SPICE: discovery of phenotype-determining component interplays.

BMC Systems Biology
Zhengzhang ChenNagiza F Samatova

Abstract

A latent behavior of a biological cell is complex. Deriving the underlying simplicity, or the fundamental rules governing this behavior has been the Holy Grail of systems biology. Data-driven prediction of the system components and their component interplays that are responsible for the target system's phenotype is a key and challenging step in this endeavor. The proposed approach, which we call System Phenotype-related Interplaying Components Enumerator (SPICE), iteratively enumerates statistically significant system components that are hypothesized (1) to play an important role in defining the specificity of the target system's phenotype(s); (2) to exhibit a functionally coherent behavior, namely, act in a coordinated manner to perform the phenotype-specific function; and (3) to improve the predictive skill of the system's phenotype(s) when used collectively in the ensemble of predictive models. SPICE can be applied to both instance-based data and network-based data. When validated, SPICE effectively identified system components related to three target phenotypes: biohydrogen production, motility, and cancer. Manual results curation agreed with the known phenotype-related system components reported in literature. Additionally...Continue Reading

References

May 1, 1992·Journal of Bacteriology·C SteffesB P Rosen
Nov 1, 1996·Archives of Microbiology·U Härtel, W Buckel
Apr 29, 1998·Annals of Oncology : Official Journal of the European Society for Medical Oncology·T KarakasL Bergmann
Dec 11, 1999·Nature·L H HartwellA W Murray
Oct 12, 2000·Proceedings of the National Academy of Sciences of the United States of America·A J ButteI S Kohane
Aug 29, 2001·FEMS Microbiology Reviews·P M VignaisJ Meyer
Oct 16, 2002·The Journal of Biological Chemistry·Athanasios PaschosAugust Böck
Nov 7, 2002·Journal of Molecular Biology·Christian MotzJoachim Rassow
Jan 28, 2003·Current Biology : CB·Mitchell LevesquePhilip N Benfey
Mar 13, 2003·Proceedings of the National Academy of Sciences of the United States of America·Ariel BlockerShin-Ichi Aizawa
Sep 13, 2003·BMC Bioinformatics·Roman L TatusovDarren A Natale
Sep 21, 2004·Applied Microbiology and Biotechnology·Kaushik Nath, Debabrata Das
Oct 7, 2004·Bioinformatics·Marcel Dettling
Mar 8, 2005·IEEE Transactions on Pattern Analysis and Machine Intelligence·Xiaofei HeHong-Jiang Zhang
Jun 14, 2005·Trends in Biotechnology·R Keira CurtisAntonio Vidal-Puig
Jan 10, 2006·BMC Bioinformatics·Ramón Díaz-Uriarte, Sara Alvarez de Andrés
May 30, 2006·Molecular Systems Biology·Noam SlonimSaeed Tavazoie
Oct 14, 2006·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·Mehmet KoyutürkAnanth Grama
Jan 16, 2007·Applied and Environmental Microbiology·Federico E ReyCaroline S Harwood
Feb 3, 2007·BMC Bioinformatics·Franck RapaportJean-Philippe Vert
Feb 6, 2007·IEEE/ACM Transactions on Computational Biology and Bioinformatics·Lipo WangWei Xie
Aug 2, 2007·Molecular Systems Biology·Seesandra V RajagopalaPeter Uetz
Aug 21, 2007·Journal of Molecular Biology·Yasuhito ShomuraYoshiki Higuchi
Aug 28, 2007·Bioinformatics·Yvan SaeysPedro Larrañaga
Sep 25, 2007·Applied Microbiology and Biotechnology·Dominik AntoniWolfgang H Schwarz
Oct 18, 2007·Molecular Systems Biology·Han-Yu ChuangTrey Ideker
Nov 13, 2007·Analytical Biochemistry·M Kalim Akhtar, Patrik R Jones
May 23, 2008·Proceedings of the National Academy of Sciences of the United States of America·Amoolya H SinghAdam P Arkin
Oct 23, 2008·Nucleic Acids Research·Lars J JensenChristian von Mering
Jan 27, 2010·BMC Bioinformatics·Taeho HwangGwan-Su Yi
Mar 23, 2010·Applied and Environmental Microbiology·Yue HuangZhihua Zhou
May 22, 2010·BMC Bioinformatics·Shuangge MaBen-Chang Shia
Jun 19, 2010·Proceedings of the National Academy of Sciences of the United States of America·James B McKinlay, Caroline S Harwood
Jul 10, 2010·Proceedings of the National Academy of Sciences of the United States of America·Michael KöpkePeter Dürre
Aug 10, 2010·Journal of Environmental Management·Patrick C Hallenbeck, Dipankar Ghosh

❮ Previous
Next ❯

Citations

Nov 2, 2013·NeuroImage. Clinical·Gowtham AtluriVipin Kumar
Oct 22, 2018··Zhichun LiCheng Cao

❮ Previous
Next ❯

Methods Mentioned

BETA
phylogenetic
phylogenetic profile
phylogenetic profiles
PCA

Software Mentioned

GO TERM FINDER
CART
PAM
MULE
Spice
RFE
System Phenotype - related Interplaying Components Enumerator ...
DENSE
varSelRF
Matlab

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.