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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.
MT-ND5 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
2942.8
Number of samples
99
Samples
Sample
Description
TPM
TCGA-DA-A960-01A
0 years, male, white, stage:Stage IIB, alive, 804 days
12998.8
TCGA-EB-A553-01A
0 years, male, white, stage:Stage IIC, alive, 226 days
9638.3
TCGA-YG-AA3N-01A
0 years, male, stage:Stage IIC, alive, 306 days
8585.1
TCGA-ER-A194-01A
0 years, male, white, stage:'--, dead, 1354 days
7171.8
TCGA-BF-A5ER-01A
0 years, male, white, stage:Stage IIC, alive, 327 days
7027.0
TCGA-D3-A5GT-01A
0 years, male, white, stage:Stage IIIC, alive, 487 days
6910.3
TCGA-EB-A85I-01A
0 years, male, white, stage:Stage IIC, alive, 362 days
6501.6
TCGA-D9-A4Z5-01A
0 years, male, white, stage:Stage IIB, alive, 218 days
6368.0
TCGA-EB-A24D-01A
0 years, male, white, stage:Stage IIIB, alive, 645 days
6155.2
TCGA-EB-A551-01A
0 years, female, white, stage:Stage IIIC, alive, 590 days
5976.6
TCGA-EB-A3XB-01A
0 years, male, white, stage:Stage II, alive, 796 days
5901.1
TCGA-BF-AAP7-01A
0 years, female, white, stage:Stage IIC, alive, 318 days
5431.5
TCGA-FW-A5DX-01A
0 years, male, white, stage:Stage IIIC, alive, 640 days
4887.1
TCGA-EB-A5UM-01A
0 years, female, white, stage:Stage IIC, alive, 779 days
4741.6
TCGA-EB-A6QY-01A
0 years, male, white, stage:Stage IIC, alive, 382 days
4677.2
TCGA-EB-A4OY-01A
0 years, female, white, stage:Stage IIIB, alive, 977 days
4669.0
TCGA-BF-A5EQ-01A
0 years, male, white, stage:Stage IIC, alive, 323 days
4523.4
TCGA-EB-A4OZ-01A
0 years, female, white, stage:Stage IIIC, alive, 620 days
4466.4
TCGA-GN-A263-01A
0 years, male, white, stage:Stage IV, dead, 467 days
4252.1
TCGA-EB-A42Z-01A
0 years, male, asian, stage:Stage IIIC, alive, 441 days
4221.5
TCGA-BF-A3DL-01A
0 years, female, white, stage:Stage IIIB, alive, 769 days
4203.5
TCGA-EB-A44P-01A
0 years, female, white, stage:Stage IIC, alive, 741 days
3892.5
TCGA-EB-A5FP-01A
0 years, female, white, stage:Stage IV, dead, 454 days
3766.7
TCGA-EB-A24C-01A
0 years, male, white, stage:'--, alive, 632 days
3742.3
TCGA-EB-A3Y6-01A
0 years, female, white, stage:Stage IIC, alive, 126 days
3595.0
TCGA-D9-A4Z2-01A
0 years, male, white, stage:Stage IIIC, dead, 190 days
3588.1
TCGA-BF-A5EP-01A
0 years, female, white, stage:Stage IIIC, alive, 335 days
3534.0
TCGA-FR-A728-01A
0 years, female, white, stage:Stage IIIB, alive, 583 days
3485.6
TCGA-BF-A1PX-01A
0 years, male, white, stage:Stage IIIB, dead, 282 days
3456.0
TCGA-GN-A4U5-01A
0 years, female, white, stage:Stage IB, alive, 1156 days
3430.1
TCGA-XV-AAZW-01A
0 years, female, white, stage:Stage II, dead, 393 days
3307.9
TCGA-BF-A9VF-01A
0 years, male, white, stage:Stage IIC, alive, 440 days
3254.4
TCGA-BF-AAOU-01A
0 years, female, white, stage:Stage IIC, alive, 476 days
3183.1
TCGA-GF-A2C7-01A
0 years, male, white, stage:Stage IIC, alive, 21 days
2927.5
TCGA-EB-A97M-01A
0 years, male, white, stage:Stage IIC, alive, 414 days
2907.7
TCGA-EB-A3XE-01A
0 years, female, white, stage:Stage IIA, alive, 180 days
2879.7
TCGA-EB-A3Y7-01A
0 years, female, white, stage:Stage IIIB, dead, 326 days
2873.7
TCGA-GN-A8LN-01A
0 years, male, white, stage:Stage IIC, alive, 772 days
2850.7
TCGA-EB-A3XD-01A
0 years, female, white, stage:Stage IIC, alive, 1160 days
2836.1
TCGA-XV-A9W5-01A
0 years, male, white, stage:Not Reported, alive, 392 days
2780.5
TCGA-FR-A2OS-01A
0 years, female, white, stage:Stage IIC, dead, 368 days
2701.9
TCGA-ER-A19K-01A
0 years, female, white, stage:Stage IIC, dead, 469 days
2695.6
TCGA-XV-AAZY-01A
0 years, female, white, stage:Stage IIIC, alive, 405 days
2669.9
TCGA-XV-A9W2-01A
0 years, male, white, stage:Stage I, alive, 417 days
2666.4
TCGA-WE-A8K4-01A
0 years, male, white, stage:Stage IIB, alive, 614 days
2609.3
TCGA-BF-AAOX-01A
0 years, male, white, stage:Stage IIC, alive, 444 days
2607.1
TCGA-BF-A5EO-01A
0 years, male, white, stage:Stage IIC, alive, 703 days
2519.5
TCGA-FS-A1ZN-01A
0 years, male, white, stage:Stage IIIA, dead, 730 days
2496.5
TCGA-BF-AAP2-01A
0 years, male, white, stage:Stage IIB, alive, 405 days
2494.2
TCGA-EB-A4IS-01A
0 years, male, white, stage:Stage IIB, alive, 774 days
2489.1
TCGA-EB-A431-01A
0 years, male, white, stage:Stage IIC, alive, 568 days
2471.0
TCGA-EB-A6QZ-01A
0 years, female, white, stage:Stage IIA, dead, 352 days
2406.6
TCGA-BF-AAP8-01A
0 years, male, white, stage:Stage IIC, alive, 447 days
2401.0
TCGA-D9-A3Z4-01A
0 years, male, white, stage:Stage IIIC, dead, 519 days
2373.7
TCGA-BF-A3DJ-01A
0 years, female, white, stage:Stage IIIB, alive, 464 days
2319.9
TCGA-XV-AAZV-01A
0 years, female, white, stage:Stage II, alive, 412 days
2240.9
TCGA-EB-A1NK-01A
0 years, male, white, stage:Stage IIC, alive, 1039 days
2219.3
TCGA-BF-A1PZ-01A
0 years, female, white, stage:Stage IIB, alive, 853 days
2214.8
TCGA-BF-AAP4-01A
0 years, male, white, stage:Stage IIC, alive, 335 days
2211.3
TCGA-EB-A3HV-01A
0 years, male, white, stage:Stage IIC, alive, 39 days
2172.2
TCGA-EB-A57M-01A
0 years, male, asian, stage:Stage IIIB, dead, 472 days
2090.7
TCGA-EB-A299-01A
0 years, male, white, stage:Stage IIA, alive, 378 days
2053.0
TCGA-BF-AAP1-01A
0 years, male, white, stage:Stage IIC, alive, 409 days
1984.6
TCGA-EB-A51B-01A
0 years, male, white, stage:Stage IIC, alive, 931 days
1959.5
TCGA-EB-A4P0-01A
0 years, male, white, stage:Stage IIC, dead, 326 days
1902.9
TCGA-BF-AAP6-01A
0 years, male, white, stage:Stage III, alive, 325 days
1875.1
TCGA-EB-A4IQ-01A
0 years, female, asian, stage:Stage IIIB, dead, 636 days
1830.2
TCGA-BF-A5ES-01A
0 years, female, white, stage:Stage IIC, alive, 490 days
1821.9
TCGA-BF-A3DN-01A
0 years, female, white, stage:Stage IIIC, alive, 717 days
1694.9
TCGA-EB-A5SF-01A
0 years, female, white, stage:Stage IIC, dead, 369 days
1635.9
TCGA-IH-A3EA-01A
0 years, male, white, stage:Stage IIC, alive, 524 days
1634.3
TCGA-BF-A1PU-01A
0 years, female, white, stage:Stage IIC, alive, 387 days
1595.7
TCGA-EB-A4XL-01A
0 years, female, white, stage:Stage IIC, alive, 777 days
1586.9
TCGA-D9-A4Z3-01A
0 years, female, white, stage:Stage IIIC, alive, 505 days
1448.4
TCGA-GF-A769-01A
0 years, male, white, stage:Stage IIC, dead, 1070 days
1406.3
TCGA-EB-A3XF-01A
0 years, male, white, stage:Stage IIC, alive, 278 days
1405.4
TCGA-EB-A6R0-01A
0 years, female, white, stage:Stage IIC, dead, 608 days
1361.2
TCGA-EB-A82B-01A
0 years, female, asian, stage:Stage III, alive, 390 days
1295.7
TCGA-EB-A550-01A
0 years, female, white, stage:Stage IIC, dead, 264 days
1265.4
TCGA-EB-A5VU-01A
0 years, male, asian, stage:Stage IIIB, dead, 321 days
1204.0
TCGA-EB-A44N-01A
0 years, male, white, stage:Stage IIC, dead, 205 days
1194.4
TCGA-BF-A1PV-01A
0 years, female, white, stage:Stage IIC, alive, 14 days
1166.0
TCGA-EB-A82C-01A
0 years, female, asian, stage:Stage IIC, alive, 17 days
1153.1
TCGA-EB-A44O-01A
0 years, male, white, stage:Stage IIB, alive, 81 days
1147.8
TCGA-EB-A85J-01A
0 years, female, white, stage:Stage IIB, alive, 360 days
1099.6
TCGA-ER-A2NB-01A
0 years, male, white, stage:Stage IIIB, dead, 857 days
1073.7
TCGA-ER-A2NF-01A
0 years, male, white, stage:Stage IIIB, dead, 877 days
1051.3
TCGA-ER-A19T-01A
0 years, male, white, stage:Stage IV, dead, 270 days
958.1
TCGA-FR-A3R1-01A
0 years, male, white, stage:Stage IIC, alive, 685 days
923.3
TCGA-ER-A196-01A
0 years, female, white, stage:Stage IIC, alive, 1785 days
868.1
TCGA-EB-A42Y-01A
0 years, female, asian, stage:Stage IIC, dead, 721 days
858.8
TCGA-BF-A1Q0-01A
0 years, male, white, stage:Stage IIC, alive, 831 days
835.1
TCGA-EB-A5SE-01A
0 years, male, white, stage:Stage IIB, dead, 401 days
517.4
TCGA-EB-A41B-01A
0 years, female, white, stage:Stage IIC, alive, 291 days
487.1
TCGA-GN-A26C-01A
0 years, male, white, stage:Stage IIIC, dead, 821 days
414.0
TCGA-EB-A3XC-01A
0 years, male, white, stage:Stage IIC, alive, 650 days
404.2
TCGA-BF-A3DM-01A
0 years, male, white, stage:Stage IIA, alive, 601 days
340.8
TCGA-ER-A42H-01A
0 years, male, white, stage:'--, dead, 426 days
273.7
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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
