Matúš Medo
YOU?
Author Swipe
View article: Replicability of bulk RNA-Seq differential expression and enrichment analysis results for small cohort sizes
Replicability of bulk RNA-Seq differential expression and enrichment analysis results for small cohort sizes Open
The high-dimensional and heterogeneous nature of transcriptomics data from RNA sequencing (RNA-Seq) experiments poses a challenge to routine downstream analysis steps, such as differential expression analysis and enrichment analysis. Addit…
View article: Table S2 from E2F1-Associated Purine Synthesis Pathway Is a Major Component of the MET-DNA Damage Response Network
Table S2 from E2F1-Associated Purine Synthesis Pathway Is a Major Component of the MET-DNA Damage Response Network Open
Differential expression analysis of the GTL-16 and EBC-1 transcriptomics data.
View article: Figure S6 from E2F1-Associated Purine Synthesis Pathway Is a Major Component of the MET-DNA Damage Response Network
Figure S6 from E2F1-Associated Purine Synthesis Pathway Is a Major Component of the MET-DNA Damage Response Network Open
GART protein expression upon MAPK and PI3K targeting: GART protein levels in untreated GTL-16 and EBC-1 cells and after MAPK (AZD6244) and PI3K (LY294002) pathways inhibition. ß Actin was used as a loading control.
View article: Figure S6 from E2F1-Associated Purine Synthesis Pathway Is a Major Component of the MET-DNA Damage Response Network
Figure S6 from E2F1-Associated Purine Synthesis Pathway Is a Major Component of the MET-DNA Damage Response Network Open
GART protein expression upon MAPK and PI3K targeting: GART protein levels in untreated GTL-16 and EBC-1 cells and after MAPK (AZD6244) and PI3K (LY294002) pathways inhibition. ß Actin was used as a loading control.
View article: Table S4 from E2F1-Associated Purine Synthesis Pathway Is a Major Component of the MET-DNA Damage Response Network
Table S4 from E2F1-Associated Purine Synthesis Pathway Is a Major Component of the MET-DNA Damage Response Network Open
Summary of the significance analysis for the survival analyses.
View article: Figure S2 from E2F1-Associated Purine Synthesis Pathway Is a Major Component of the MET-DNA Damage Response Network
Figure S2 from E2F1-Associated Purine Synthesis Pathway Is a Major Component of the MET-DNA Damage Response Network Open
Suppementary metabolomics data: (A) Heat map determining top hits of metabolite ions in all cell lines at 24 hrs time-point post METi (|log2FC| > 0.5; adj.P value < 0.01). (B) Differences in metabolite ions (dots) abundance in METi-…
View article: Table S3 from E2F1-Associated Purine Synthesis Pathway Is a Major Component of the MET-DNA Damage Response Network
Table S3 from E2F1-Associated Purine Synthesis Pathway Is a Major Component of the MET-DNA Damage Response Network Open
Basic statistics of the downloaded TCGA data.
View article: Table S1 from E2F1-Associated Purine Synthesis Pathway Is a Major Component of the MET-DNA Damage Response Network
Table S1 from E2F1-Associated Purine Synthesis Pathway Is a Major Component of the MET-DNA Damage Response Network Open
Differential abundance analysis and ion annotation matches for non-targeted metabolomics measurements.
View article: Table S3 from E2F1-Associated Purine Synthesis Pathway Is a Major Component of the MET-DNA Damage Response Network
Table S3 from E2F1-Associated Purine Synthesis Pathway Is a Major Component of the MET-DNA Damage Response Network Open
Basic statistics of the downloaded TCGA data.
View article: Figure S3 from E2F1-Associated Purine Synthesis Pathway Is a Major Component of the MET-DNA Damage Response Network
Figure S3 from E2F1-Associated Purine Synthesis Pathway Is a Major Component of the MET-DNA Damage Response Network Open
Supplementations with glutamine, serine, and folic acid: (A) Proliferation of GTL-16 and EBC-1 cells upon supplementation with glutamine, serine or folic acid. (B) Apoptosis (caspase-3 activation) in GTL-16 and EBC-1 cells upon supplementa…
View article: Figure S5 from E2F1-Associated Purine Synthesis Pathway Is a Major Component of the MET-DNA Damage Response Network
Figure S5 from E2F1-Associated Purine Synthesis Pathway Is a Major Component of the MET-DNA Damage Response Network Open
GART and E2F1 mRNA levels following METi combined with IR: mRNA levels of GART (left) and E2F1 (right) following METi (50nM, 24 hr), IR (10 Gy, 1 hr) and their combination in GTL-16 and EBC-1 cells.
View article: Table S2 from E2F1-Associated Purine Synthesis Pathway Is a Major Component of the MET-DNA Damage Response Network
Table S2 from E2F1-Associated Purine Synthesis Pathway Is a Major Component of the MET-DNA Damage Response Network Open
Differential expression analysis of the GTL-16 and EBC-1 transcriptomics data.
View article: Figure S3 from E2F1-Associated Purine Synthesis Pathway Is a Major Component of the MET-DNA Damage Response Network
Figure S3 from E2F1-Associated Purine Synthesis Pathway Is a Major Component of the MET-DNA Damage Response Network Open
Supplementations with glutamine, serine, and folic acid: (A) Proliferation of GTL-16 and EBC-1 cells upon supplementation with glutamine, serine or folic acid. (B) Apoptosis (caspase-3 activation) in GTL-16 and EBC-1 cells upon supplementa…
View article: Table S4 from E2F1-Associated Purine Synthesis Pathway Is a Major Component of the MET-DNA Damage Response Network
Table S4 from E2F1-Associated Purine Synthesis Pathway Is a Major Component of the MET-DNA Damage Response Network Open
Summary of the significance analysis for the survival analyses.
View article: Figure S4 from E2F1-Associated Purine Synthesis Pathway Is a Major Component of the MET-DNA Damage Response Network
Figure S4 from E2F1-Associated Purine Synthesis Pathway Is a Major Component of the MET-DNA Damage Response Network Open
Supplementations with nucleosides and hypoxanthine: (A) Proliferation of GTL-16 and EBC-1 cells upon supplementation with nucleosides or hypoxanthine. (B) Apoptosis (caspase-3 activation) in GTL-16 and EBC-1 upon supplementation with nucle…
View article: Figure S1 from E2F1-Associated Purine Synthesis Pathway Is a Major Component of the MET-DNA Damage Response Network
Figure S1 from E2F1-Associated Purine Synthesis Pathway Is a Major Component of the MET-DNA Damage Response Network Open
p4E-BP1 protein levels upon MET inhibition: Whole-cell lysates were subjected to Western blotting using a specific antibody against p4E-BP1 following the treatment either with vehicle or 50nM tepotinib (EMD1214063, shortly EMD) for either …
View article: Figure S1 from E2F1-Associated Purine Synthesis Pathway Is a Major Component of the MET-DNA Damage Response Network
Figure S1 from E2F1-Associated Purine Synthesis Pathway Is a Major Component of the MET-DNA Damage Response Network Open
p4E-BP1 protein levels upon MET inhibition: Whole-cell lysates were subjected to Western blotting using a specific antibody against p4E-BP1 following the treatment either with vehicle or 50nM tepotinib (EMD1214063, shortly EMD) for either …
View article: Figure S4 from E2F1-Associated Purine Synthesis Pathway Is a Major Component of the MET-DNA Damage Response Network
Figure S4 from E2F1-Associated Purine Synthesis Pathway Is a Major Component of the MET-DNA Damage Response Network Open
Supplementations with nucleosides and hypoxanthine: (A) Proliferation of GTL-16 and EBC-1 cells upon supplementation with nucleosides or hypoxanthine. (B) Apoptosis (caspase-3 activation) in GTL-16 and EBC-1 upon supplementation with nucle…
View article: Figure S5 from E2F1-Associated Purine Synthesis Pathway Is a Major Component of the MET-DNA Damage Response Network
Figure S5 from E2F1-Associated Purine Synthesis Pathway Is a Major Component of the MET-DNA Damage Response Network Open
GART and E2F1 mRNA levels following METi combined with IR: mRNA levels of GART (left) and E2F1 (right) following METi (50nM, 24 hr), IR (10 Gy, 1 hr) and their combination in GTL-16 and EBC-1 cells.
View article: Table S1 from E2F1-Associated Purine Synthesis Pathway Is a Major Component of the MET-DNA Damage Response Network
Table S1 from E2F1-Associated Purine Synthesis Pathway Is a Major Component of the MET-DNA Damage Response Network Open
Differential abundance analysis and ion annotation matches for non-targeted metabolomics measurements.
View article: Figure S2 from E2F1-Associated Purine Synthesis Pathway Is a Major Component of the MET-DNA Damage Response Network
Figure S2 from E2F1-Associated Purine Synthesis Pathway Is a Major Component of the MET-DNA Damage Response Network Open
Suppementary metabolomics data: (A) Heat map determining top hits of metabolite ions in all cell lines at 24 hrs time-point post METi (|log2FC| > 0.5; adj.P value < 0.01). (B) Differences in metabolite ions (dots) abundance in METi-…
View article: Figure S6 from HPV and p53 Status as Precision Determinants of Head and Neck Cancer Response to DNA-PKcs Inhibition in Combination with Irradiation
Figure S6 from HPV and p53 Status as Precision Determinants of Head and Neck Cancer Response to DNA-PKcs Inhibition in Combination with Irradiation Open
In-vivo tissue immunohistochemistry: (A) Tumor collection day post treatment (top panel), growth control (bottom) and (B) Ki67 (proliferation), TUNEL (DNA fragmentation), and β-gal (senescence) stainings (representative pictures (top panel…
View article: Data from HPV and p53 Status as Precision Determinants of Head and Neck Cancer Response to DNA-PKcs Inhibition in Combination with Irradiation
Data from HPV and p53 Status as Precision Determinants of Head and Neck Cancer Response to DNA-PKcs Inhibition in Combination with Irradiation Open
Major risk factors of head and neck squamous cell carcinoma (HNSCC) are tobacco use and human papillomavirus (HPV). HPV E6 oncoprotein leads to p53 degradation, whereas HPV-negative cancers are frequently associated with TP53 mutati…
View article: Figure S2 from HPV and p53 Status as Precision Determinants of Head and Neck Cancer Response to DNA-PKcs Inhibition in Combination with Irradiation
Figure S2 from HPV and p53 Status as Precision Determinants of Head and Neck Cancer Response to DNA-PKcs Inhibition in Combination with Irradiation Open
Cell cycle distribution and colony-forming assays: (A-C) Cell cycle distribution data at 7 hours (A), 24 hours (B), and 36 hours (C) after treatment (p values are not shown). (D) Colony-forming assay (two-way ANOVA with post hoc multiple c…
View article: Figure S3 from HPV and p53 Status as Precision Determinants of Head and Neck Cancer Response to DNA-PKcs Inhibition in Combination with Irradiation
Figure S3 from HPV and p53 Status as Precision Determinants of Head and Neck Cancer Response to DNA-PKcs Inhibition in Combination with Irradiation Open
Live-dead assays and apoptosis: (A) Live/Dead assay performed 5 days after the indicated treatments. Right panels: Representative pictures of dead (red; Ethidium homodimer-1) and living (green; calcein-AM) cells. Left panels: Quantificatio…
View article: Figure S1 from HPV and p53 Status as Precision Determinants of Head and Neck Cancer Response to DNA-PKcs Inhibition in Combination with Irradiation
Figure S1 from HPV and p53 Status as Precision Determinants of Head and Neck Cancer Response to DNA-PKcs Inhibition in Combination with Irradiation Open
Cell proliferation (crystal violet assays): (A) Representative images of crystal violet assay. (B) Response (1.0 - cell proliferation) as a function of the IR dose for treated (Peposertib) and untreated (Control) cell lines. Data is repres…
View article: Figure S5 from HPV and p53 Status as Precision Determinants of Head and Neck Cancer Response to DNA-PKcs Inhibition in Combination with Irradiation
Figure S5 from HPV and p53 Status as Precision Determinants of Head and Neck Cancer Response to DNA-PKcs Inhibition in Combination with Irradiation Open
In-vivo tumor growth: (A) In-vivo study treatment setup (Created with BioRender.com) (B) Tumor growth curves for each individual animal (n = 7) in all experimental and treatment groups. (C) Average animal weight gain (Mean (%) ± SEM) throu…
View article: Figure S4 from HPV and p53 Status as Precision Determinants of Head and Neck Cancer Response to DNA-PKcs Inhibition in Combination with Irradiation
Figure S4 from HPV and p53 Status as Precision Determinants of Head and Neck Cancer Response to DNA-PKcs Inhibition in Combination with Irradiation Open
Representative images of RAD51 and yH2AX foci in the nucleus (DAPI) of UM-SCC-74A (p53 wild-type), UM-SCC-14A (p53-mutated) and UM-SCC-104 (HPV+) cell lines 3 h, 24 h and 48 hours after treatment.
View article: HPV and p53 Status as Precision Determinants of Head and Neck Cancer Response to DNA-PKcs Inhibition in Combination with Irradiation
HPV and p53 Status as Precision Determinants of Head and Neck Cancer Response to DNA-PKcs Inhibition in Combination with Irradiation Open
Major risk factors of head and neck squamous cell carcinoma (HNSCC) are tobacco use and human papillomavirus (HPV). HPV E6 oncoprotein leads to p53 degradation, whereas HPV-negative cancers are frequently associated with TP53 mutations. Pe…
View article: A comprehensive comparison of tools for fitting mutational signatures
A comprehensive comparison of tools for fitting mutational signatures Open
Mutational signatures connect characteristic mutational patterns in the genome with biological or chemical processes that take place in cancers. Analysis of mutational signatures can help elucidate tumor evolution, prognosis, and therapeut…