Commonly used medications and endometrial cancer survival: a population-based cohort study.

Genomic Identification of Significant Targets (GISTIC) outputs for Circular Binary Segmentation (CBS) - or Piecewise Constant Fit (PCF) - segmented input data. The number of peaks attained by GISTIC on the y-axis is plotted against the two changing parameters α for CBS and γ for PCF on the x-axis. GISTIC peaks of amplification applying CBS-segmented data are illustrated in pink and PCF-segmented data in red, respectively. Deletion peaks are colored in green for CBS-segmented input data and in blue for PCF-segmented data. From top to bottom are shown GISTIC focal peaks for breast, ovarian, endometrial, and cervical cancers, to the left for PCF-segmented input data (A, C, E, and G) and to the right for CBS-segmented input data (B, D, F and H), respectively. For further analysis are the selected α and γ highlighted with a colored square. (PDF 362 kb

Additional file 14: Figure S5. of A systematic comparison of copy number alterations in four types of female cancer

A schematic view of two common genes among female cancers. This schematic view shows the genomic positions of two genes that were found common among female cancers. The figure further suggests an explanation about the lack of any common genes for the focal aberrations at 8q24.3. (XLSX 493 kb

Additional file 11: Table S6. of A systematic comparison of copy number alterations in four types of female cancer

GISTIC focal peaks for joint regions of CBS and PCF gains and losses. This table shows the GISTIC focal peaks of the overlapping regions between CBS and PCF. (XLSX 15 kb

Additional file 10: Figure S4. of A systematic comparison of copy number alterations in four types of female cancer

Focal peaks of GISTIC for female cancers based on PCF-segmented input data (amplifications and deletions). Panel A represents the aberrations of female cancers in a circular format for PCF-segmented input data to GISTIC. In clockwise direction, breast, ovarian, endometrial, and cervical cancers are displayed in pink (breast), green (ovarian), purple (endometrial), or brown (cervical) cancers. From top of the circles are displayed 23 chromosomes for each cohort, each chromosome’s cytobands colored differently. Rearrangements are represented by lines connecting the overlapping cytobands between the different female cancers. The width of lines is matched with the size of each cytoband. Amplification lines are colored in red and deletion lines in blue, respectively. Panel B focuses separately on each chromosome. (PDF 330 kb

Additional file 7: Table S5. of A systematic comparison of copy number alterations in four types of female cancer

GISTIC focal peaks for selected α (CBS) and γ (PCF) - gains and losses. Table S5 reveals the GISTIC focal peaks of the selected values in Table S4. Indicated by asterisks (*) are the joint regions between cancer types for at least two cancers displaying a common genomic region, and (n) representing the number of events in each cohort. (XLSX 37 kb

Additional file 3: Table S2. of A systematic comparison of copy number alterations in four types of female cancer

GISTIC focal peaks for simulated data – gains and losses. Table S2A exemplifies the number of focal peaks of simulation data for PCF-segmented input data to GISTIC and variable γ from 10 to 90. Table S2B represents GISTIC focal peaks of simulated data for CBS-segmented input data to GISTIC and α varied from 0.00001 to 0.1. (XLSX 10 kb

Additional file 9: Figure S3. of A systematic comparison of copy number alterations in four types of female cancer

Focal peaks of GISTIC for female cancers based on CBS-segmented data (amplifications and deletions). Panel A represents the aberrations of various female cancers for CBS-segmented input data to GISTIC in a circos-plot. In clockwise direction, breast (B, pink), ovarian (O, green), endometrial (E, purple), or cervical (C, brown) cancers are displayed. From the top of circles with 23 chromosomes presented for each cohort with each chromosome’s cytobands is colored differently. Aberrations are represented by lines linking the overlapping cytobands between the various female cancers. The width of lines is matched to the size of each cytoband. Amplification lines are colored in red and deletion lines are illustrated in blue. Panel B focuses separately on each chromosome. (PDF 329 kb