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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
56.3
Number of samples
153
Samples
Sample
Description
FPKM
TCGA-06-0749-01A
50 years, male, black or african american, dead, 82 days
118.0
TCGA-28-1753-01A
53 years, male, white, alive, 37 days
117.9
TCGA-76-4928-01B
85 years, female, white, dead, 94 days
113.3
TCGA-06-0644-01A
71 years, male, black or african american, dead, 384 days
108.2
TCGA-02-0055-01A
62 years, female, white, dead, 76 days
106.1
TCGA-28-5218-01A
63 years, male, white, dead, 157 days
102.1
TCGA-12-3652-01A
60 years, male, white, dead, 1062 days
101.7
TCGA-32-1980-01A
72 years, male, white, dead, 36 days
99.5
TCGA-06-5411-01A
51 years, male, white, dead, 254 days
95.3
TCGA-06-0190-01A
62 years, male, white, dead, 317 days
94.0
TCGA-06-0132-01A
49 years, male, white, dead, 771 days
92.7
TCGA-28-2514-01A
45 years, male, asian, alive, 160 days
85.9
TCGA-06-5412-01A
78 years, female, white, dead, 138 days
85.6
TCGA-32-2632-01A
80 years, male, white, dead, 269 days
84.5
TCGA-41-4097-01A
63 years, female, white, dead, 6 days
82.8
TCGA-06-5410-01A
72 years, female, white, dead, 108 days
82.6
TCGA-28-2513-01A
69 years, female, white, alive, 222 days
82.6
TCGA-27-2524-01A
56 years, male, white, dead, 231 days
82.3
TCGA-27-2523-01A
63 years, male, white, dead, 489 days
80.3
TCGA-14-0871-01A
75 years, female, white, dead, 880 days
78.7
TCGA-06-0168-01A
59 years, female, white, dead, 598 days
78.6
TCGA-14-0789-01A
54 years, male, white, dead, 342 days
78.2
TCGA-06-0141-01A
62 years, male, white, dead, 313 days
77.9
TCGA-41-2572-01A
67 years, male, white, dead, 406 days
76.3
TCGA-28-5208-01A
52 years, male, white, dead, 544 days
75.6
TCGA-14-0787-01A
69 years, male, asian, dead, 68 days
74.3
TCGA-06-0686-01A
53 years, male, white, dead, 432 days
72.3
TCGA-12-0616-01A
36 years, female, white, dead, 448 days
70.5
TCGA-06-0184-01A
63 years, male, white, dead, 2126 days
69.4
TCGA-41-2571-01A
89 years, male, white, dead, 26 days
68.5
TCGA-19-1390-01A
63 years, female, white, dead, 772 days
68.4
TCGA-12-3650-01A
46 years, male, white, dead, 333 days
68.2
TCGA-14-0781-01B
49 years, male, black or african american, dead, 29 days
68.1
TCGA-32-2638-01A
67 years, male, white, dead, 766 days
68.0
TCGA-41-3915-01A
48 years, male, white, dead, 360 days
68.0
TCGA-19-2620-01A
70 years, male, white, dead, 148 days
67.8
TCGA-06-0747-01A
53 years, male, white, dead, 82 days
67.4
TCGA-06-0745-01A
59 years, male, white, dead, 239 days
66.9
TCGA-26-5139-01A
65 years, female, white, alive, 48 days
66.9
TCGA-06-2563-01A
72 years, female, white, alive, 932 days
66.2
TCGA-15-0742-01A
65 years, male, white, dead, 419 days
65.8
TCGA-06-0750-01A
43 years, male, white, dead, 28 days
65.3
TCGA-06-0139-01A
40 years, male, white, dead, 362 days
65.2
TCGA-32-2616-01A
48 years, female, white, dead, 224 days
65.1
TCGA-76-4927-01A
58 years, male, white, dead, 535 days
64.4
TCGA-06-0130-01A
54 years, male, white, dead, 394 days
63.9
TCGA-12-1597-01B
62 years, female, white, dead, 675 days
63.6
TCGA-06-0882-01A
30 years, male, white, dead, 632 days
62.4
TCGA-12-5295-01A
60 years, female, white, dead, 454 days
61.9
TCGA-06-0645-01A
56 years, female, white, dead, 175 days
61.2
TCGA-32-1970-01A
59 years, male, white, dead, 468 days
61.2
TCGA-12-0619-01A
60 years, male, white, dead, 1062 days
60.3
TCGA-06-0158-01A
73 years, male, white, dead, 329 days
59.6
TCGA-28-2509-01A
77 years, female, white, alive, 145 days
59.4
TCGA-32-1982-01A
76 years, female, white, dead, 142 days
59.2
TCGA-27-2521-01A
34 years, male, white, dead, 510 days
59.0
TCGA-19-2625-01A
76 years, female, white, dead, 124 days
58.3
TCGA-06-0744-01A
67 years, male, white, dead, 1426 days
57.3
TCGA-28-5209-01A
66 years, female, white, alive, 77 days
57.3
TCGA-14-1034-01A
60 years, female, dead, 485 days
57.1
TCGA-06-0174-01A
54 years, male, white, dead, 98 days
56.9
TCGA-06-0238-01A
46 years, male, white, dead, 405 days
56.8
TCGA-06-0649-01B
73 years, female, black or african american, dead, 64 days
56.2
TCGA-19-2619-01A
55 years, female, black or african american, alive, 294 days
55.1
TCGA-16-0846-01A
85 years, male, white, dead, 119 days
54.9
TCGA-26-5134-01A
74 years, male, white, alive, 167 days
54.6
TCGA-06-0211-01B
47 years, male, white, dead, 360 days
54.5
TCGA-28-5207-01A
71 years, male, white, dead, 343 days
53.9
TCGA-12-3653-01A
34 years, female, white, dead, 442 days
53.7
TCGA-16-1045-01B
49 years, female, white, dead, 883 days
53.2
TCGA-06-1804-01A
81 years, female, white, dead, 414 days
53.1
TCGA-28-5216-01A
52 years, male, white, alive, 415 days
53.1
TCGA-26-5135-01A
72 years, female, white, dead, 270 days
52.6
TCGA-14-0817-01A
69 years, female, white, dead, 164 days
52.6
TCGA-02-2483-01A
43 years, male, asian, alive, 466 days
51.9
TCGA-06-0743-01A
69 years, male, white, dead, 803 days
51.7
TCGA-12-5299-01A
56 years, female, white, dead, 98 days
51.6
TCGA-27-2526-01A
79 years, female, white, dead, 87 days
51.5
TCGA-12-0618-01A
49 years, male, white, dead, 395 days
51.3
TCGA-27-1832-01A
59 years, female, white, dead, 300 days
51.1
TCGA-19-2624-01A
51 years, male, white, dead, 5 days
51.0
TCGA-06-0125-01A
63 years, female, white, dead, 1448 days
50.7
TCGA-06-5416-01A
23 years, female, white, alive, 204 days
50.6
TCGA-19-5960-01A
56 years, male, white, dead, 455 days
50.6
TCGA-27-1837-01A
36 years, male, white, dead, 427 days
50.4
TCGA-06-2562-01A
81 years, male, white, dead, 382 days
50.1
TCGA-76-4931-01A
70 years, female, white, dead, 279 days
49.8
TCGA-06-2567-01A
65 years, male, white, dead, 133 days
49.8
TCGA-26-5132-01A
74 years, male, white, alive, 286 days
49.7
TCGA-28-5204-01A
72 years, male, white, dead, 454 days
49.4
TCGA-02-2486-01A
64 years, male, white, dead, 618 days
49.0
TCGA-06-2565-01A
59 years, male, asian, dead, 506 days
49.0
TCGA-06-2557-01A
76 years, male, black or african american, dead, 33 days
48.8
TCGA-06-5408-01A
54 years, female, white, dead, 357 days
48.8
TCGA-06-0157-01A
63 years, female, white, dead, 97 days
48.6
TCGA-28-5215-01A
62 years, female, white, dead, 335 days
48.2
TCGA-06-2558-01A
75 years, female, white, dead, 380 days
47.7
TCGA-32-2615-01A
62 years, male, white, dead, 485 days
47.3
TCGA-32-4213-01A
47 years, female, white, alive, 604 days
47.1
TCGA-26-5133-01A
59 years, male, white, alive, 452 days
47.1
TCGA-08-0386-01A
74 years, male, white, dead, 548 days
47.1
TCGA-06-5413-01A
67 years, male, white, alive, 268 days
46.9
TCGA-27-2528-01A
62 years, male, white, dead, 480 days
46.8
TCGA-32-2634-01A
82 years, male, white, alive, 693 days
46.8
TCGA-06-5859-01A
63 years, male, white, alive, 139 days
46.4
TCGA-28-2499-01A
59 years, male, white, dead, 95 days
46.3
TCGA-06-0156-01A
57 years, male, white, dead, 178 days
45.9
TCGA-06-0878-01A
74 years, male, white, alive, 218 days
45.8
TCGA-28-1747-01C
44 years, male, white, dead, 77 days
45.4
TCGA-02-2485-01A
53 years, male, black or african american, alive, 470 days
45.3
TCGA-27-1835-01A
53 years, female, white, dead, 648 days
45.0
TCGA-06-0210-01A
72 years, female, white, dead, 225 days
44.8
TCGA-28-5213-01A
72 years, male, white, alive, 951 days
43.5
TCGA-14-2554-01A
52 years, female, white, dead, 532 days
43.1
TCGA-06-5856-01A
58 years, male, white, dead, 114 days
42.6
TCGA-76-4926-01B
68 years, male, white, dead, 138 days
42.5
TCGA-06-5414-01A
61 years, male, white, alive, 273 days
41.6
TCGA-19-4065-01A
36 years, male, white, alive, 214 days
41.6
TCGA-06-0646-01A
61 years, male, white, dead, 175 days
41.6
TCGA-19-2629-01A
60 years, male, white, dead, 737 days
41.6
TCGA-06-2569-01A
24 years, female, black or african american, alive, 13 days
41.1
TCGA-02-0047-01A
78 years, male, white, dead, 448 days
41.0
TCGA-12-0821-01A
62 years, male, white, dead, 323 days
41.0
TCGA-14-1825-01A
70 years, male, white, dead, 232 days
40.9
TCGA-76-4932-01A
50 years, female, white, dead, 1458 days
40.0
TCGA-14-0790-01B
64 years, female, white, dead, 419 days
39.9
TCGA-06-0129-01A
30 years, male, asian, dead, 1024 days
38.6
TCGA-76-4929-01A
76 years, female, white, dead, 111 days
38.6
TCGA-06-0138-01A
43 years, male, white, dead, 737 days
38.1
TCGA-06-5418-01A
75 years, female, white, dead, 83 days
38.1
TCGA-06-2564-01A
50 years, male, white, alive, 181 days
37.9
TCGA-06-0187-01A
69 years, male, white, dead, 828 days
37.5
TCGA-26-1442-01A
43 years, male, white, alive, 953 days
37.0
TCGA-27-1830-01A
57 years, male, white, dead, 154 days
36.6
TCGA-06-2570-01A
21 years, female, white, alive, 958 days
35.9
TCGA-19-1787-01B
49 years, male, white, dead, 385 days
35.9
TCGA-15-1444-01A
21 years, male, white, dead, 1537 days
35.5
TCGA-06-0178-01A
39 years, male, white, dead, 2681 days
35.4
TCGA-06-2561-01A
53 years, female, white, dead, 537 days
34.5
TCGA-32-5222-01A
66 years, male, white, dead, 585 days
33.7
TCGA-06-0219-01A
67 years, male, white, dead, 22 days
32.5
TCGA-06-5858-01A
45 years, female, white, alive, 187 days
32.3
TCGA-41-5651-01A
59 years, female, black or african american, dead, 460 days
32.1
TCGA-28-5220-01A
67 years, male, white, dead, 388 days
30.7
TCGA-76-4925-01A
76 years, male, white, dead, 146 days
30.6
TCGA-27-2519-01A
48 years, male, white, dead, 550 days
30.5
TCGA-27-1834-01A
56 years, male, white, dead, 1233 days
29.9
TCGA-06-2559-01A
83 years, male, white, dead, 150 days
29.5
TCGA-14-1829-01A
57 years, male, black or african american, alive, 218 days
28.9
TCGA-26-5136-01B
78 years, female, white, dead, 577 days
28.8
TCGA-06-5417-01A
45 years, female, white, alive, 155 days
26.6
TCGA-14-1823-01A
58 years, female, white, dead, 543 days
23.5
TCGA-27-1831-01A
66 years, male, white, dead, 505 days
17.8
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GLIOMA - 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
