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PATHOLOGY TESTIS CANCER Show tissue menu
BREAST CANCER CARCINOID CERVICAL CANCER COLORECTAL CANCER ENDOMETRIAL CANCER GLIOMA HEAD AND NECK CANCER LIVER CANCER LUNG CANCER LYMPHOMA
MELANOMA OVARIAN CANCER PANCREATIC CANCER PROSTATE CANCER RENAL CANCER SKIN CANCER STOMACH CANCER TESTIS CANCER THYROID CANCER UROTHELIAL CANCER
Dictionary
Testis cancer
Human pathology
Testis cancer
TESTICULAR GERM CELL TUMOR (TGCT) - Interactive survival scatter ploti

The Survival Scatter plot shows the clinical status (i.e. dead or alive) for all individuals in the patient cohort, based on the same data that underlies the corresponding Kaplan-Meier plots. Patients that are alive at last time for follow-up are shown in blue and patients who have died during the study are shown in red.

The x-axis shows the expression levels (FPKM) of the investigated gene in the tumor tissue at the time of diagnosis. The y-axis shows the follow-up time after diagnosis (years). Both axes are complimented with kernel density curves demonstrating the data density over the axes. The top density plot shows the expression levels (FPKM) distribution among dead (red) and alive patients (blue). The right density plot shows the data density of the survived years of dead patients with high and low expression levels respectively, stratified using the cutoff indicated by the vertical dashed line through the Survival Scatter plot. This cutoff is automatically defined based on the FPKM cutoff that minimizes the p-score. The cutoff can be changed by dragging the vertical line or by entering a cutoff value in the square labeled "Current cut-off".

Under the Survival Scatter plot the p-score landscape (black curve; left axis) is shown together with dead median separation (red curve; right axis). Dead median separation is the difference in median mRNA expression between patients who have died with high and low expression, respectively. It is calculated as follows: median FPKM expression of dead patients with high expression - median FPKM expression of dead patients with low expression. This is intended to aid the user in visually exploring custom cutoffs and the associated p-scores and dead median separation.

Individual patient data is displayed and can be filtered by clicking on one or more of the category buttons on the top of the page. Categories describing expression level and patient information include: high, low, alive, dead, female, male and tumor stages. The scale of the x-axis can be toggled between linear and log-scale by clicking on the "x log" button. Mouse-over function shows TCGA ID, patient information and mRNA expression (FPKM) for each patient.

& Survival analysisi

Kaplan-Meier plots summarize results from analysis of correlation between mRNA expression level and patient survival. Patients were divided based on level of expression into one of the two groups "low" (under cut off) or "high" (over cut off). X-axis shows time for survival (years) and y-axis shows the probability of survival, where 1.0 corresponds to 100 percent.




Stage:


Survival analysis
Current cut offi

Current cut-off shows the cut-off (FPKM) currently selected. It may be changed manually. When the current cut-off is changed, the vertical dashed line indicating cut-off, the interactive survival scatter plot and the Kaplan-Meier curve will be automatically adjusted to show results accordingly.

:
Best expression cut offi

Based on the FPKM value of each gene, patients were classified into two groups and association between prognosis (survival) and gene expression (FPKM) was examined. The best expression cut-off refers the FPKM value that yields maximal difference with regard to survival between the two groups at the lowest log-rank P-value. Best expression cut-off was selected based on survival analysis .

When clicking on this number, the vertical dashed line indicating cut-off, the interactive survival plot, and the Kaplan-Meier curve will be adjusted to show results based on the best expression cut-off.

: 67.25
Median expressioni

Median expression refers to the median FPKM value calculated based on the gene expression (FPKM) data from all patients in this dataset. When clicking on this number, the vertical dashed line indicating cut-off, the interactive survival plot, and the Kaplan-Meier curve will be adjusted to show results based on the median expression.

: N/A
Median follow up timei

Median follow up time refers to the median time (years) after diagnosis with this type of cancer, based on clinical data from all patients in this dataset.

: N/A
P scorei

Log-rank P value for Kaplan-Meier plot showing results from analysis of correlation between mRNA expression level and patient survival.

N/A
5-year survival highi

5-year survival for patients with higher expression than the expression cutoff.

For melanoma and glioma, 3-year survival is shown.

N/A
5-year survival lowi

5-year survival for patients with lower expression than the expression cutoff.

For melanoma and glioma, 3-year survival is shown.

N/A
TCGA RNA samplesi

RNA-seq data is reported as average FPKM (number Fragments Per Kilobase of exon per Million reads), generated by the The Cancer Genome Atlas (TCGA) .

Normal distribution across the dataset is visualized with box plots, shown as median and 25th and 75th percentiles. Points are displayed as outliers if they are above or below 1.5 times the interquartile range. FPKM values of the individual samples are presented next to the box plot.

Average FPKM 56.4
Number of samples 134
Samples
Sample Description FPKM
TCGA-2G-AAG8-01A 21 years, male, white, stage:ib, alive, 2289 days 115.0
TCGA-VF-A8AD-01A 36 years, male, white, stage:ib, alive, 1006 days 97.9
TCGA-2G-AAGA-01A 38 years, male, white, stage:iia, alive, 2439 days 96.8
TCGA-X3-A8G4-01A 33 years, male, white, stage:is, alive, 856 days 91.5
TCGA-2G-AAFV-01A 31 years, male, white, stage:is, alive, 1389 days 91.1
TCGA-2G-AAL7-01A 32 years, male, white, stage:is, alive, 3991 days 86.3
TCGA-2G-AAGN-01A 41 years, male, white, stage:iiib, alive, 3656 days 85.4
TCGA-2G-AAG7-01A 33 years, male, white, stage:is, alive, 2475 days 84.0
TCGA-2G-AAFL-01A 35 years, male, white, stage:ib, alive, 750 days 82.3
TCGA-XY-A8S3-01B 24 years, male, white, stage:is, alive, 843 days 80.3
TCGA-2G-AAFO-01A 33 years, male, white, stage:iia, alive, 685 days 79.6
TCGA-2G-AAGK-01A 20 years, male, white, stage:is, alive, 3621 days 78.5
TCGA-2G-AAGC-01A 28 years, male, white, stage:is, alive, 2585 days 78.2
TCGA-YU-AA4L-01A 27 years, male, black or african american, stage:iiic, alive, 1573 days 77.3
TCGA-2G-AAGO-01A 41 years, male, white, stage:is, alive, 4026 days 77.3
TCGA-2G-AALP-01A 43 years, male, white, stage:iiib, alive, 2645 days 76.6
TCGA-2G-AAFN-01A 26 years, male, white, stage:iiib, alive, 773 days 75.2
TCGA-WZ-A7V5-01A 27 years, male, white, stage:i, alive, 1061 days 75.1
TCGA-VF-A8A8-01A 18 years, male, white, stage:ia, alive, 1131 days 74.7
TCGA-2G-AAKL-01A 26 years, male, white, stage:ii, alive, 7023 days 74.5
TCGA-2G-AAGT-01A 30 years, male, white, stage:is, alive, 4406 days 73.7
TCGA-XE-A8H1-01A 24 years, male, white, stage:is, alive, 209 days 71.9
TCGA-2G-AAFZ-01A 32 years, male, white, stage:iii, alive, 1353 days 71.8
TCGA-2G-AAFI-01A 41 years, male, white, stage:ib, alive, 675 days 71.6
TCGA-2G-AAG0-01A 23 years, male, white, stage:is, alive, 1529 days 70.7
TCGA-W4-A7U4-01A 23 years, male, white, alive, 738 days 70.5
TCGA-2G-AAGI-01A 33 years, male, white, stage:is, alive, 3137 days 70.4
TCGA-2G-AAKG-01A 22 years, male, white, stage:i, alive, 6598 days 69.5
TCGA-2G-AAKH-01A 19 years, male, white, stage:ii, alive, 6862 days 69.0
TCGA-YU-A90P-01A 25 years, male, white, stage:ia, alive, 2069 days 68.9
TCGA-2G-AAF6-01A 28 years, male, white, stage:is, alive, 3491 days 68.2
TCGA-2G-AAFM-01A 31 years, male, white, stage:iia, alive, 503 days 68.1
TCGA-VF-A8A9-01A 31 years, male, white, stage:ia, alive, 1119 days 67.9
TCGA-SN-A84Y-01A 18 years, male, white, stage:is, alive, 524 days 67.6
TCGA-2G-AAF8-01A 33 years, male, white, stage:ia, alive, 3911 days 67.4
TCGA-2G-AAKM-01A 14 years, male, white, stage:ii, dead, 6972 days 67.1
TCGA-2G-AAGE-01A 21 years, male, white, stage:is, alive, 2478 days 66.8
TCGA-2G-AAGM-01A 51 years, male, white, stage:is, alive, 3891 days 65.7
TCGA-2G-AAGG-01A 20 years, male, white, stage:iiic, alive, 2611 days 65.6
TCGA-YU-A90Y-01A 23 years, male, black or african american, stage:iiic, dead, 17 days 64.6
TCGA-YU-A94I-01A 66 years, male, stage:ia, alive, 536 days 64.1
TCGA-SN-A84X-01A 21 years, male, white, stage:is, alive, 312 days 63.4
TCGA-2G-AAGF-01A 28 years, male, white, stage:is, alive, 2734 days 63.3
TCGA-2G-AAH0-01A 30 years, male, white, stage:is, alive, 5477 days 62.4
TCGA-W4-A7U2-01A 26 years, male, white, alive, 1263 days 62.3
TCGA-2G-AAGZ-01A 27 years, male, white, stage:iiia, alive, 5233 days 62.3
TCGA-2G-AAL5-01A 31 years, male, white, stage:i, alive, 7437 days 62.2
TCGA-XE-AAOC-01A 31 years, male, white, stage:ia, alive, 270 days 62.0
TCGA-XY-A8S2-01A 67 years, male, white, stage:i, alive, 672 days 62.0
TCGA-VF-A8AE-01A 39 years, male, white, stage:ia, alive, 727 days 61.6
TCGA-XE-AAOB-01A 27 years, male, white, stage:is, dead, 513 days 61.3
TCGA-2G-AAH4-01A 34 years, male, white, stage:ii, alive, 6210 days 60.7
TCGA-W4-A7U3-01A 26 years, male, white, alive, 149 days 60.4
TCGA-4K-AAAL-01A 31 years, male, white, stage:is, alive, 483 days 59.3
TCGA-2G-AAFY-01A 24 years, male, white, stage:iia, alive, 1099 days 59.1
TCGA-2G-AAGP-01A 33 years, male, white, stage:iia, alive, 4018 days 58.4
TCGA-2G-AAFG-01A 30 years, male, white, stage:is, alive, 6183 days 58.1
TCGA-YU-AA61-01A 29 years, male, white, stage:is, alive, 864 days 57.9
TCGA-2G-AAH2-01A 20 years, male, white, stage:is, alive, 6060 days 57.9
TCGA-VF-A8AB-01A 31 years, male, black or african american, stage:ia, alive, 760 days 57.7
TCGA-4K-AA1G-01A 34 years, male, white, stage:is, alive, 436 days 57.2
TCGA-2G-AAGS-01A 39 years, male, white, stage:iiib, alive, 4816 days 57.1
TCGA-2G-AAG6-01A 24 years, male, white, stage:is, alive, 2231 days 56.8
TCGA-XY-A9T9-01A 37 years, male, white, stage:is, alive, 281 days 56.7
TCGA-SN-A84W-01A 30 years, male, white, stage:is, alive, 293 days 56.6
TCGA-2G-AAHG-01A 25 years, male, white, stage:i, alive, 1819 days 55.5
TCGA-2G-AAG5-01A 36 years, male, white, stage:is, alive, 2299 days 55.3
TCGA-2G-AAHP-01A 31 years, male, white, stage:is, alive, 5667 days 55.1
TCGA-XE-AAO3-01A 33 years, male, asian, stage:i, alive, 2857 days 54.9
TCGA-2G-AAFH-01A 38 years, male, white, stage:iib, alive, 1375 days 54.8
TCGA-2G-AAKD-01A 18 years, male, white, stage:iii, alive, 6340 days 54.7
TCGA-2G-AAH8-01A 45 years, male, white, stage:iiic, alive, 2248 days 53.9
TCGA-2G-AAGW-01A 38 years, male, white, stage:is, alive, 4899 days 53.6
TCGA-XE-A8H4-01A 23 years, male, white, stage:ia, alive, 559 days 53.6
TCGA-SB-A76C-01A 38 years, male, white, alive, 42 days 53.4
TCGA-XE-AANI-01A 37 years, male, white, stage:is, alive, 1041 days 52.8
TCGA-ZM-AA0B-01A 32 years, male, white, stage:ia, alive, 838 days 52.3
TCGA-WZ-A7V3-01A 20 years, male, white, stage:i, alive, 753 days 52.1
TCGA-2G-AAHL-01A 26 years, male, white, stage:i, alive, 7081 days 51.9
TCGA-XE-AAOD-01A 39 years, male, white, stage:ib, alive, 2058 days 51.8
TCGA-2G-AAF4-01A 30 years, male, white, stage:i, alive, 2315 days 51.1
TCGA-WZ-A7V4-01A 28 years, male, white, stage:i, alive, 894 days 51.0
TCGA-VF-A8AA-01A 51 years, male, white, stage:i, alive, 1146 days 50.7
TCGA-XE-AANR-01A 24 years, male, white, stage:i, alive, 14 days 50.6
TCGA-2G-AAGV-01A 23 years, male, white, alive, 4527 days 50.3
TCGA-XE-AANV-01A 52 years, male, stage:ib, alive, 1701 days 50.3
TCGA-4K-AA1I-01A 26 years, male, white, stage:ia, alive, 3 days 50.2
TCGA-2G-AAFE-01A 37 years, male, white, stage:iia, alive, 4702 days 50.1
TCGA-2G-AAFJ-01A 23 years, male, asian, alive, 792 days 50.0
TCGA-2G-AAEX-01A 38 years, male, white, stage:is, alive, 1259 days 49.3
TCGA-XE-AAOJ-01A 24 years, male, white, stage:is, alive, 1550 days 48.7
TCGA-2G-AAGY-01A 28 years, male, white, stage:is, alive, 5329 days 47.7
TCGA-S6-A8JY-01A 27 years, male, white, stage:is, alive, 278 days 46.7
TCGA-2G-AAGJ-01A 28 years, male, black or african american, stage:ia, alive, 2938 days 46.4
TCGA-2G-AAGX-01A 22 years, male, white, stage:ia, alive, 5514 days 46.3
TCGA-ZM-AA0N-01A 44 years, male, white, stage:ib, alive, 634 days 46.2
TCGA-2G-AAG9-01A 25 years, male, white, stage:iiib, alive, 2234 days 45.7
TCGA-2G-AAHN-01A 32 years, male, white, stage:i, alive, 6445 days 45.3
TCGA-YU-A94D-01A 28 years, male, stage:iiib, alive, 2167 days 44.5
TCGA-XE-AAO4-01A 40 years, male, white, stage:ia, alive, 367 days 44.3
TCGA-XE-AAOF-01A 50 years, male, asian, stage:ia, alive, 1268 days 44.1
TCGA-2G-AAEW-01A 31 years, male, white, stage:is, dead, 618 days 43.8
TCGA-4K-AA1H-01A 26 years, male, white, stage:ia, alive, 518 days 43.3
TCGA-XE-A9SE-01A 35 years, male, white, stage:ia, alive, 708 days 43.0
TCGA-VF-A8AC-01A 29 years, male, white, stage:ia, alive, 1083 days 42.9
TCGA-2X-A9D5-01A 49 years, male, white, stage:i, alive, 435 days 42.6
TCGA-YU-A90Q-01A 21 years, male, stage:ib, alive, 1964 days 42.2
TCGA-2G-AAH3-01A 20 years, male, white, stage:i, alive, 1822 days 41.8
TCGA-ZM-AA0D-01A 34 years, male, white, stage:ia, alive, 848 days 40.9
TCGA-ZM-AA0F-01A 35 years, male, white, stage:ia, alive, 681 days 39.4
TCGA-2G-AAF1-01A 28 years, male, asian, stage:is, alive, 1403 days 39.3
TCGA-2G-AAHC-01A 33 years, male, white, stage:is, alive, 5539 days 39.2
TCGA-XY-A89B-01A 35 years, male, white, stage:ia, alive, 471 days 39.2
TCGA-SN-A6IS-01A 26 years, male, white, stage:is, alive, 496 days 39.0
TCGA-SB-A6J6-01A 22 years, male, white, stage:ia, alive, 413 days 38.8
TCGA-YU-A912-01A 34 years, male, black or african american, stage:iiic, alive, 866 days 38.0
TCGA-SO-A8JP-01A 29 years, male, white, stage:i, alive, 540 days 37.5
TCGA-YU-A90S-01A 26 years, male, white, stage:ia, alive, 971 days 37.4
TCGA-WZ-A8D5-01A 38 years, male, white, alive, 774 days 36.2
TCGA-XE-AAO6-01A 47 years, male, white, stage:ia, alive, 240 days 35.7
TCGA-2X-A9D6-01A 42 years, male, white, stage:i, alive, 607 days 35.6
TCGA-ZM-AA0E-01A 39 years, male, white, stage:ia, alive, 811 days 35.0
TCGA-S6-A8JW-01A 37 years, male, white, stage:is, alive, 698 days 34.5
TCGA-2G-AAHA-01A 48 years, male, white, stage:ib, alive, 3349 days 33.9
TCGA-2G-AAHT-01A 32 years, male, white, stage:is, alive, 542 days 33.6
TCGA-XE-A8H5-01A 29 years, male, stage:is, alive, 1217 days 33.6
TCGA-XE-AANJ-01A 39 years, male, white, stage:is, alive, 2007 days 33.5
TCGA-YU-A90W-01A 45 years, male, white, stage:ia, alive, 1113 days 33.5
TCGA-2G-AAG3-01A 53 years, male, white, stage:is, alive, 1593 days 32.6
TCGA-S6-A8JX-01A 27 years, male, white, stage:ib, alive, 552 days 32.3
TCGA-ZM-AA0H-01A 50 years, male, white, stage:is, alive, 1736 days 29.0
TCGA-ZM-AA06-01A 45 years, male, white, stage:ib, alive, 1498 days 26.5
TCGA-ZM-AA05-01A 36 years, male, white, stage:iic, alive, 1126 days 25.9
TCGA-XE-AAOL-01A 38 years, male, black or african american, stage:i, alive, 13 days 14.8
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