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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.
PGF 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.
: 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 TPM
31.6
Number of samples
99
Samples
Sample
Description
TPM
TCGA-BF-A3DN-01A
0 years, female, white, stage:Stage IIIC, alive, 717 days
262.9
TCGA-XV-A9W5-01A
0 years, male, white, stage:Not Reported, alive, 392 days
226.4
TCGA-BF-A1PU-01A
0 years, female, white, stage:Stage IIC, alive, 387 days
205.0
TCGA-GF-A769-01A
0 years, male, white, stage:Stage IIC, dead, 1070 days
151.9
TCGA-BF-A3DM-01A
0 years, male, white, stage:Stage IIA, alive, 601 days
150.9
TCGA-EB-A1NK-01A
0 years, male, white, stage:Stage IIC, alive, 1039 days
119.6
TCGA-EB-A3Y6-01A
0 years, female, white, stage:Stage IIC, alive, 126 days
93.0
TCGA-EB-A3XB-01A
0 years, male, white, stage:Stage II, alive, 796 days
92.4
TCGA-XV-AAZV-01A
0 years, female, white, stage:Stage II, alive, 412 days
69.9
TCGA-D9-A4Z5-01A
0 years, male, white, stage:Stage IIB, alive, 218 days
67.2
TCGA-EB-A24C-01A
0 years, male, white, stage:'--, alive, 632 days
64.1
TCGA-EB-A3XE-01A
0 years, female, white, stage:Stage IIA, alive, 180 days
63.6
TCGA-EB-A5VU-01A
0 years, male, asian, stage:Stage IIIB, dead, 321 days
63.5
TCGA-EB-A550-01A
0 years, female, white, stage:Stage IIC, dead, 264 days
59.0
TCGA-EB-A42Z-01A
0 years, male, asian, stage:Stage IIIC, alive, 441 days
55.0
TCGA-D9-A3Z4-01A
0 years, male, white, stage:Stage IIIC, dead, 519 days
54.3
TCGA-EB-A44N-01A
0 years, male, white, stage:Stage IIC, dead, 205 days
49.1
TCGA-EB-A97M-01A
0 years, male, white, stage:Stage IIC, alive, 414 days
48.3
TCGA-EB-A24D-01A
0 years, male, white, stage:Stage IIIB, alive, 645 days
47.8
TCGA-ER-A196-01A
0 years, female, white, stage:Stage IIC, alive, 1785 days
46.9
TCGA-EB-A57M-01A
0 years, male, asian, stage:Stage IIIB, dead, 472 days
41.0
TCGA-EB-A4OZ-01A
0 years, female, white, stage:Stage IIIC, alive, 620 days
40.4
TCGA-ER-A42H-01A
0 years, male, white, stage:'--, dead, 426 days
38.4
TCGA-FW-A5DX-01A
0 years, male, white, stage:Stage IIIC, alive, 640 days
36.8
TCGA-EB-A551-01A
0 years, female, white, stage:Stage IIIC, alive, 590 days
35.2
TCGA-BF-AAP7-01A
0 years, female, white, stage:Stage IIC, alive, 318 days
32.9
TCGA-EB-A5SF-01A
0 years, female, white, stage:Stage IIC, dead, 369 days
32.8
TCGA-BF-A5EP-01A
0 years, female, white, stage:Stage IIIC, alive, 335 days
30.2
TCGA-BF-AAP1-01A
0 years, male, white, stage:Stage IIC, alive, 409 days
27.4
TCGA-EB-A3XD-01A
0 years, female, white, stage:Stage IIC, alive, 1160 days
27.1
TCGA-EB-A82B-01A
0 years, female, asian, stage:Stage III, alive, 390 days
27.0
TCGA-GN-A4U5-01A
0 years, female, white, stage:Stage IB, alive, 1156 days
26.9
TCGA-BF-AAP8-01A
0 years, male, white, stage:Stage IIC, alive, 447 days
26.8
TCGA-BF-A1PX-01A
0 years, male, white, stage:Stage IIIB, dead, 282 days
26.5
TCGA-ER-A2NB-01A
0 years, male, white, stage:Stage IIIB, dead, 857 days
25.6
TCGA-EB-A5UM-01A
0 years, female, white, stage:Stage IIC, alive, 779 days
24.6
TCGA-ER-A194-01A
0 years, male, white, stage:'--, dead, 1354 days
24.4
TCGA-EB-A4XL-01A
0 years, female, white, stage:Stage IIC, alive, 777 days
24.2
TCGA-EB-A431-01A
0 years, male, white, stage:Stage IIC, alive, 568 days
24.1
TCGA-FS-A1ZN-01A
0 years, male, white, stage:Stage IIIA, dead, 730 days
24.1
TCGA-FR-A728-01A
0 years, female, white, stage:Stage IIIB, alive, 583 days
23.4
TCGA-EB-A3HV-01A
0 years, male, white, stage:Stage IIC, alive, 39 days
21.4
TCGA-GF-A2C7-01A
0 years, male, white, stage:Stage IIC, alive, 21 days
20.8
TCGA-EB-A44P-01A
0 years, female, white, stage:Stage IIC, alive, 741 days
18.8
TCGA-EB-A3XF-01A
0 years, male, white, stage:Stage IIC, alive, 278 days
18.3
TCGA-BF-A5EO-01A
0 years, male, white, stage:Stage IIC, alive, 703 days
18.2
TCGA-EB-A4IQ-01A
0 years, female, asian, stage:Stage IIIB, dead, 636 days
17.9
TCGA-BF-A5EQ-01A
0 years, male, white, stage:Stage IIC, alive, 323 days
17.3
TCGA-XV-AAZW-01A
0 years, female, white, stage:Stage II, dead, 393 days
16.6
TCGA-FR-A2OS-01A
0 years, female, white, stage:Stage IIC, dead, 368 days
16.0
TCGA-EB-A85J-01A
0 years, female, white, stage:Stage IIB, alive, 360 days
15.7
TCGA-EB-A299-01A
0 years, male, white, stage:Stage IIA, alive, 378 days
15.5
TCGA-XV-A9W2-01A
0 years, male, white, stage:Stage I, alive, 417 days
15.0
TCGA-GN-A8LN-01A
0 years, male, white, stage:Stage IIC, alive, 772 days
14.6
TCGA-D9-A4Z2-01A
0 years, male, white, stage:Stage IIIC, dead, 190 days
13.2
TCGA-EB-A553-01A
0 years, male, white, stage:Stage IIC, alive, 226 days
13.2
TCGA-XV-AAZY-01A
0 years, female, white, stage:Stage IIIC, alive, 405 days
12.3
TCGA-EB-A6QY-01A
0 years, male, white, stage:Stage IIC, alive, 382 days
12.3
TCGA-ER-A2NF-01A
0 years, male, white, stage:Stage IIIB, dead, 877 days
11.3
TCGA-EB-A4P0-01A
0 years, male, white, stage:Stage IIC, dead, 326 days
11.1
TCGA-BF-AAOU-01A
0 years, female, white, stage:Stage IIC, alive, 476 days
10.8
TCGA-BF-AAP6-01A
0 years, male, white, stage:Stage III, alive, 325 days
10.7
TCGA-BF-A3DL-01A
0 years, female, white, stage:Stage IIIB, alive, 769 days
10.5
TCGA-BF-AAP4-01A
0 years, male, white, stage:Stage IIC, alive, 335 days
10.0
TCGA-BF-AAOX-01A
0 years, male, white, stage:Stage IIC, alive, 444 days
9.8
TCGA-EB-A42Y-01A
0 years, female, asian, stage:Stage IIC, dead, 721 days
9.6
TCGA-EB-A6QZ-01A
0 years, female, white, stage:Stage IIA, dead, 352 days
8.9
TCGA-BF-A1PZ-01A
0 years, female, white, stage:Stage IIB, alive, 853 days
8.2
TCGA-BF-A1PV-01A
0 years, female, white, stage:Stage IIC, alive, 14 days
7.9
TCGA-EB-A3XC-01A
0 years, male, white, stage:Stage IIC, alive, 650 days
7.5
TCGA-EB-A85I-01A
0 years, male, white, stage:Stage IIC, alive, 362 days
7.5
TCGA-BF-A3DJ-01A
0 years, female, white, stage:Stage IIIB, alive, 464 days
7.2
TCGA-EB-A4IS-01A
0 years, male, white, stage:Stage IIB, alive, 774 days
6.3
TCGA-EB-A82C-01A
0 years, female, asian, stage:Stage IIC, alive, 17 days
6.1
TCGA-EB-A3Y7-01A
0 years, female, white, stage:Stage IIIB, dead, 326 days
6.0
TCGA-WE-A8K4-01A
0 years, male, white, stage:Stage IIB, alive, 614 days
6.0
TCGA-EB-A5FP-01A
0 years, female, white, stage:Stage IV, dead, 454 days
5.7
TCGA-EB-A4OY-01A
0 years, female, white, stage:Stage IIIB, alive, 977 days
5.2
TCGA-ER-A19K-01A
0 years, female, white, stage:Stage IIC, dead, 469 days
4.8
TCGA-EB-A41B-01A
0 years, female, white, stage:Stage IIC, alive, 291 days
4.6
TCGA-BF-A1Q0-01A
0 years, male, white, stage:Stage IIC, alive, 831 days
4.2
TCGA-EB-A44O-01A
0 years, male, white, stage:Stage IIB, alive, 81 days
4.1
TCGA-BF-A5ES-01A
0 years, female, white, stage:Stage IIC, alive, 490 days
3.9
TCGA-EB-A5SE-01A
0 years, male, white, stage:Stage IIB, dead, 401 days
3.9
TCGA-DA-A960-01A
0 years, male, white, stage:Stage IIB, alive, 804 days
3.0
TCGA-BF-A5ER-01A
0 years, male, white, stage:Stage IIC, alive, 327 days
2.2
TCGA-GN-A263-01A
0 years, male, white, stage:Stage IV, dead, 467 days
1.9
TCGA-IH-A3EA-01A
0 years, male, white, stage:Stage IIC, alive, 524 days
1.8
TCGA-BF-A9VF-01A
0 years, male, white, stage:Stage IIC, alive, 440 days
1.8
TCGA-EB-A6R0-01A
0 years, female, white, stage:Stage IIC, dead, 608 days
1.8
TCGA-EB-A51B-01A
0 years, male, white, stage:Stage IIC, alive, 931 days
1.7
TCGA-D9-A4Z3-01A
0 years, female, white, stage:Stage IIIC, alive, 505 days
1.4
TCGA-FR-A3R1-01A
0 years, male, white, stage:Stage IIC, alive, 685 days
1.4
TCGA-D3-A5GT-01A
0 years, male, white, stage:Stage IIIC, alive, 487 days
0.9
TCGA-GN-A26C-01A
0 years, male, white, stage:Stage IIIC, dead, 821 days
0.0
TCGA-YG-AA3N-01A
0 years, male, stage:Stage IIC, alive, 306 days
0.0
TCGA-ER-A19T-01A
0 years, male, white, stage:Stage IV, dead, 270 days
0.0
TCGA-BF-AAP2-01A
0 years, male, white, stage:Stage IIB, alive, 405 days
0.0
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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
