Supplementary Material of manuscript, title: "A Global Genome-wide Scan with Optimal Cutoff Mining for Emerging Biomarkers in Head and Neck Squamous Cell Carcinoma"
pvalueTex_R_lite.tar.gz, including
Sep 8 2020 15:03 main_marginSFP_HNSCC.R # main code
Sep 8 2020 10:45 TCGA_HNSCC_marginSFP.R # step 1
May 20 2020 10:55 cutofFinder_func_HNSCC.R # cutoff finding procedure (FDR)
Jul 3 2021 10:58 analysis_export.R. # step 2 (Bonferroni)
Sep 19 2020 02:59 volcano_plot.R
Jul 2 2021 22:00 Validation_GSE65858_survival.R # final validation
Jun 26 2021 20:45 Bayes_survival.R # LASSO regression with Cox (RLassoCox)
..
2021/07/22 all R script R_script_2020July.zip
(first version at manuscript submitted on 2020/09/19) (final version at manuscript submitted on 2021/07/04) JPM
Sep 8 2020 15:01 HNSCC.clinical.Fire.Rda # HNSCC clinical dataset from TCGA
Aug 14 2019 HNSCC.clinical.RNAseq.Fire.Rda (size: 85031069byte; HNSCC RNA-Seq 20500 genes
Aug 14 2019 HNSCC.clinical.RNAseq_tobacco.Fire.Rda # HNSCC clinical dataset (with tobacco exposure)
Aug 14 2019 whole_genome.Rda # "gene ID" of 20500 protein coding genesAug 11 2021 jpm-11-00782-v2.pdf # publised article, https://www.mdpi.com/2075-4426/11/8/782
Aug 15 2021 KOMA_Script_MDPI_jpm_1309345_Keynote_VideoAbstract.pdf # keynote for Video abstract
Video is also available at YouTube: https://youtu.be/VK5F43fusDA
Intermediate_data:
Sep 8 2019 HNSCC.survival.marginS.20500.tar.gz # resulting survival tables of each gene (.Rda + .xlsx), size 933Mb
Sep 8 2019 file20500_list.txt # gene ID and filename list of HNSCC.survival.marginS.20500.tar.gz
Mar 8 2020 HNSCC_OS_marginS_6429.csv # survival tables of 6429 genes (uncorrected P-value < 0.05), with FDR correction
Sep 19 2020 08:18 HNSCC.survival.marginS.candidate20.tar.gz # survival tables of 20 candidate genes (.xlsx)
Mar 8 2020 HNSCC_OS_marginS_10bad_candidates.csv # gene ID list of "bad" candidates
Mar 8 2020 HNSCC_OS_marginS_10good_candidates.csv # gene ID list of "good" candidates
Oct 7 2020 CI_genes.Rda candidate gene set belongs to the immune system process and immune response
Jun 6 2021 HNSCC.mRNA.Exp.SLC35E2.Fire.Rda mRNA data of SLC35E2 (containing SLC35E2A and SLC35E2B)
Supplementary Figures:
Feb 2 2021 cancers-1082127_supplementaryFigure123.pdf
Aug 4 2021 MDPI_JPM_1309345-10_supplementary.pdfThe implementation by Rstudio shiny App, supporting all TCGA diseases, with custom feature.
We use Semantic Versioning to identify each release. (https://semver.org)
The content of this material is licensed under the GNU General Public License v3.0 or later.
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