Computational Biology / Bioinformatics/microarray data

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Question
Hello there,
I was wondering if you know anything about microarray technology . If you do a cDNA microarray analysis to determine whether hepatic genes  are differentially expressed in C57BL/6J male mice fed a high-fat diet (HFD)  versus a low fat diet, and genes are considered differentially expressed at a 2-fold threshold, does this mean that a gene is expressed two times as much in one group over the other? How reliable is the microarray data for genes expressed at a 2-fold threshold? Thanks for any help you can offer!

Answer
Hi Kat,

Until recently micro array technology was extensively used for detecting deferentially  expressed genes. It is based on measuring the light signal from hybridized probes, and indirectly allows comparing relative gene expression between an experimental treatment and control. If a two fold threshold is used, then it means that the 2-fold relative gene expression cutoff was chosen then all the genes with more than 2-fold relative gene expression are considered deferentially expressed between the treatment and control. So a deferentially expressed gene can have two fold or more than two fold expression in treatment or control. Theoretically the relative expression value should reflect the actual difference in expression, however there are several technical and biological variables which affect this, leading to many false positives. The problem is much more in the detection of differential expression for lowly expressing genes. So usually many people take higher thresholds (more conservative), like 4-fold. In general the reliability of the differential expression results can be increased by increasing replication.

Computational Biology / Bioinformatics

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Sridhar Acharya Malkaram

Expertise

Sequence and Structural Analysis, Next generation sequencing, Illumina, SOLiD, CHiP-sequencing, RNA sequencing, miRNA sequencing analysis, Molecular Dynamics, Protein and Nucleic acid simulations, computational methods, Bioinformatics tools, Biological Databases, Search techniques, Protein comparative modelling, Mutation analysis

Experience

about fifteen (15) years

Education/Credentials
Bachelor of Science in Agriculture Master of Science in Biotechnology Ph.D in computational Biology

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