PMID: 9331369Oct 23, 1997

The significance of digital gene expression profiles

Genome Research
S Audic, J M Claverie

Abstract

Genes differentially expressed in different tissues, during development, or during specific pathologies are of foremost interest to both basic and pharmaceutical research. "Transcript profiles" or "digital Northerns" are generated routinely by partially sequencing thousands of randomly selected clones from relevant cDNA libraries. Differentially expressed genes can then be detected from variations in the counts of their cognate sequence tags. Here we present the first systematic study on the influence of random fluctuations and sampling size on the reliability of this kind of data. We establish a rigorous significance test and demonstrate its use on publicly available transcript profiles. The theory links the threshold of selection of putatively regulated genes (e.g., the number of pharmaceutical leads) to the fraction of false positive clones one is willing to risk. Our results delineate more precisely and extend the limits within which digital Northern data can be used.

References

Feb 5, 2000·Journal of Neuroscience Research·C ColantuoniJ Pevsner
May 31, 2002·Molecular Plant-microbe Interactions : MPMI·Warren M KrugerGary J Muehlbauer
Aug 15, 2002·Genome Génome / Conseil National De Recherches Canada·Cheryl GrangerRandy C Shoemaker
Jul 11, 2003·Proceedings of the National Academy of Sciences of the United States of America·Rentao Song, Joachim Messing
Jul 23, 2004·American Journal of Respiratory Cell and Molecular Biology
Sep 28, 2004·The Plant Journal : for Cell and Molecular Biology·Hangning ZhangAndreas Graner
Feb 11, 2005·Human Molecular Genetics·Juanliang CaiMichael Lovett
Apr 12, 2005·Plant Molecular Biology·Nathalie PavyJohn Mackay
Dec 29, 2005·Parasitology Research·Bartel VanholmeGodelieve Gheysen
Aug 31, 2006·BMC Genomics·Jae Yong HanHeebal Kim
Dec 22, 2006·The Journal of Immunology : Official Journal of the American Association of Immunologists·Dorothée MisséFrancisco Veas
Mar 21, 2007·PLoS Pathogens·Guanggan HuJames W Kronstad
Mar 22, 2008·Genome Génome / Conseil National De Recherches Canada·Cesar A SommerFlavio Henrique-Silva
Feb 12, 2008·Current Protocols in Molecular Biology·Seth BlackshawLi Cai
Jun 7, 2008·Molecular Plant-microbe Interactions : MPMI·Johana RinconesGonçalo A G Pereira
Apr 23, 2008·Current Protocols in Human Genetics·Seth BlackshawLi Cai
Feb 26, 2009·Proteome Science·Paulo C CarvalhoValmir C Barbosa
Jun 11, 2008·Proceedings of the National Academy of Sciences of the United States of America·Marie Sémon, Kenneth H Wolfe
Aug 5, 2008·Molecular Microbiology·Guanggan HuJames W Kronstad
Oct 13, 2009·Applied Microbiology and Biotechnology·Xin LiuZhonghua Ma
May 5, 2010·Genetics·Paul L Auer, R W Doerge
Jun 3, 2010·The EMBO Journal·Gong-Hong WeiJussi Taipale
Jul 14, 2010·Journal of Biomedicine & Biotechnology·Valerio CostaAlfredo Ciccodicola

Citations

Jan 1, 1992·Mammalian Genome : Official Journal of the International Mammalian Genome Society·T M GressH Lehrach
Feb 13, 1992·Nature·M D AdamsJ C Venter
Oct 1, 1991·Trends in Genetics : TIG·G Lennon, H Lehrach
Oct 20, 1995·Science·R Nowak
Oct 20, 1995·Science·V E VelculescuK W Kinzler
Aug 29, 1995·Proceedings of the National Academy of Sciences of the United States of America·Norman H LeeA R Kerlavage
Aug 1, 1995·Nature Genetics·M S Boguski, G D Schuler
Jan 1, 1995·Analytical Biochemistry·R S MatsonP Coassin
Dec 1, 1993·Current Opinion in Biotechnology·K Matsubara, K Okubo
May 1, 1996·Nature Genetics
Sep 1, 1996·Genome Research·L D HillierMarco A Marra
Dec 18, 1996·Journal of the National Cancer Institute·B Kuska
Mar 1, 1997·Molecular Medicine Today·C O'Brien
Jun 1, 1996·Nature Biotechnology·W Bains

Related Concepts

Confidence Intervals
Fluctuation
Isoactin
Brain
Gene Expression
Sequencing
Sample Size
Pathology
Two-Parameter Models
Bayesian Prediction

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.

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.

Synapse Loss as Therapeutic Target in MS

As we age, the number of synapses present in the human brain starts to decline, but in neurodegenerative diseases this occurs at an accelerated rate. In MS, it has been shown that there is a reduction in synaptic density, which presents a potential target for treatment. Here is the latest research on synapse loss as a therapeutic target in MS.

Artificial Intelligence in Cardiac Imaging

Artificial intelligence (ai) techniques are increasingly applied to cardiovascular (cv) medicine in cardiac imaging analysis. 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.

Social Learning

Social learning involves learning new behaviors through observation, imitation and modeling. Follow this feed to stay up to date on the latest research.

Cell Atlas of the Human Eye

Constructing a cell atlas of the human eye will require transcriptomic and histologic analysis over the lifespan. This understanding will aid in the study of development and disease. Find the latest research pertaining to the Cell Atlas of the Human Eye here.

Single Cell Chromatin Profiling

Techniques like ATAC-seq and CUT&Tag have the potential to allow single cell profiling of chromatin accessibility, histones, and TFs. This will provide novel insight into cellular heterogeneity and cell states. Discover the latest research on single cell chromatin profiling here.

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.