Additional file 8 of Gene expression variability in long-term survivors of childhood cancer and cancer-free controls in response to ionizing irradiation
Creators: name: Grandt, Caine Lucas
name: Brackmann, Lara Kim
name: Foraita, Ronja
name: Schwarz, Heike
name: Hummel-Bartenschlager, Willempje
name: Hankeln, Thomas
name: Kraemer, Christiane
name: Zahnreich, Sebastian
name: Drees, Philipp
name: Mirsch, Johanna
name: Spix, Claudia
name: Blettner, Maria
name: Schmidberger, Heinz
name: Binder, Harald
name: Hess, Moritz
name: Galetzka, Danuta
name: Marini, Federico
name: Poplawski, Alicia
name: Marron, Manuela
Publisher: name: figshare
Year: 2024
Subjects: subject: Cell Biology
subject: Genetics
subject: FOS: Biological sciences
subject: Molecular Biology
subject: Physiology
subject: Immunology
subject: FOS: Clinical medicine
subject: Biological Sciences not elsewhere classified
subject: Cancer
subject: Virology

description: Additional file 8. Stratified_Analyses. a: Violin and jitter plots comparing results of the analyses for bimodally expressed genes stratified by radiation dose and sex. With respect to the reduced sample size due to the stratification, the cut-off was increased to 1.3 (dashed line). Nevertheless, these sample sizes (female: n = 81, male: n = 75) could still not have been sufficient to provide adequate power for the detection of bimodally expressed genes. b: Comparison of expressional variation by sex. The scatterplot compares the sex-specific EV per gene and radiation dose. The black line indicates the linear regression model (adjusted r2: 0.779; Kendall’s tau: 0.786). Only genes with a bimodal index &lt; 1.3 were included in the analysis. c: Bar charts showing the number of genes per classification using the whole data set and the number of genes with stable classification after cross-validation per radiation dose. Data shown here were stratified by sex. Only genes with a bimodal index &lt; 1.3 were included in the analyses. N0 = fibroblasts of cancer-free controls, N1 = fibroblasts of long-term survivors of childhood cancer without a second primary neoplasm, and N2 +  = fibroblasts of long-term survivors of childhood cancer with at least one second primary neoplasm. d: Intersect graphs of overlapping gene classifications: Data are stratified by variability classification, donor group (N0 = fibroblasts of cancer-free controls, N1 = fibroblasts of long-term survivors of childhood cancer without a second primary neoplasm, N2 +  = fibroblasts of long-term survivors of childhood cancer with at least one second primary neoplasm), sex, and radiation dose. Connected rows implicate that genes were identically classified in these data sets. Bars denote the summed number of identically classified genes among the vertically connected rows of data. e: Violin and jitter plots comparing results of the analyses for bimodally expressed genes stratified by radiation dose and consumption information on smoking and alcohol. Data used here were donor triplets without heavy smokers (&gt; 10 pack years) and/or alcohol consumption (&gt; 2 alcoholic beverages per day), termed “healthy” for brevity; as well as triplets that contained at least one donor with the above-described lifestyle, shortly termed “unhealthy”. To ensure validity, the cut-off was increased to 1.3 due to the reduced sample size. Nevertheless, these sample sizes (Donors from triplets without any heavy smokers or drinkers: n = 60, donors from triplets with at least one heavy drinker or smoker: n = 54) might not be sufficient to provide adequate power for the detection of bimodally expressed genes with the given cut-off. f: Bar charts showing the number of genes per classification using the whole data set and the number of genes with stable classification after cross-validation per radiation dose. Data used here were donor triplets without heavy smokers (&gt; 10 pack years) and/or alcohol consumption (&gt; 2 alcoholic beverages per day), termed”healthy”; as well as triplets that contained at least one donor with the above-described lifestyle, termed “unhealthy” for brevity. Only genes with a bimodal index &lt; 1.3 were included in the analyses. N0 = fibroblasts of cancer-free controls, N1 = fibroblasts of long-term survivors of childhood cancer without a second primary neoplasm, and N2 +  = fibroblasts of long-term survivors of childhood cancer with at least one second primary neoplasm. g: Comparison of the EV per gene and radiation dose comparison donor triplets with and without heavy smokers (&gt; 10 pack years) and/or alcohol consumption (&gt; 2 alcoholic beverages per day). The red line indicates the linear regression model (adjusted r2: 0.377; Kendall’s tau: 0.683). Only genes with a bimodal index &lt; 1.3 were included in the analysis. h: Intersect graphs of overlapping gene classifications: Data are stratified by variability classification, donor group (N0 = fibroblasts of cancer-free controls, N1 = fibroblasts of long-term survivors of childhood cancer without a second primary neoplasm, N2 +  = fibroblasts of long-term survivors of childhood cancer with at least one second primary neoplasm), radiation dose, and additionally computed using only the 20 donor triplets (n = 60) without heavy smokers (&gt; 10 pack years) and/or alcohol consumption (&gt; 2 alcoholic beverages per day). Connected rows implicate that genes were identically classified in these data sets. Bars denote the summed number of identically classified genes among the vertically connected rows of data.