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Gene Expression and Profiling

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Application of Clinical Bioinformatics

Part of the book series: Translational Bioinformatics ((TRBIO,volume 11))

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Abstract

Transcriptomics analysis has been widely applied to explore the unknown genes or factors in various biological processes, traits, diseases, and drug treatment. By screening entire RNAs, this technique implicates novel genes and pathways related to a particular condition. Two major types of transcriptomic profiling methods are microarray and RNA sequencing. The two approaches generates and preprocess their respective raw data quite differently, but further analysis is nearly identical. In this chapter, we briefly describe the principles of both methods and compare the differences between them. Since RNA quality is a key practical factor in transcriptomic study, we also introduce isolation and quality control methods and popular software packages for each step in the data analysis process. Finally, we provide an example of a clinical project which used transcriptomics approach to study a disease etiology.

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Abbreviations

BH:

Benjamini-hochberg

CLL:

Chronic lymphocytic leukemia

DEG:

Differentially expressed gene

EBI:

European bioinformatics institute

eQTL:

Expression quantitative trait loci

FDR:

False discovery rate

FPKM:

Fragments per kilobase of transcript per million mapped reads

GAPDH:

Glyceraldehyde-3-phosphate dehydrogenase

GO:

Gene ontology

GSEA:

Gene set enrichment analysis

GWAS:

Genome-wide association studies

ICGC:

International cancer genome consortium

LOD:

Logarithm of the odds

MM:

Mismatch probes

NCBI:

National Center for Biotechnology Information

PBMC:

Peripheral blood mononuclear cells

PM:

Perfect match probes

RIN:

Rna integrity number

RMA:

Robust microarray average

RNA-Seq:

RNA sequencing

RPKM:

Reads per kilobase of transcript per million mapped reads

SAM:

Significance analysis of microarrays

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Correspondence to Hong-Wen Deng .

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© 2016 Springer Science+Business Media Dordrecht

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Zhou, Y., Xu, C., Zhang, J., Deng, HW. (2016). Gene Expression and Profiling. In: Wang, X., Baumgartner, C., Shields, D., Deng, HW., Beckmann, J. (eds) Application of Clinical Bioinformatics. Translational Bioinformatics, vol 11. Springer, Dordrecht. https://doi.org/10.1007/978-94-017-7543-4_3

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