ArticleMarine biotechnology (New York, N.Y.)2017
Bias and Correction in RNA-seq Data for Marine Species.
Article in Marine biotechnology (New York, N.Y.), 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
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Who cites it
18 citing papers in PubMed.
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- Transcriptome Analysis Reveals the Response Mechanism ofInternational journal of molecular sciences · 2022Article
- Identification of a novel autophagy-related prognostic signature and small molecule drugs for glioblastoma by bioinformatics.BMC medical genomics · 2022Article
- Identification and validation of an immune-related prognostic signature and key gene in papillary thyroid carcinoma.Cancer cell international · 2021Article
- Deciphering the Pyroptosis-Related Prognostic Signature and Immune Cell Infiltration Characteristics of Colon Cancer.Frontiers in genetics · 2021Article
- Identification of Genes Related to Immune Infiltration in the Tumor Microenvironment of Cutaneous Melanoma.Frontiers in oncology · 2021Article
- Integrative Analysis of Biomarkers Through Machine Learning Identifies Stemness Features in Colorectal Cancer.Frontiers in cell and developmental biology · 2021Article
- Genomic Landscape of Mutational Biases in the Pacific Oyster Crassostrea gigas.Genome biology and evolution · 2020Article
- New insights into the Manila clam and PAMPs interaction based on RNA-seq analysis of clam through in vitro challenges with LPS, PGN, and poly(I:C).BMC genomics · 2020Article
- Identification of Key Genes Related to Lung Squamous Cell Carcinoma Using Bioinformatics Analysis.International journal of molecular sciences · 2020Article
- Relationship Among Intron Length, Gene Expression, and Nucleotide Diversity in the Pacific Oyster Crassostrea gigas.Marine biotechnology (New York, N.Y.) · 2018Article
- Gonadal Transcriptome Analysis of Pacific Abalone Haliotis discus discus: Identification of Genes Involved in Germ Cell Development.Marine biotechnology (New York, N.Y.) · 2018Article
- Characterization of Spleen Transcriptome of Schizothorax prenanti during Aeromonas hydrophila Infection.Marine biotechnology (New York, N.Y.) · 2018Article
- Comparative Transcriptome Analysis Reveals Growth-Related Genes in Juvenile Chinese Sea Cucumber, Russian Sea Cucumber, and Their Hybrids.Marine biotechnology (New York, N.Y.) · 2018Article
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Authors and funding
3 authors.
Funding
Abstract
RNA-seq is a recently developed approach widely used for transcriptome profiling in biological analyses that use next-generation sequencing technologies. Accurate estimation of gene expression levels is critical for answering biological questions. Here, we show that the commonly used measure of gene expression levels, fragments per kilobase of transcript per million mapped reads (FPKM), is biased in transcript length, GC content, and dinucleotide frequencies in the RNA-seq analysis of marine species. We used a generalized linear model to correct the observed biases of FPKM. We used RNA-seq data sets from eight species obtained by different sequencing methods to evaluate the correction methods. Our work contributes to the understanding of potential technical artifacts in RNA-seq experiments for marine species, and presents a means by which more accurate gene expression measures can be obtained.
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