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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.
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.
: 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
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.
N/A
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.
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
16.2
Number of samples
102
Samples
Sample
Description
FPKM
TCGA-BF-A5ER-01A
63 years, male, white, stage:iic, alive, 327 days
40.1
TCGA-BF-A5EO-01A
65 years, male, white, stage:iic, alive, 703 days
38.7
TCGA-XV-AAZY-01A
76 years, female, white, stage:iiic, alive, 405 days
35.3
TCGA-BF-A3DM-01A
63 years, male, white, stage:iia, alive, 601 days
34.8
TCGA-BF-AAP6-01A
55 years, male, white, stage:iii, alive, 325 days
30.9
TCGA-EB-A42Y-01A
73 years, female, asian, stage:iic, dead, 721 days
29.9
TCGA-EB-A82C-01A
70 years, female, asian, stage:iic, alive, 17 days
28.6
TCGA-EB-A1NK-01A
48 years, male, white, stage:iic, alive, 1039 days
26.2
TCGA-EB-A6R0-01A
58 years, female, white, stage:iic, dead, 608 days
26.2
TCGA-BF-A1PV-01A
74 years, female, white, stage:iic, alive, 14 days
26.1
TCGA-BF-A3DL-01A
84 years, female, white, stage:iiib, alive, 769 days
24.4
TCGA-EB-A6QZ-01A
76 years, female, white, stage:iia, dead, 352 days
24.1
TCGA-BF-A5ES-01A
76 years, female, white, stage:iic, alive, 490 days
24.0
TCGA-YG-AA3N-01A
67 years, male, stage:iic, alive, 306 days
23.1
TCGA-EB-A3XD-01A
53 years, female, white, stage:iic, alive, 1160 days
22.7
TCGA-GN-A8LN-01A
68 years, male, white, stage:iic, alive, 772 days
22.5
TCGA-HR-A5NC-01A
90 years, female, alive, 1000 days
22.4
TCGA-IH-A3EA-01A
61 years, male, white, stage:iic, alive, 524 days
22.3
TCGA-EB-A3XF-01A
57 years, male, white, stage:iic, alive, 278 days
22.2
TCGA-EB-A3XE-01A
77 years, female, white, stage:iia, alive, 180 days
22.2
TCGA-FR-A2OS-01A
49 years, female, white, stage:iic, dead, 368 days
22.1
TCGA-BF-A1PX-01A
56 years, male, white, stage:iiib, dead, 282 days
21.8
TCGA-EB-A5FP-01A
65 years, female, white, stage:iv, dead, 454 days
21.5
TCGA-EB-A4IS-01A
77 years, male, white, stage:iib, alive, 774 days
21.3
TCGA-BF-A1Q0-01A
80 years, male, white, stage:iic, alive, 831 days
20.9
TCGA-BF-A1PZ-01A
71 years, female, white, stage:iib, alive, 853 days
20.6
TCGA-EB-A85I-01A
66 years, male, white, stage:iic, alive, 362 days
20.4
TCGA-EB-A5SE-01A
73 years, male, white, stage:iib, dead, 401 days
18.5
TCGA-EB-A41A-01A
90 years, male, white, stage:iic, alive, 262 days
18.3
TCGA-D9-A4Z2-01A
50 years, male, white, stage:iiic, dead, 190 days
18.2
TCGA-EB-A3Y7-01A
86 years, female, white, stage:iiib, dead, 326 days
18.2
TCGA-XV-A9VZ-01A
90 years, female, white, stage:ii, alive, 11 days
18.2
TCGA-ER-A42H-01A
77 years, male, white, dead, 426 days
18.1
TCGA-ER-A196-01A
64 years, female, white, stage:iic, alive, 1785 days
17.8
TCGA-EB-A4IQ-01A
42 years, female, asian, stage:iiib, dead, 636 days
17.5
TCGA-BF-A5EP-01A
75 years, female, white, stage:iiic, alive, 335 days
17.1
TCGA-BF-A5EQ-01A
63 years, male, white, stage:iic, alive, 323 days
16.9
TCGA-XV-AAZW-01A
62 years, female, white, stage:ii, dead, 393 days
16.7
TCGA-XV-AAZV-01A
56 years, female, white, stage:ii, alive, 412 days
16.7
TCGA-GN-A26C-01A
77 years, male, white, stage:iiic, dead, 821 days
16.6
TCGA-EB-A44P-01A
58 years, female, white, stage:iic, alive, 741 days
16.5
TCGA-D9-A4Z3-01A
73 years, female, white, stage:iiic, alive, 505 days
16.5
TCGA-EB-A3XC-01A
74 years, male, white, stage:iic, alive, 650 days
16.5
TCGA-EB-A97M-01A
66 years, male, white, stage:iic, alive, 414 days
16.3
TCGA-EB-A5SF-01A
78 years, female, white, stage:iic, dead, 369 days
16.2
TCGA-EB-A44O-01A
69 years, male, white, stage:iib, alive, 81 days
16.0
TCGA-BF-A3DJ-01A
36 years, female, white, stage:iiib, alive, 464 days
16.0
TCGA-FS-A1ZN-01A
43 years, male, white, stage:iiia, dead, 730 days
15.5
TCGA-EB-A51B-01A
53 years, male, white, stage:iic, alive, 931 days
15.4
TCGA-BF-AAP2-01A
62 years, male, white, stage:iib, alive, 405 days
15.3
TCGA-ER-A19K-01A
79 years, female, white, stage:iic, dead, 469 days
15.3
TCGA-EB-A85J-01A
66 years, female, white, stage:iib, alive, 360 days
15.2
TCGA-EB-A3HV-01A
37 years, male, white, stage:iic, alive, 39 days
15.1
TCGA-EB-A5UM-01A
48 years, female, white, stage:iic, alive, 779 days
14.9
TCGA-EB-A4OZ-01A
42 years, female, white, stage:iiic, alive, 620 days
14.8
TCGA-EB-A6QY-01A
71 years, male, white, stage:iic, alive, 382 days
14.4
TCGA-EB-A299-01A
63 years, male, white, stage:iia, alive, 378 days
14.4
TCGA-FW-A5DX-01A
71 years, male, white, stage:iiic, alive, 640 days
14.4
TCGA-EB-A550-01A
75 years, female, white, stage:iic, dead, 264 days
13.8
TCGA-EB-A57M-01A
56 years, male, asian, stage:iiib, dead, 472 days
13.7
TCGA-BF-A3DN-01A
81 years, female, white, stage:iiic, alive, 717 days
13.5
TCGA-FR-A728-01A
54 years, female, white, stage:iiib, alive, 583 days
13.4
TCGA-ER-A2NB-01A
57 years, male, white, stage:iiib, dead, 857 days
13.4
TCGA-ER-A194-01A
77 years, male, white, dead, 1354 days
13.4
TCGA-GF-A769-01A
39 years, male, white, stage:iic, dead, 1070 days
13.3
TCGA-XV-A9W2-01A
81 years, male, white, stage:i, alive, 417 days
13.3
TCGA-GF-A2C7-01A
48 years, male, white, stage:iic, alive, 21 days
13.2
TCGA-EB-A4OY-01A
65 years, female, white, stage:iiib, alive, 977 days
13.2
TCGA-EB-A4P0-01A
82 years, male, white, stage:iic, dead, 326 days
12.8
TCGA-BF-A1PU-01A
46 years, female, white, stage:iic, alive, 387 days
12.7
TCGA-D9-A4Z5-01A
68 years, male, white, stage:iib, alive, 218 days
12.3
TCGA-BF-AAP4-01A
61 years, male, white, stage:iic, alive, 335 days
11.9
TCGA-EB-A44N-01A
59 years, male, white, stage:iic, dead, 205 days
11.6
TCGA-EB-A41B-01A
76 years, female, white, stage:iic, alive, 291 days
11.3
TCGA-BF-AAP7-01A
76 years, female, white, stage:iic, alive, 318 days
11.3
TCGA-BF-AAOX-01A
83 years, male, white, stage:iic, alive, 444 days
11.0
TCGA-GN-A263-01A
24 years, male, white, stage:iv, dead, 467 days
10.8
TCGA-EB-A24D-01A
72 years, male, white, stage:iiib, alive, 645 days
10.8
TCGA-EB-A24C-01A
56 years, male, white, alive, 632 days
10.8
TCGA-D9-A3Z4-01A
54 years, male, white, stage:iiic, dead, 519 days
10.5
TCGA-EB-A4XL-01A
56 years, female, white, stage:iic, alive, 777 days
10.5
TCGA-EB-A5VU-01A
56 years, male, asian, stage:iiib, dead, 321 days
10.3
TCGA-EB-A551-01A
78 years, female, white, stage:iiic, alive, 590 days
9.7
TCGA-BF-A9VF-01A
77 years, male, white, stage:iic, alive, 440 days
9.6
TCGA-ER-A2NF-01A
53 years, male, white, stage:iiib, dead, 877 days
9.1
TCGA-XV-A9W5-01A
51 years, male, white, stage:i/ii nos, alive, 392 days
9.0
TCGA-WE-A8K4-01A
85 years, male, white, stage:iib, alive, 614 days
8.9
TCGA-EB-A3XB-01A
63 years, male, white, stage:ii, alive, 796 days
8.8
TCGA-EB-A42Z-01A
49 years, male, asian, stage:iiic, alive, 441 days
8.7
TCGA-BF-AAP1-01A
86 years, male, white, stage:iic, alive, 409 days
8.7
TCGA-GN-A4U5-01A
61 years, female, white, stage:ib, alive, 1156 days
8.7
TCGA-BF-AAP8-01A
58 years, male, white, stage:iic, alive, 447 days
8.7
TCGA-EB-A82B-01A
58 years, female, asian, stage:iii, alive, 390 days
8.6
TCGA-FR-A3R1-01A
69 years, male, white, stage:iic, alive, 685 days
8.6
TCGA-FR-A726-01A
90 years, male, white, stage:iic, dead, 305 days
8.4
TCGA-EB-A3Y6-01A
56 years, female, white, stage:iic, alive, 126 days
8.4
TCGA-DA-A960-01A
73 years, male, white, stage:iib, alive, 804 days
8.2
TCGA-EB-A431-01A
34 years, male, white, stage:iic, alive, 568 days
6.2
TCGA-BF-AAOU-01A
73 years, female, white, stage:iic, alive, 476 days
5.9
TCGA-ER-A19T-01A
51 years, male, white, stage:iv, dead, 270 days
5.8
TCGA-EB-A553-01A
62 years, male, white, stage:iic, alive, 226 days
4.4
TCGA-D3-A5GT-01A
43 years, male, white, stage:iiic, alive, 487 days
3.4
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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.
Antibody stainingi
Antibody staining in the annotated cell types in the current human tissue is reported as not detected, low, medium, or high, based on conventional immunohistochemistry profiling in selected tissues. This score is based on the combination of the staining intensity and fraction of stained cells.
Each image is clickable and will lead to virtual microscopy that enables deeper exploration of all samples and also displays staining intensity scores, fraction scores and subcellular localization as well as patient and tissue information for each sample.
The Human Protein Atlas project is funded
