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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
571.3
Number of samples
153
Samples
Sample
Description
FPKM
TCGA-14-1829-01A
57 years, male, black or african american, alive, 218 days
3095.1
TCGA-14-0817-01A
69 years, female, white, dead, 164 days
1861.5
TCGA-27-2526-01A
79 years, female, white, dead, 87 days
1643.9
TCGA-27-1831-01A
66 years, male, white, dead, 505 days
1544.8
TCGA-27-2524-01A
56 years, male, white, dead, 231 days
1495.0
TCGA-06-0644-01A
71 years, male, black or african american, dead, 384 days
1346.3
TCGA-12-5295-01A
60 years, female, white, dead, 454 days
1312.1
TCGA-02-0055-01A
62 years, female, white, dead, 76 days
1302.6
TCGA-76-4928-01B
85 years, female, white, dead, 94 days
1273.6
TCGA-32-4213-01A
47 years, female, white, alive, 604 days
1211.4
TCGA-32-5222-01A
66 years, male, white, dead, 585 days
1161.5
TCGA-06-0178-01A
39 years, male, white, dead, 2681 days
1160.5
TCGA-02-2486-01A
64 years, male, white, dead, 618 days
1148.1
TCGA-06-0744-01A
67 years, male, white, dead, 1426 days
1121.9
TCGA-06-5418-01A
75 years, female, white, dead, 83 days
1091.6
TCGA-28-5213-01A
72 years, male, white, alive, 951 days
1083.5
TCGA-19-2625-01A
76 years, female, white, dead, 124 days
1079.9
TCGA-06-0747-01A
53 years, male, white, dead, 82 days
1045.5
TCGA-28-2499-01A
59 years, male, white, dead, 95 days
1029.8
TCGA-19-4065-01A
36 years, male, white, alive, 214 days
1027.0
TCGA-14-0781-01B
49 years, male, black or african american, dead, 29 days
1004.5
TCGA-06-0219-01A
67 years, male, white, dead, 22 days
992.4
TCGA-06-0141-01A
62 years, male, white, dead, 313 days
968.5
TCGA-76-4932-01A
50 years, female, white, dead, 1458 days
935.7
TCGA-12-0619-01A
60 years, male, white, dead, 1062 days
929.1
TCGA-06-0184-01A
63 years, male, white, dead, 2126 days
919.8
TCGA-27-2523-01A
63 years, male, white, dead, 489 days
852.2
TCGA-12-0616-01A
36 years, female, white, dead, 448 days
834.8
TCGA-06-0749-01A
50 years, male, black or african american, dead, 82 days
819.1
TCGA-26-5132-01A
74 years, male, white, alive, 286 days
784.1
TCGA-28-5216-01A
52 years, male, white, alive, 415 days
769.1
TCGA-06-5412-01A
78 years, female, white, dead, 138 days
763.6
TCGA-28-5208-01A
52 years, male, white, dead, 544 days
759.5
TCGA-06-0750-01A
43 years, male, white, dead, 28 days
731.0
TCGA-26-5136-01B
78 years, female, white, dead, 577 days
709.4
TCGA-06-0168-01A
59 years, female, white, dead, 598 days
699.8
TCGA-32-2616-01A
48 years, female, white, dead, 224 days
693.3
TCGA-06-5410-01A
72 years, female, white, dead, 108 days
685.5
TCGA-12-3652-01A
60 years, male, white, dead, 1062 days
680.9
TCGA-06-0211-01B
47 years, male, white, dead, 360 days
679.9
TCGA-32-2615-01A
62 years, male, white, dead, 485 days
675.8
TCGA-28-2509-01A
77 years, female, white, alive, 145 days
666.2
TCGA-28-5209-01A
66 years, female, white, alive, 77 days
657.0
TCGA-32-2632-01A
80 years, male, white, dead, 269 days
655.4
TCGA-41-4097-01A
63 years, female, white, dead, 6 days
647.7
TCGA-28-5204-01A
72 years, male, white, dead, 454 days
644.6
TCGA-41-2572-01A
67 years, male, white, dead, 406 days
643.1
TCGA-12-5299-01A
56 years, female, white, dead, 98 days
635.1
TCGA-06-5414-01A
61 years, male, white, alive, 273 days
630.7
TCGA-06-0743-01A
69 years, male, white, dead, 803 days
628.4
TCGA-06-0130-01A
54 years, male, white, dead, 394 days
626.5
TCGA-06-0190-01A
62 years, male, white, dead, 317 days
622.1
TCGA-06-0139-01A
40 years, male, white, dead, 362 days
617.4
TCGA-14-0787-01A
69 years, male, asian, dead, 68 days
610.9
TCGA-06-0187-01A
69 years, male, white, dead, 828 days
609.3
TCGA-32-2638-01A
67 years, male, white, dead, 766 days
602.2
TCGA-19-2620-01A
70 years, male, white, dead, 148 days
600.4
TCGA-14-2554-01A
52 years, female, white, dead, 532 days
597.4
TCGA-19-2619-01A
55 years, female, black or african american, alive, 294 days
594.8
TCGA-28-2513-01A
69 years, female, white, alive, 222 days
581.9
TCGA-19-1787-01B
49 years, male, white, dead, 385 days
580.5
TCGA-06-0878-01A
74 years, male, white, alive, 218 days
568.7
TCGA-27-1832-01A
59 years, female, white, dead, 300 days
563.3
TCGA-32-1982-01A
76 years, female, white, dead, 142 days
563.2
TCGA-06-0210-01A
72 years, female, white, dead, 225 days
562.4
TCGA-19-2629-01A
60 years, male, white, dead, 737 days
559.5
TCGA-14-1823-01A
58 years, female, white, dead, 543 days
554.6
TCGA-27-1830-01A
57 years, male, white, dead, 154 days
553.8
TCGA-28-5220-01A
67 years, male, white, dead, 388 days
546.6
TCGA-27-1837-01A
36 years, male, white, dead, 427 days
545.0
TCGA-06-0158-01A
73 years, male, white, dead, 329 days
544.1
TCGA-06-5416-01A
23 years, female, white, alive, 204 days
528.4
TCGA-15-0742-01A
65 years, male, white, dead, 419 days
515.2
TCGA-41-3915-01A
48 years, male, white, dead, 360 days
515.1
TCGA-28-5218-01A
63 years, male, white, dead, 157 days
511.0
TCGA-06-0882-01A
30 years, male, white, dead, 632 days
509.1
TCGA-06-0125-01A
63 years, female, white, dead, 1448 days
502.9
TCGA-12-3650-01A
46 years, male, white, dead, 333 days
498.9
TCGA-26-5139-01A
65 years, female, white, alive, 48 days
495.0
TCGA-06-0745-01A
59 years, male, white, dead, 239 days
487.3
TCGA-14-0789-01A
54 years, male, white, dead, 342 days
481.4
TCGA-27-1834-01A
56 years, male, white, dead, 1233 days
467.0
TCGA-76-4931-01A
70 years, female, white, dead, 279 days
459.2
TCGA-06-0645-01A
56 years, female, white, dead, 175 days
432.1
TCGA-06-2562-01A
81 years, male, white, dead, 382 days
422.6
TCGA-06-5413-01A
67 years, male, white, alive, 268 days
422.5
TCGA-02-0047-01A
78 years, male, white, dead, 448 days
416.5
TCGA-06-0686-01A
53 years, male, white, dead, 432 days
414.6
TCGA-06-0132-01A
49 years, male, white, dead, 771 days
414.5
TCGA-32-1980-01A
72 years, male, white, dead, 36 days
413.7
TCGA-06-0238-01A
46 years, male, white, dead, 405 days
406.1
TCGA-28-1747-01C
44 years, male, white, dead, 77 days
400.8
TCGA-06-2559-01A
83 years, male, white, dead, 150 days
395.7
TCGA-06-0156-01A
57 years, male, white, dead, 178 days
394.4
TCGA-76-4926-01B
68 years, male, white, dead, 138 days
392.7
TCGA-16-0846-01A
85 years, male, white, dead, 119 days
390.4
TCGA-76-4927-01A
58 years, male, white, dead, 535 days
385.1
TCGA-06-2565-01A
59 years, male, asian, dead, 506 days
361.2
TCGA-76-4925-01A
76 years, male, white, dead, 146 days
358.7
TCGA-06-2564-01A
50 years, male, white, alive, 181 days
353.8
TCGA-14-1034-01A
60 years, female, dead, 485 days
353.4
TCGA-06-2561-01A
53 years, female, white, dead, 537 days
352.7
TCGA-27-2528-01A
62 years, male, white, dead, 480 days
352.3
TCGA-06-0138-01A
43 years, male, white, dead, 737 days
340.2
TCGA-06-5408-01A
54 years, female, white, dead, 357 days
338.5
TCGA-14-0790-01B
64 years, female, white, dead, 419 days
323.3
TCGA-28-2514-01A
45 years, male, asian, alive, 160 days
318.7
TCGA-32-1970-01A
59 years, male, white, dead, 468 days
313.7
TCGA-19-2624-01A
51 years, male, white, dead, 5 days
311.5
TCGA-28-5207-01A
71 years, male, white, dead, 343 days
308.3
TCGA-15-1444-01A
21 years, male, white, dead, 1537 days
307.2
TCGA-06-1804-01A
81 years, female, white, dead, 414 days
305.2
TCGA-26-5134-01A
74 years, male, white, alive, 167 days
303.9
TCGA-76-4929-01A
76 years, female, white, dead, 111 days
302.7
TCGA-06-0649-01B
73 years, female, black or african american, dead, 64 days
302.1
TCGA-02-2483-01A
43 years, male, asian, alive, 466 days
295.0
TCGA-06-2567-01A
65 years, male, white, dead, 133 days
293.9
TCGA-02-2485-01A
53 years, male, black or african american, alive, 470 days
293.8
TCGA-12-3653-01A
34 years, female, white, dead, 442 days
273.3
TCGA-27-2519-01A
48 years, male, white, dead, 550 days
272.5
TCGA-32-2634-01A
82 years, male, white, alive, 693 days
269.9
TCGA-06-2558-01A
75 years, female, white, dead, 380 days
269.9
TCGA-06-5411-01A
51 years, male, white, dead, 254 days
269.6
TCGA-27-2521-01A
34 years, male, white, dead, 510 days
266.6
TCGA-41-2571-01A
89 years, male, white, dead, 26 days
263.0
TCGA-26-5135-01A
72 years, female, white, dead, 270 days
260.6
TCGA-16-1045-01B
49 years, female, white, dead, 883 days
260.6
TCGA-28-5215-01A
62 years, female, white, dead, 335 days
244.6
TCGA-06-2557-01A
76 years, male, black or african american, dead, 33 days
243.6
TCGA-06-5859-01A
63 years, male, white, alive, 139 days
234.9
TCGA-06-0646-01A
61 years, male, white, dead, 175 days
233.3
TCGA-12-0821-01A
62 years, male, white, dead, 323 days
232.3
TCGA-06-5858-01A
45 years, female, white, alive, 187 days
230.5
TCGA-06-0174-01A
54 years, male, white, dead, 98 days
227.5
TCGA-06-5856-01A
58 years, male, white, dead, 114 days
222.5
TCGA-28-1753-01A
53 years, male, white, alive, 37 days
218.4
TCGA-14-1825-01A
70 years, male, white, dead, 232 days
209.2
TCGA-26-5133-01A
59 years, male, white, alive, 452 days
208.5
TCGA-12-1597-01B
62 years, female, white, dead, 675 days
206.9
TCGA-26-1442-01A
43 years, male, white, alive, 953 days
199.3
TCGA-08-0386-01A
74 years, male, white, dead, 548 days
189.0
TCGA-06-0157-01A
63 years, female, white, dead, 97 days
187.9
TCGA-06-2570-01A
21 years, female, white, alive, 958 days
168.9
TCGA-06-5417-01A
45 years, female, white, alive, 155 days
156.9
TCGA-27-1835-01A
53 years, female, white, dead, 648 days
141.0
TCGA-12-0618-01A
49 years, male, white, dead, 395 days
140.1
TCGA-06-2563-01A
72 years, female, white, alive, 932 days
132.5
TCGA-14-0871-01A
75 years, female, white, dead, 880 days
128.7
TCGA-19-5960-01A
56 years, male, white, dead, 455 days
125.9
TCGA-06-0129-01A
30 years, male, asian, dead, 1024 days
112.0
TCGA-41-5651-01A
59 years, female, black or african american, dead, 460 days
107.6
TCGA-19-1390-01A
63 years, female, white, dead, 772 days
79.4
TCGA-06-2569-01A
24 years, female, black or african american, alive, 13 days
27.7
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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
