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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
385.1
Number of samples
102
Samples
Sample
Description
FPKM
TCGA-BF-A5ER-01A
63 years, male, white, stage:iic, alive, 327 days
1164.1
TCGA-EB-A82C-01A
70 years, female, asian, stage:iic, alive, 17 days
1069.3
TCGA-IH-A3EA-01A
61 years, male, white, stage:iic, alive, 524 days
841.7
TCGA-BF-A1Q0-01A
80 years, male, white, stage:iic, alive, 831 days
776.6
TCGA-EB-A4OY-01A
65 years, female, white, stage:iiib, alive, 977 days
638.1
TCGA-D9-A4Z3-01A
73 years, female, white, stage:iiic, alive, 505 days
632.4
TCGA-FR-A3R1-01A
69 years, male, white, stage:iic, alive, 685 days
629.4
TCGA-EB-A4IQ-01A
42 years, female, asian, stage:iiib, dead, 636 days
603.3
TCGA-EB-A5FP-01A
65 years, female, white, stage:iv, dead, 454 days
591.3
TCGA-EB-A85J-01A
66 years, female, white, stage:iib, alive, 360 days
585.4
TCGA-EB-A3Y7-01A
86 years, female, white, stage:iiib, dead, 326 days
557.8
TCGA-BF-A1PV-01A
74 years, female, white, stage:iic, alive, 14 days
554.1
TCGA-EB-A57M-01A
56 years, male, asian, stage:iiib, dead, 472 days
531.1
TCGA-BF-AAP1-01A
86 years, male, white, stage:iic, alive, 409 days
523.6
TCGA-BF-A9VF-01A
77 years, male, white, stage:iic, alive, 440 days
519.7
TCGA-EB-A6QZ-01A
76 years, female, white, stage:iia, dead, 352 days
497.0
TCGA-EB-A3XC-01A
74 years, male, white, stage:iic, alive, 650 days
495.1
TCGA-BF-AAP2-01A
62 years, male, white, stage:iib, alive, 405 days
493.0
TCGA-BF-A5EO-01A
65 years, male, white, stage:iic, alive, 703 days
487.4
TCGA-EB-A431-01A
34 years, male, white, stage:iic, alive, 568 days
478.5
TCGA-XV-AAZY-01A
76 years, female, white, stage:iiic, alive, 405 days
458.0
TCGA-ER-A194-01A
77 years, male, white, dead, 1354 days
457.4
TCGA-BF-A5EQ-01A
63 years, male, white, stage:iic, alive, 323 days
447.7
TCGA-EB-A82B-01A
58 years, female, asian, stage:iii, alive, 390 days
442.6
TCGA-EB-A41A-01A
90 years, male, white, stage:iic, alive, 262 days
439.3
TCGA-BF-A3DM-01A
63 years, male, white, stage:iia, alive, 601 days
434.5
TCGA-HR-A5NC-01A
90 years, female, alive, 1000 days
431.0
TCGA-BF-AAP7-01A
76 years, female, white, stage:iic, alive, 318 days
424.6
TCGA-BF-A1PX-01A
56 years, male, white, stage:iiib, dead, 282 days
423.6
TCGA-YG-AA3N-01A
67 years, male, stage:iic, alive, 306 days
420.1
TCGA-ER-A19K-01A
79 years, female, white, stage:iic, dead, 469 days
419.2
TCGA-FR-A726-01A
90 years, male, white, stage:iic, dead, 305 days
403.8
TCGA-EB-A6R0-01A
58 years, female, white, stage:iic, dead, 608 days
403.0
TCGA-GF-A2C7-01A
48 years, male, white, stage:iic, alive, 21 days
401.6
TCGA-EB-A24D-01A
72 years, male, white, stage:iiib, alive, 645 days
398.8
TCGA-EB-A42Z-01A
49 years, male, asian, stage:iiic, alive, 441 days
396.6
TCGA-EB-A1NK-01A
48 years, male, white, stage:iic, alive, 1039 days
395.9
TCGA-FS-A1ZN-01A
43 years, male, white, stage:iiia, dead, 730 days
392.2
TCGA-ER-A42H-01A
77 years, male, white, dead, 426 days
391.8
TCGA-BF-A1PU-01A
46 years, female, white, stage:iic, alive, 387 days
388.8
TCGA-BF-A5EP-01A
75 years, female, white, stage:iiic, alive, 335 days
388.8
TCGA-XV-A9W2-01A
81 years, male, white, stage:i, alive, 417 days
388.1
TCGA-EB-A4OZ-01A
42 years, female, white, stage:iiic, alive, 620 days
385.2
TCGA-BF-AAP4-01A
61 years, male, white, stage:iic, alive, 335 days
384.1
TCGA-BF-A5ES-01A
76 years, female, white, stage:iic, alive, 490 days
382.1
TCGA-EB-A5UM-01A
48 years, female, white, stage:iic, alive, 779 days
380.0
TCGA-EB-A3XF-01A
57 years, male, white, stage:iic, alive, 278 days
379.1
TCGA-EB-A51B-01A
53 years, male, white, stage:iic, alive, 931 days
378.5
TCGA-EB-A42Y-01A
73 years, female, asian, stage:iic, dead, 721 days
370.7
TCGA-FW-A5DX-01A
71 years, male, white, stage:iiic, alive, 640 days
368.9
TCGA-XV-A9VZ-01A
90 years, female, white, stage:ii, alive, 11 days
367.3
TCGA-FR-A2OS-01A
49 years, female, white, stage:iic, dead, 368 days
361.0
TCGA-EB-A5SE-01A
73 years, male, white, stage:iib, dead, 401 days
358.8
TCGA-EB-A44O-01A
69 years, male, white, stage:iib, alive, 81 days
357.5
TCGA-EB-A97M-01A
66 years, male, white, stage:iic, alive, 414 days
357.2
TCGA-XV-A9W5-01A
51 years, male, white, stage:i/ii nos, alive, 392 days
356.8
TCGA-XV-AAZW-01A
62 years, female, white, stage:ii, dead, 393 days
356.8
TCGA-ER-A196-01A
64 years, female, white, stage:iic, alive, 1785 days
354.5
TCGA-EB-A4IS-01A
77 years, male, white, stage:iib, alive, 774 days
350.5
TCGA-BF-A1PZ-01A
71 years, female, white, stage:iib, alive, 853 days
349.9
TCGA-BF-AAOX-01A
83 years, male, white, stage:iic, alive, 444 days
345.5
TCGA-BF-A3DL-01A
84 years, female, white, stage:iiib, alive, 769 days
326.4
TCGA-EB-A41B-01A
76 years, female, white, stage:iic, alive, 291 days
326.3
TCGA-EB-A3XD-01A
53 years, female, white, stage:iic, alive, 1160 days
321.7
TCGA-EB-A4P0-01A
82 years, male, white, stage:iic, dead, 326 days
319.9
TCGA-EB-A5VU-01A
56 years, male, asian, stage:iiib, dead, 321 days
313.6
TCGA-EB-A44N-01A
59 years, male, white, stage:iic, dead, 205 days
312.9
TCGA-ER-A2NF-01A
53 years, male, white, stage:iiib, dead, 877 days
307.4
TCGA-GN-A8LN-01A
68 years, male, white, stage:iic, alive, 772 days
305.7
TCGA-GN-A26C-01A
77 years, male, white, stage:iiic, dead, 821 days
302.4
TCGA-ER-A19T-01A
51 years, male, white, stage:iv, dead, 270 days
297.3
TCGA-EB-A3XE-01A
77 years, female, white, stage:iia, alive, 180 days
297.3
TCGA-EB-A5SF-01A
78 years, female, white, stage:iic, dead, 369 days
291.4
TCGA-EB-A3Y6-01A
56 years, female, white, stage:iic, alive, 126 days
288.6
TCGA-GF-A769-01A
39 years, male, white, stage:iic, dead, 1070 days
285.3
TCGA-EB-A85I-01A
66 years, male, white, stage:iic, alive, 362 days
282.2
TCGA-D3-A5GT-01A
43 years, male, white, stage:iiic, alive, 487 days
279.1
TCGA-FR-A728-01A
54 years, female, white, stage:iiib, alive, 583 days
278.8
TCGA-EB-A3HV-01A
37 years, male, white, stage:iic, alive, 39 days
275.5
TCGA-D9-A4Z2-01A
50 years, male, white, stage:iiic, dead, 190 days
264.9
TCGA-EB-A6QY-01A
71 years, male, white, stage:iic, alive, 382 days
258.4
TCGA-GN-A263-01A
24 years, male, white, stage:iv, dead, 467 days
255.7
TCGA-EB-A3XB-01A
63 years, male, white, stage:ii, alive, 796 days
253.9
TCGA-EB-A4XL-01A
56 years, female, white, stage:iic, alive, 777 days
245.0
TCGA-D9-A3Z4-01A
54 years, male, white, stage:iiic, dead, 519 days
242.4
TCGA-BF-A3DN-01A
81 years, female, white, stage:iiic, alive, 717 days
241.8
TCGA-BF-A3DJ-01A
36 years, female, white, stage:iiib, alive, 464 days
232.5
TCGA-XV-AAZV-01A
56 years, female, white, stage:ii, alive, 412 days
229.6
TCGA-EB-A44P-01A
58 years, female, white, stage:iic, alive, 741 days
228.4
TCGA-DA-A960-01A
73 years, male, white, stage:iib, alive, 804 days
226.1
TCGA-ER-A2NB-01A
57 years, male, white, stage:iiib, dead, 857 days
224.1
TCGA-EB-A553-01A
62 years, male, white, stage:iic, alive, 226 days
222.5
TCGA-EB-A299-01A
63 years, male, white, stage:iia, alive, 378 days
220.6
TCGA-D9-A4Z5-01A
68 years, male, white, stage:iib, alive, 218 days
213.8
TCGA-EB-A24C-01A
56 years, male, white, alive, 632 days
213.5
TCGA-EB-A551-01A
78 years, female, white, stage:iiic, alive, 590 days
212.7
TCGA-WE-A8K4-01A
85 years, male, white, stage:iib, alive, 614 days
211.8
TCGA-GN-A4U5-01A
61 years, female, white, stage:ib, alive, 1156 days
202.5
TCGA-BF-AAOU-01A
73 years, female, white, stage:iic, alive, 476 days
189.7
TCGA-EB-A550-01A
75 years, female, white, stage:iic, dead, 264 days
181.6
TCGA-BF-AAP6-01A
55 years, male, white, stage:iii, alive, 325 days
171.8
TCGA-BF-AAP8-01A
58 years, male, white, stage:iic, alive, 447 days
170.4
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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.