Journal: Cancer immunology research

Article Title: Head and neck cancers promote an inflammatory transcriptome through co-activation of classical and alternative NF-κB pathways

doi: 10.1158/2326-6066.CIR-18-0832

Figure Lengend Snippet: (A) Correlation between (CNV) and mRNA expression in HNSCC with different HPV status. Scatterplots for 20 selected genes showing significant CNV and gene expression correlation in HNSCC TCGA datasets (n = 279), including 243 HPV(–) (gray circles), and 36 HPV(+) specimens (red triangles). Pearson correlation coefficient significance test, with P values presented. X axis, log2 CN ratio; 0 is diploid, −1 is one-copy loss, 0.585 is one-copy gain, and values larger than 1 are amplifications. Y axis, log2 transformed RNA-Seq RSEM values. (B). The genes with statistical significance in distribution of various CNV between HPV(–) samples (blue bar) and HPV(+) samples (orange bar). The percentage of each CNV types in their respective HPV status groups were calculated based on the HNSCC sample counts. Statistical analysis was conducted by Fisher exact test.

Article Snippet: Parallel analyses of HNSCC TCGA datasets and molecular features of cell lines Datasets of the 279 HNSCC tumor plus 16 normal mucosa tissues in the TCGA cohorts including level 3 RNA sequencing data (log2 transformed RPKM value, as reads per kilobase of transcript per million mapped reads), HPV status, and clinic data were downloaded from the Broad Institute Firebrowse website ( http://firebrowse.org/ ).

Techniques: Expressing, Gene Expression, Transformation Assay, RNA Sequencing

Journal: Cancer immunology research

Article Title: Head and neck cancers promote an inflammatory transcriptome through co-activation of classical and alternative NF-κB pathways

doi: 10.1158/2326-6066.CIR-18-0832

Figure Lengend Snippet: Altered gene expression between 279 HNSCC specimens and 16 normal mucosa specimens from TCGA (left panels), as well as 26 HNSCC cell lines and 3 HOK lines (right panels) were compared from RNA-seq. Mean expression levels of genes were compared between tumor [including both HPV(–) and HPV(+) samples] and normal tissues, as well as between tumors with different HPV status. The 28 most altered genes are presented by the relative gene expression levels as mean± standard errors (SE). Statistical difference was calculated by Student t-test (P<0.05). * indicates statistical significances when compared mean expression of genes between tumor [including both HPV(–) and HPV(+) samples] with normal tissues, and # indicates significance when the comparison between tumor samples of different HPV status. The gene expression of 26 HNSCC cell lines were compared with the mean of the three HOK lines, as well as between tumor lines with different HPV status (right panels). The data analysis was performed in the same way as for HNSCC TCGA data.

Article Snippet: Parallel analyses of HNSCC TCGA datasets and molecular features of cell lines Datasets of the 279 HNSCC tumor plus 16 normal mucosa tissues in the TCGA cohorts including level 3 RNA sequencing data (log2 transformed RPKM value, as reads per kilobase of transcript per million mapped reads), HPV status, and clinic data were downloaded from the Broad Institute Firebrowse website ( http://firebrowse.org/ ).

Techniques: Gene Expression, RNA Sequencing, Expressing, Comparison