItamar Simon
May 8, 2004·Bioinformatics·Ziv Bar-Joseph
Jan 13, 2006·Nature Biotechnology·Atul J Butte, Isaac S Kohane
Sep 20, 2006·Nucleic Acids Research·Philip GrothBertram Weiss
Apr 3, 2007·BMC Bioinformatics·Ido PrinessIrad Ben-Gal
Aug 2, 2007·IEEE/ACM Transactions on Computational Biology and Bioinformatics·Michael A Lones, Andy M Tyrrell
May 1, 2008·Annual Review of Plant Biology·Neil R Baker
Oct 11, 2008·Nature Biotechnology·Jay Shendure, Hanlee Ji
Jul 28, 2009·Cognitive Neuropsychiatry·Robert M BilderRussell A Poldrack
Jun 22, 2010·Bioinformatics·Philip GrothBertram Weiss
Aug 31, 2010·Bioinformatics·Paul D McNicholas, Thomas Brendan Murphy
Nov 17, 2010·Plant Physiology·David M Kramer, John R Evans
Feb 19, 2011·Nature Reviews. Genetics·Günter P Wagner, Jianzhi Zhang
Jun 21, 2011·Bioinformatics·Julia SivriverNir Friedman
Jul 23, 2011·Methods in Molecular Biology·Philip GrothBertram Weiss
Dec 6, 2011·Nucleic Acids Research·Philippe LameschEva Huala
Jun 7, 2012·Bioinformatics·Moysés NascimentoAna Carolina C Nascimento
Mar 9, 2013·TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik·Joshua N CobbSusan McCouch
Apr 9, 2013·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·Hua WangChris Ding
Feb 26, 2014·BMC Systems Biology·Oliver L TessmerJin Chen
Jan 27, 2015·Bioinformatics·Lei XuJin Chen
May 21, 2015·Dental press journal of orthodontics·Joana Cunha-Cruz

❮ Previous
Next ❯

Citations


❮ Previous
Next ❯

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.