Selected article for: "gene normalization and normalized expression"
Author: C Langelier; MS Zinter; K Kalantar; GA Yanik; S Christenson; B Odonovan; C White; M Wilson; A Sapru; CC Dvorak; S Miller; CY Chiu; JL DeRisi
Title: Metagenomic Sequencing Detects Respiratory Pathogens in Hematopoietic Cellular Transplant Patients
  • Document date: 2017_1_24
    • ID: km0b1z64_21
    Snippet: RNA transcripts aligning to the human genome were captured by our computational pipeline as described above. Cumulative sum scaling normalization of protein-coding gene transcripts was carried out (26) and genes expressed in fewer than 30% of samples, or as outliers in only 10% of samples, were removed. Using a supervised approach, pathways related to immune functionality were selected a priori from the Molecular Signatures Database (27) and comp.....
    Document: RNA transcripts aligning to the human genome were captured by our computational pipeline as described above. Cumulative sum scaling normalization of protein-coding gene transcripts was carried out (26) and genes expressed in fewer than 30% of samples, or as outliers in only 10% of samples, were removed. Using a supervised approach, pathways related to immune functionality were selected a priori from the Molecular Signatures Database (27) and compared in terms of total normalized expression between subjects using the nonparametric Wilcoxon Rank Sum test as described in the online data supplement. These pathways contained gene biomarkers associated with antiviral response, interferons α, β, and γ, IL-6/JAK/STAT5 signaling and adaptive immunity, and have all been strongly associated with the immune response to infection (28, 29) .

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