NDLI: Gene expression rate comparison for multiple high-throughput datasets

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Gene expression rate comparison for multiple high-throughput datasets

Content Provider	IET Digital Library
Author	Chen, Chien Ming Shih, Tsan Huang Pai, Tun Wen Liu, Zhen Long Chang, Margaret Dah Tsyr Hu, Chin Hwa
Abstract	Microarray provides genome-wide transcript profiles, whereas RNA-seq is an alternative approach applied for transcript discovery and genome annotation. Both high-throughput techniques show quantitative measurement of gene expression. To explore differential gene expression rates and understand biological functions, the authors designed a system which utilises annotations from Kyoto Encyclopedia of Genes and Genomes (KEGG) biological pathways and Gene Ontology (GO) associations for integrating multiple RNA-seq or microarray datasets. The developed system is initiated by either estimating gene expression levels from mapping next generation sequencing short reads onto reference genomes or performing intensity analysis from microarray raw images. Normalisation procedures on expression levels are evaluated and compared through different approaches including Reads Per Kilobase per Million mapped reads (RPKM) and housekeeping gene selection. Such gene expression levels are shown in different colour shades and graphically displayed in designed temporal pathways. To enhance importance of functional relationships of clustered genes, representative GO terms associated with differentially expressed gene cluster are visually illustrated in a tag cloud representation.
Starting Page	135
Ending Page	142
Page Count	8
ISSN	17518849
Volume Number	7
e-ISSN	17518857
Issue Number	Issue 5, Oct (2013)
Alternate Webpage(s)	https://digital-library.theiet.org/content/journals/iet-syb/7/5
Alternate Webpage(s)	https://digital-library.theiet.org/content/journals/10.1049/iet-syb.2012.0060
Journal	IET Systems Biology
Access Restriction	Open
Rights Holder	© The Institution of Engineering and Technology
Subject Keyword	Biomolecular Structure, Configuration, Conformation, And Active Sites Colour Shades Gene Cluster Gene Expression Levels Gene Expression Rate Gene Ontology Associations Genetics Genome Annotation Genome Biological Pathways Genome-wide Transcript Profile Genomic Technique Genomics High-throughput Technique Housekeeping Gene Selection Lab-on-a-chip Macromolecular Configuration (bonds, Dimensions) Microarray Datasets Microarray Raw Image Molecular Biophysics Molecular Configurations Multiple High-throughput Datasets Multiple RNA-seq Datasets Next Generation Sequencing Quantitative Measurement Representative GO Term RNA Tag Cloud Representation Temporal Pathways Transcript Discovery
Content Type	Text
Resource Type	Article
Subject	Cell Biology Genetics Molecular Biology Modeling and Simulation Biotechnology

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