Gene Meter: Accurate abundance calculations of gene expression

Communicative & Integrative Biology
Alexander E Pozhitkov, Peter A Noble

Abstract

We previously reported that thousands of transcripts in the mouse and zebrafish significantly increased in abundance in a time series spanning from life to several days after death. Transcript abundances were determined by: calibrating each microarray probe using a dilution series of pooled RNAs, fitting the probe-responses to adsorption models, and back-calculating abundances using the probe signal intensity of a sample and the best fitting model. The accuracy of the abundance measurements was not assessed in our previous study because individual transcript concentrations in the calibration pool were not known. Accurate transcript abundances are highly desired for modeling the dynamics of biological systems and investigating how systems respond to perturbations. In this study, we show that accurate transcript abundances can be determined by calibrating the probes using a calibration pool of transcripts with known concentrations. Instructions for determining accurate transcript abundances using the Gene Meter approach are provided.

References

Feb 16, 2019·FEBS Letters·Hanane Hadj-MoussaKenneth B Storey
Aug 9, 2017·BioEssays : News and Reviews in Molecular, Cellular and Developmental Biology·Alexander E Pozhitkov, Peter A Noble
Sep 16, 2018·BMC Genomics·Peter A Noble, Alexander E Pozhitkov

Citations

Oct 22, 2002·Proceedings of the National Academy of Sciences of the United States of America·Y TuU Klein
Nov 6, 2010·Molecular Ecology·Anthony S AmendThomas D Bruns
Jan 12, 2013·Nucleic Acids Research·Andrew HarrisonAlexander E Pozhitkov
Oct 9, 2016·Journal of Microbiological Methods·M Colby HunterPeter A Noble
Jan 27, 2017·Open Biology·Alex E PozhitkovPeter A Noble
Mar 23, 2017·Forensic Science International : Synergy·M Colby HunterPeter A Noble

Related Concepts

Study
Genes
Cessation of Life
Adsorption
Gene Expression
Meters (Physical Object)
Zebrafish
Probes
Dilution Technique
Transcript

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.

Sexual Dimorphism in Neurodegeneration

There exist sex differences in neurodevelopmental and neurodegenerative disorders. For instance, multiple sclerosis is more common in women, whereas Parkinson’s disease is more common in men. Here is the latest research on sexual dimorphism in neurodegeneration

HLA Genetic Variation

HLA genetic variation has been found to confer risk for a wide variety of diseases. Identifying these associations and understanding their molecular mechanisms is ongoing and holds promise for the development of therapeutics. Find the latest research on HLA genetic variation here.

Super-resolution Microscopy

Super-resolution microscopy is the term commonly given to fluorescence microscopy techniques with resolutions that are not limited by the diffraction of light. Here are the latest discoveries pertaining to super-resolution microscopy.

Genetic Screens in iPSC-derived Brain Cells

Genetic screening is a critical tool that can be employed to define and understand gene function and interaction. This feed focuses on genetic screens conducted using induced pluripotent stem cell (iPSC)-derived brain cells.

Brain Lower Grade Glioma

Low grade gliomas in the brain form from oligodendrocytes and astrocytes and are the slowest-growing glioma in adults. Discover the latest research on these brain tumors here.

CD4/CD8 Signaling

Cluster of differentiation 4 and 8 (CD8 and CD8) are glycoproteins founds on the surface of immune cells. Here is the latest research on their role in cell signaling pathways.

Alignment-free Sequence Analysis Tools

Alignment-free sequence analyses have been applied to problems ranging from whole-genome phylogeny to the classification of protein families, identification of horizontally transferred genes, and detection of recombined sequences. Here is the latest research.

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.