Additional file 4: Figure S3. of SPAG6 and L1TD1 are transcriptionally regulated by DNA methylation in non-small cell lung cancers

SPAG6 and L1TD1 SNVs and deletions in NSCLC patients. TCGA LUAD and LUSC datasets were analysed with Caleydo software (version April 2014). Mutation of TP53 was used to demonstrate reliability of TCGA data analysis. ADC, adenocarcinoma patients; SCC, squamous carcinoma patients. (TIF 90 kb

Additional file 3: Figure S2. of SPAG6 and L1TD1 are transcriptionally regulated by DNA methylation in non-small cell lung cancers

Impact of SPAG6 and L1TD1 mRNA expression on OS of NSCLC patients. (A) A shorter OS of squamous cell carcinoma patients with low SPAG6 mRNA expression (N = 155) compared to high SPAG6 mRNA expression (N = 267) was observed. (B) Adenocarcinoma patients with low L1TD1 mRNA expression (N = 138) showed a shorter OS compared to adenocarcinoma patients with high L1TD1 mRNA expression (N = 350). Gene expression microarray datasets (Affymetrix IDs 210032_s_at and 219955_at) were analysed and Kaplan-Meier plots were generated using all datasets and default settings of KM plotter. The cut-off values for “low” and “high” SPAG6 and L1TD1 mRNA expression were automatically defined by KM plotter software (Version 2013). (TIF 50 kb

Additional file 1: Table S1. of SPAG6 and L1TD1 are transcriptionally regulated by DNA methylation in non-small cell lung cancers

Description of NSCLC cell lines used in this study. Information about histology, origin and disease stage of donors was obtained from ATCC catalogue ( https://www.lgcstandards-atcc.org ). EGFR, KRAS and TP53 mutational status and MET amplification according to supplementary references (1–3). *activating EGFR mutation in exon 19 (E746-E749 del), **activating EGFR mutation in exon 21 (L858R). N/A, not available; wt, wildtype; mut, mutated. Table S2. Clinico-pathological characteristics of 983 NSCLC patients. Overview of gender, histology, stage of disease and ethnicity of NSCLC patients obtained from TCGA database and used for mutation and copy number changes analyses of SPAG6 and L1TD1 is shown. ADC, adenocarcinoma; SCC, squamous cell carcinoma. Clinical data based on Caleydo software version 16/04/14. Table S3. Primer sequences. Summary of oligonucleotide sequences used for mRNA expression, MS-HRM, BGS analyses and construction of pCMV6-GFP expression vector. Y, random integration of C or T in fwd primer; R, random integration of G or A in rev primer. Table S4. Methylation of SPAG6 and L1TD1 in tumor cells of other tumor types. *Morphology, histology and origin of cell lines according to ATCC catalogue ( https://www.lgcstandards-atcc.org ). Percentage of methylation was calculated as described previously (4). (DOCX 33 kb

Additional file 2: Figure S1. of SPAG6 and L1TD1 are transcriptionally regulated by DNA methylation in non-small cell lung cancers

SPAG6 and L1TD1 mRNA expression in different datasets of TCGA database. SPAG6 and L1TD1 mRNA expression was analysed using IlluminaHiSeq RNAseq data from TCGA database. Datasets LUAD and LUSC (lung), BRCA (breast), COADREAD (colorectal), HNSC (head and neck), KIRC (kidney), LIHC (liver) and PRAD (prostate) were analysed. Normalized log2 mRNA expression values are shown. Each dot represents a single sample. (TIF 176 kb