Information for the HNSCC training set was obtained from TCGA on November 13, 2016 (18 (link)). Gene expression data were extracted from IlluminaHiSeq_RNASeqV2 platform and normalized by RSEM method (19 (link)). In addition, we performed quality control with a total of 20530 genes. Genes with more than half of values as zero were removed, 17711 genes remained with quantile normalization. Patients with complete follow-up information and gene expression values for tumor tissues were included in the study. Information for the HNSCC testing set was collected from GSE65858 (20 (link)) in GEO. Gene expression data were extracted from Illumina HumanHT-12 V4.0 expression beadchip and normalized using the robust spline normalization (RSN) method (21 (link)). Consecutive patients with primary and metachronous secondary HNSCC of oral cavity, larynx, oro- and hypopharynx were included, while tumor cell lines and those with low quality assays were excluded. All gene expression values were log2-transformed and standardized for comparability between the training and testing sets.
Protocol detail
HNSCC Gene Expression Data Analysis
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Assays
Gene expression
Genes
Genes control
Hnscc
Hypopharynx
Larynx
Oral cavity
Patients
Tissues
Tumor cell lines
Tumor gene
Corresponding Organization :
Other organizations : Nanjing Medical University, Shanghai Institute of Planned Parenthood Research
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Variable analysis
independent variables
- Gene expression data extracted from the IlluminaHiSeq_RNASeqV2 platform and normalized by the RSEM method
- Gene expression data extracted from the Illumina HumanHT-12 V4.0 expression beadchip and normalized using the robust spline normalization (RSN) method
- Patients with complete follow-up information and gene expression values for tumor tissues
- Genes with more than half of values as zero were removed, 17711 genes remained with quantile normalization
- Consecutive patients with primary and metachronous secondary HNSCC of oral cavity, larynx, oro- and hypopharynx were included, while tumor cell lines and those with low quality assays were excluded
- All gene expression values were log2-transformed and standardized for comparability between the training and testing sets
- No positive or negative controls were explicitly mentioned in the information provided.
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