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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.
MT2A is not prognostic in Skin Cuteneous Melanoma (TCGA)
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.
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.
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.
: 1.23
P scorei
Log-rank P value for Kaplan-Meier plot showing results from analysis of correlation between mRNA expression level and patient survival.
0.19
3-year survival highi
5-year survival for patients with higher expression than the expression cutoff.
For melanoma and glioma, 3-year survival is shown.
25%
3-year survival lowi
5-year survival for patients with lower expression than the expression cutoff.
For melanoma and glioma, 3-year survival is shown.
43%
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 TPM
1937.3
Number of samples
99
Samples
Sample
Description
TPM
TCGA-EB-A42Z-01A
49 years, male, asian, stage:Stage IIIC, alive, 441 days
10043.7
TCGA-XV-A9W5-01A
51 years, male, white, stage:Not Reported, alive, 392 days
6575.1
TCGA-XV-AAZV-01A
56 years, female, white, stage:Stage II, alive, 412 days
6264.2
TCGA-IH-A3EA-01A
61 years, male, white, stage:Stage IIC, alive, 524 days
5912.6
TCGA-EB-A85I-01A
66 years, male, white, stage:Stage IIC, alive, 362 days
5248.0
TCGA-BF-A3DL-01A
84 years, female, white, stage:Stage IIIB, alive, 769 days
5196.0
TCGA-EB-A3HV-01A
37 years, male, white, stage:Stage IIC, alive, 39 days
4756.8
TCGA-EB-A42Y-01A
73 years, female, asian, stage:Stage IIC, dead, 721 days
4730.9
TCGA-D9-A4Z5-01A
68 years, male, white, stage:Stage IIB, alive, 218 days
4507.8
TCGA-BF-A3DJ-01A
36 years, female, white, stage:Stage IIIB, alive, 464 days
4261.7
TCGA-EB-A3XF-01A
57 years, male, white, stage:Stage IIC, alive, 278 days
4190.4
TCGA-BF-A1Q0-01A
80 years, male, white, stage:Stage IIC, alive, 831 days
4088.8
TCGA-GN-A26C-01A
77 years, male, white, stage:Stage IIIC, dead, 821 days
3936.9
TCGA-EB-A299-01A
63 years, male, white, stage:Stage IIA, alive, 378 days
3925.8
TCGA-BF-AAOU-01A
73 years, female, white, stage:Stage IIC, alive, 476 days
3610.4
TCGA-EB-A3Y7-01A
86 years, female, white, stage:Stage IIIB, dead, 326 days
3560.3
TCGA-EB-A44N-01A
59 years, male, white, stage:Stage IIC, dead, 205 days
3320.4
TCGA-EB-A553-01A
62 years, male, white, stage:Stage IIC, alive, 226 days
3200.9
TCGA-XV-A9W2-01A
81 years, male, white, stage:Stage I, alive, 417 days
3052.7
TCGA-EB-A82B-01A
58 years, female, asian, stage:Stage III, alive, 390 days
2992.3
TCGA-GN-A8LN-01A
68 years, male, white, stage:Stage IIC, alive, 772 days
2916.3
TCGA-XV-AAZW-01A
62 years, female, white, stage:Stage II, dead, 393 days
2853.9
TCGA-BF-A5EP-01A
75 years, female, white, stage:Stage IIIC, alive, 335 days
2833.6
TCGA-GF-A769-01A
39 years, male, white, stage:Stage IIC, dead, 1070 days
2816.8
TCGA-EB-A44P-01A
58 years, female, white, stage:Stage IIC, alive, 741 days
2698.2
TCGA-BF-A5EO-01A
65 years, male, white, stage:Stage IIC, alive, 703 days
2675.9
TCGA-EB-A3Y6-01A
56 years, female, white, stage:Stage IIC, alive, 126 days
2643.4
TCGA-EB-A3XB-01A
63 years, male, white, stage:Stage II, alive, 796 days
2324.0
TCGA-BF-A5ER-01A
63 years, male, white, stage:Stage IIC, alive, 327 days
2212.0
TCGA-WE-A8K4-01A
85 years, male, white, stage:Stage IIB, alive, 614 days
2187.5
TCGA-FR-A2OS-01A
49 years, female, white, stage:Stage IIC, dead, 368 days
2132.3
TCGA-GN-A4U5-01A
61 years, female, white, stage:Stage IB, alive, 1156 days
2018.1
TCGA-YG-AA3N-01A
67 years, male, stage:Stage IIC, alive, 306 days
1875.5
TCGA-EB-A4XL-01A
56 years, female, white, stage:Stage IIC, alive, 777 days
1818.8
TCGA-EB-A3XC-01A
74 years, male, white, stage:Stage IIC, alive, 650 days
1814.6
TCGA-FR-A3R1-01A
69 years, male, white, stage:Stage IIC, alive, 685 days
1806.6
TCGA-EB-A5SF-01A
78 years, female, white, stage:Stage IIC, dead, 369 days
1803.9
TCGA-ER-A2NB-01A
57 years, male, white, stage:Stage IIIB, dead, 857 days
1789.2
TCGA-EB-A97M-01A
66 years, male, white, stage:Stage IIC, alive, 414 days
1780.2
TCGA-EB-A4OZ-01A
41 years, female, white, stage:Stage IIIC, alive, 620 days
1731.2
TCGA-BF-AAP7-01A
76 years, female, white, stage:Stage IIC, alive, 318 days
1689.3
TCGA-EB-A51B-01A
53 years, male, white, stage:Stage IIC, alive, 931 days
1667.0
TCGA-BF-A3DM-01A
63 years, male, white, stage:Stage IIA, alive, 601 days
1587.3
TCGA-XV-AAZY-01A
76 years, female, white, stage:Stage IIIC, alive, 405 days
1541.4
TCGA-BF-AAP4-01A
61 years, male, white, stage:Stage IIC, alive, 335 days
1527.4
TCGA-BF-AAP2-01A
62 years, male, white, stage:Stage IIB, alive, 405 days
1519.4
TCGA-EB-A550-01A
75 years, female, white, stage:Stage IIC, dead, 264 days
1513.7
TCGA-EB-A44O-01A
69 years, male, white, stage:Stage IIB, alive, 81 days
1484.5
TCGA-EB-A85J-01A
66 years, female, white, stage:Stage IIB, alive, 360 days
1402.3
TCGA-BF-A3DN-01A
81 years, female, white, stage:Stage IIIC, alive, 717 days
1363.7
TCGA-EB-A6QZ-01A
76 years, female, white, stage:Stage IIA, dead, 352 days
1327.2
TCGA-BF-A1PU-01A
46 years, female, white, stage:Stage IIC, alive, 387 days
1324.2
TCGA-D9-A4Z2-01A
50 years, male, white, stage:Stage IIIC, dead, 190 days
1267.1
TCGA-ER-A196-01A
64 years, female, white, stage:Stage IIC, alive, 1785 days
1246.5
TCGA-D9-A3Z4-01A
54 years, male, white, stage:Stage IIIC, dead, 519 days
1164.3
TCGA-EB-A6R0-01A
58 years, female, white, stage:Stage IIC, dead, 608 days
1150.4
TCGA-FS-A1ZN-01A
43 years, male, white, stage:Stage IIIA, dead, 730 days
1102.5
TCGA-EB-A1NK-01A
48 years, male, white, stage:Stage IIC, alive, 1039 days
1083.4
TCGA-EB-A431-01A
34 years, male, white, stage:Stage IIC, alive, 568 days
1064.7
TCGA-EB-A4IS-01A
77 years, male, white, stage:Stage IIB, alive, 774 days
1050.0
TCGA-EB-A82C-01A
70 years, female, asian, stage:Stage IIC, alive, 17 days
1035.9
TCGA-EB-A57M-01A
56 years, male, asian, stage:Stage IIIB, dead, 472 days
997.4
TCGA-BF-A1PV-01A
74 years, female, white, stage:Stage IIC, alive, 14 days
996.9
TCGA-D3-A5GT-01A
43 years, male, white, stage:Stage IIIC, alive, 487 days
985.6
TCGA-BF-A5EQ-01A
63 years, male, white, stage:Stage IIC, alive, 323 days
968.3
TCGA-EB-A5VU-01A
56 years, male, asian, stage:Stage IIIB, dead, 321 days
926.1
TCGA-D9-A4Z3-01A
73 years, female, white, stage:Stage IIIC, alive, 505 days
917.1
TCGA-EB-A3XE-01A
77 years, female, white, stage:Stage IIA, alive, 180 days
891.2
TCGA-EB-A6QY-01A
71 years, male, white, stage:Stage IIC, alive, 382 days
890.8
TCGA-BF-AAP1-01A
86 years, male, white, stage:Stage IIC, alive, 409 days
851.6
TCGA-BF-A1PX-01A
56 years, male, white, stage:Stage IIIB, dead, 282 days
843.6
TCGA-DA-A960-01A
73 years, male, white, stage:Stage IIB, alive, 804 days
841.2
TCGA-BF-A9VF-01A
77 years, male, white, stage:Stage IIC, alive, 440 days
814.5
TCGA-ER-A42H-01A
76 years, male, white, stage:'--, dead, 426 days
803.9
TCGA-BF-A5ES-01A
76 years, female, white, stage:Stage IIC, alive, 490 days
798.5
TCGA-EB-A5SE-01A
73 years, male, white, stage:Stage IIB, dead, 401 days
784.1
TCGA-EB-A4IQ-01A
42 years, female, asian, stage:Stage IIIB, dead, 636 days
756.8
TCGA-FR-A728-01A
54 years, female, white, stage:Stage IIIB, alive, 583 days
736.5
TCGA-EB-A551-01A
78 years, female, white, stage:Stage IIIC, alive, 590 days
692.8
TCGA-EB-A41B-01A
76 years, female, white, stage:Stage IIC, alive, 291 days
653.1
TCGA-EB-A24C-01A
56 years, male, white, stage:'--, alive, 632 days
639.2
TCGA-BF-A1PZ-01A
71 years, female, white, stage:Stage IIB, alive, 853 days
558.0
TCGA-BF-AAP6-01A
55 years, male, white, stage:Stage III, alive, 325 days
556.1
TCGA-EB-A5FP-01A
65 years, female, white, stage:Stage IV, dead, 454 days
529.4
TCGA-EB-A4P0-01A
82 years, male, white, stage:Stage IIC, dead, 326 days
529.2
TCGA-BF-AAOX-01A
83 years, male, white, stage:Stage IIC, alive, 444 days
477.3
TCGA-BF-AAP8-01A
58 years, male, white, stage:Stage IIC, alive, 447 days
435.6
TCGA-EB-A3XD-01A
53 years, female, white, stage:Stage IIC, alive, 1160 days
433.5
TCGA-GF-A2C7-01A
48 years, male, white, stage:Stage IIC, alive, 21 days
413.7
TCGA-EB-A24D-01A
72 years, male, white, stage:Stage IIIB, alive, 645 days
407.2
TCGA-ER-A194-01A
77 years, male, white, stage:'--, dead, 1354 days
406.9
TCGA-FW-A5DX-01A
71 years, male, white, stage:Stage IIIC, alive, 640 days
406.8
TCGA-EB-A5UM-01A
48 years, female, white, stage:Stage IIC, alive, 779 days
372.0
TCGA-ER-A19K-01A
79 years, female, white, stage:Stage IIC, dead, 469 days
338.1
TCGA-ER-A19T-01A
51 years, male, white, stage:Stage IV, dead, 270 days
259.1
TCGA-GN-A263-01A
24 years, male, white, stage:Stage IV, dead, 467 days
258.4
TCGA-ER-A2NF-01A
53 years, male, white, stage:Stage IIIB, dead, 877 days
241.7
TCGA-EB-A4OY-01A
65 years, female, white, stage:Stage IIIB, alive, 977 days
225.9
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MELANOMA - Protein expressioni
A mouse-over function shows sample information and annotation data. Click on an image to view it in a full screen mode. Samples can be filtered based on level of antibody staining by selecting one or several of the following categories: high, medium, low and not detected. The assay and annotation is described here.
Note that samples used for immunohistochemistry by the Human Protein Atlas do not correspond to samples in the TCGA dataset.
The Human Protein Atlas project is funded
