Machine learning approaches to supporting the identification of photoreceptor-enriched genes based on expression data

BMC Bioinformatics
Haiying WangFrancisco Azuaje

Abstract

Retinal photoreceptors are highly specialised cells, which detect light and are central to mammalian vision. Many retinal diseases occur as a result of inherited dysfunction of the rod and cone photoreceptor cells. Development and maintenance of photoreceptors requires appropriate regulation of the many genes specifically or highly expressed in these cells. Over the last decades, different experimental approaches have been developed to identify photoreceptor enriched genes. Recent progress in RNA analysis technology has generated large amounts of gene expression data relevant to retinal development. This paper assesses a machine learning methodology for supporting the identification of photoreceptor enriched genes based on expression data. Based on the analysis of publicly-available gene expression data from the developing mouse retina generated by serial analysis of gene expression (SAGE), this paper presents a predictive methodology comprising several in silico models for detecting key complex features and relationships encoded in the data, which may be useful to distinguish genes in terms of their functional roles. In order to understand temporal patterns of photoreceptor gene expression during retinal development, a two-way...Continue Reading

References

Oct 1, 1988·Proceedings of the National Academy of Sciences of the United States of America·C BlattR R Reed
Oct 20, 1995·Science·V E VelculescuK W Kinzler
May 23, 1997·Science·L ZhangK W Kinzler
Mar 4, 2000·Human Molecular Genetics·P M D'CruzD Vollrath
Jun 14, 2000·Clinical Genetics·G ClarkeR R McInnes
Apr 13, 2001·Bioinformatics·K Y YeungW L Ruzzo
Oct 23, 2002·Proceedings of the National Academy of Sciences of the United States of America·Nicholas KatsanisJames R Lupski
Mar 5, 2003·BioTechniques·A I SaeedJ Quackenbush
Jul 1, 2004·PLoS Biology·Seth BlackshawConstance L Cepko
Jul 9, 2004·Genome Biology·Li CaiWing H Wong
Oct 13, 2007·Science·Laura D WoodBert Vogelstein
Jan 25, 2008·Neural Development·Eric M MorrowConstance L Cepko

❮ Previous
Next ❯

Citations

Sep 30, 2008·BioData Mining·Jesús S Aguilar-RuizMarylyn D Ritchie
Sep 30, 2008·BioData Mining·Haiying WangFrancisco Azuaje

❮ Previous
Next ❯

Methods Mentioned

BETA
in silico methods

Software Mentioned

SAGE
FOM
Weka
KStar

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.

Related Papers

Proceedings of the National Academy of Sciences of the United States of America
Akishi OnishiSeth Blackshaw
Proceedings of the National Academy of Sciences of the United States of America
Joseph C CorboConstance L Cepko
PLoS Biology
Seth BlackshawConstance L Cepko
Reproduction : the Official Journal of the Society for the Study of Fertility
Helen White-Cooper
© 2021 Meta ULC. All rights reserved