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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
303.1
Number of samples
153
Samples
Sample
Description
FPKM
TCGA-06-0686-01A
53 years, male, white, dead, 432 days
875.4
TCGA-06-0238-01A
46 years, male, white, dead, 405 days
833.3
TCGA-14-1825-01A
70 years, male, white, dead, 232 days
776.2
TCGA-02-2483-01A
43 years, male, asian, alive, 466 days
719.7
TCGA-41-2571-01A
89 years, male, white, dead, 26 days
713.2
TCGA-12-3650-01A
46 years, male, white, dead, 333 days
706.8
TCGA-12-1597-01B
62 years, female, white, dead, 675 days
704.4
TCGA-76-4932-01A
50 years, female, white, dead, 1458 days
676.8
TCGA-41-5651-01A
59 years, female, black or african american, dead, 460 days
672.5
TCGA-12-0618-01A
49 years, male, white, dead, 395 days
635.6
TCGA-27-2523-01A
63 years, male, white, dead, 489 days
631.5
TCGA-06-2558-01A
75 years, female, white, dead, 380 days
605.7
TCGA-26-5134-01A
74 years, male, white, alive, 167 days
598.5
TCGA-06-0174-01A
54 years, male, white, dead, 98 days
586.9
TCGA-15-0742-01A
65 years, male, white, dead, 419 days
586.2
TCGA-06-2570-01A
21 years, female, white, alive, 958 days
573.8
TCGA-19-2624-01A
51 years, male, white, dead, 5 days
570.1
TCGA-26-5135-01A
72 years, female, white, dead, 270 days
547.9
TCGA-15-1444-01A
21 years, male, white, dead, 1537 days
535.6
TCGA-27-2521-01A
34 years, male, white, dead, 510 days
525.5
TCGA-06-5413-01A
67 years, male, white, alive, 268 days
524.2
TCGA-12-0616-01A
36 years, female, white, dead, 448 days
511.6
TCGA-32-2634-01A
82 years, male, white, alive, 693 days
506.1
TCGA-12-0821-01A
62 years, male, white, dead, 323 days
492.7
TCGA-28-5215-01A
62 years, female, white, dead, 335 days
485.5
TCGA-19-5960-01A
56 years, male, white, dead, 455 days
479.6
TCGA-06-0157-01A
63 years, female, white, dead, 97 days
475.3
TCGA-06-0178-01A
39 years, male, white, dead, 2681 days
470.1
TCGA-02-2485-01A
53 years, male, black or african american, alive, 470 days
458.5
TCGA-28-1753-01A
53 years, male, white, alive, 37 days
453.5
TCGA-06-5411-01A
51 years, male, white, dead, 254 days
451.0
TCGA-06-0745-01A
59 years, male, white, dead, 239 days
441.0
TCGA-19-2629-01A
60 years, male, white, dead, 737 days
416.3
TCGA-28-5216-01A
52 years, male, white, alive, 415 days
414.7
TCGA-06-2557-01A
76 years, male, black or african american, dead, 33 days
405.5
TCGA-06-0129-01A
30 years, male, asian, dead, 1024 days
400.2
TCGA-06-0156-01A
57 years, male, white, dead, 178 days
397.8
TCGA-76-4927-01A
58 years, male, white, dead, 535 days
394.1
TCGA-06-5858-01A
45 years, female, white, alive, 187 days
393.7
TCGA-19-1390-01A
63 years, female, white, dead, 772 days
389.1
TCGA-28-1747-01C
44 years, male, white, dead, 77 days
389.1
TCGA-76-4931-01A
70 years, female, white, dead, 279 days
388.8
TCGA-27-1837-01A
36 years, male, white, dead, 427 days
386.9
TCGA-06-5417-01A
45 years, female, white, alive, 155 days
369.3
TCGA-06-0744-01A
67 years, male, white, dead, 1426 days
368.9
TCGA-06-5416-01A
23 years, female, white, alive, 204 days
366.8
TCGA-28-5204-01A
72 years, male, white, dead, 454 days
360.3
TCGA-16-0846-01A
85 years, male, white, dead, 119 days
358.6
TCGA-76-4929-01A
76 years, female, white, dead, 111 days
356.4
TCGA-76-4925-01A
76 years, male, white, dead, 146 days
352.1
TCGA-06-2559-01A
83 years, male, white, dead, 150 days
349.0
TCGA-32-5222-01A
66 years, male, white, dead, 585 days
346.9
TCGA-14-0790-01B
64 years, female, white, dead, 419 days
345.0
TCGA-06-0138-01A
43 years, male, white, dead, 737 days
331.9
TCGA-06-0211-01B
47 years, male, white, dead, 360 days
331.5
TCGA-02-0047-01A
78 years, male, white, dead, 448 days
328.5
TCGA-32-4213-01A
47 years, female, white, alive, 604 days
314.9
TCGA-27-2519-01A
48 years, male, white, dead, 550 days
313.2
TCGA-12-5295-01A
60 years, female, white, dead, 454 days
309.0
TCGA-28-2514-01A
45 years, male, asian, alive, 160 days
303.3
TCGA-41-3915-01A
48 years, male, white, dead, 360 days
302.2
TCGA-28-5209-01A
66 years, female, white, alive, 77 days
302.0
TCGA-14-0787-01A
69 years, male, asian, dead, 68 days
298.1
TCGA-12-5299-01A
56 years, female, white, dead, 98 days
294.7
TCGA-28-5220-01A
67 years, male, white, dead, 388 days
293.4
TCGA-06-5408-01A
54 years, female, white, dead, 357 days
293.1
TCGA-27-2524-01A
56 years, male, white, dead, 231 days
289.7
TCGA-12-3653-01A
34 years, female, white, dead, 442 days
286.2
TCGA-26-1442-01A
43 years, male, white, alive, 953 days
285.8
TCGA-06-0646-01A
61 years, male, white, dead, 175 days
285.7
TCGA-06-5856-01A
58 years, male, white, dead, 114 days
283.7
TCGA-28-5208-01A
52 years, male, white, dead, 544 days
281.2
TCGA-06-0125-01A
63 years, female, white, dead, 1448 days
280.1
TCGA-26-5133-01A
59 years, male, white, alive, 452 days
279.4
TCGA-27-1830-01A
57 years, male, white, dead, 154 days
277.9
TCGA-14-0817-01A
69 years, female, white, dead, 164 days
268.8
TCGA-06-2565-01A
59 years, male, asian, dead, 506 days
267.2
TCGA-06-0743-01A
69 years, male, white, dead, 803 days
264.2
TCGA-14-0871-01A
75 years, female, white, dead, 880 days
262.4
TCGA-12-3652-01A
60 years, male, white, dead, 1062 days
259.0
TCGA-32-2616-01A
48 years, female, white, dead, 224 days
252.7
TCGA-06-2564-01A
50 years, male, white, alive, 181 days
250.0
TCGA-06-0219-01A
67 years, male, white, dead, 22 days
248.2
TCGA-06-2563-01A
72 years, female, white, alive, 932 days
247.7
TCGA-32-1970-01A
59 years, male, white, dead, 468 days
240.5
TCGA-28-5207-01A
71 years, male, white, dead, 343 days
240.5
TCGA-08-0386-01A
74 years, male, white, dead, 548 days
238.1
TCGA-06-0645-01A
56 years, female, white, dead, 175 days
236.9
TCGA-28-5218-01A
63 years, male, white, dead, 157 days
236.7
TCGA-26-5136-01B
78 years, female, white, dead, 577 days
235.6
TCGA-06-0749-01A
50 years, male, black or african american, dead, 82 days
234.7
TCGA-19-2625-01A
76 years, female, white, dead, 124 days
233.8
TCGA-06-0187-01A
69 years, male, white, dead, 828 days
230.6
TCGA-19-1787-01B
49 years, male, white, dead, 385 days
225.1
TCGA-27-2528-01A
62 years, male, white, dead, 480 days
221.3
TCGA-41-2572-01A
67 years, male, white, dead, 406 days
215.3
TCGA-06-0132-01A
49 years, male, white, dead, 771 days
209.8
TCGA-06-0158-01A
73 years, male, white, dead, 329 days
207.7
TCGA-19-2620-01A
70 years, male, white, dead, 148 days
201.4
TCGA-14-1034-01A
60 years, female, dead, 485 days
201.3
TCGA-06-5414-01A
61 years, male, white, alive, 273 days
201.3
TCGA-27-1835-01A
53 years, female, white, dead, 648 days
200.5
TCGA-26-5139-01A
65 years, female, white, alive, 48 days
199.2
TCGA-19-2619-01A
55 years, female, black or african american, alive, 294 days
195.5
TCGA-76-4926-01B
68 years, male, white, dead, 138 days
190.5
TCGA-26-5132-01A
74 years, male, white, alive, 286 days
189.1
TCGA-06-0747-01A
53 years, male, white, dead, 82 days
184.2
TCGA-06-0190-01A
62 years, male, white, dead, 317 days
179.6
TCGA-32-2638-01A
67 years, male, white, dead, 766 days
178.3
TCGA-32-1980-01A
72 years, male, white, dead, 36 days
176.8
TCGA-06-0750-01A
43 years, male, white, dead, 28 days
169.6
TCGA-28-2509-01A
77 years, female, white, alive, 145 days
166.9
TCGA-06-0184-01A
63 years, male, white, dead, 2126 days
164.9
TCGA-32-2632-01A
80 years, male, white, dead, 269 days
162.5
TCGA-12-0619-01A
60 years, male, white, dead, 1062 days
158.8
TCGA-06-5410-01A
72 years, female, white, dead, 108 days
155.2
TCGA-76-4928-01B
85 years, female, white, dead, 94 days
153.4
TCGA-32-1982-01A
76 years, female, white, dead, 142 days
151.7
TCGA-06-0882-01A
30 years, male, white, dead, 632 days
151.4
TCGA-06-0210-01A
72 years, female, white, dead, 225 days
147.2
TCGA-27-2526-01A
79 years, female, white, dead, 87 days
146.8
TCGA-14-0781-01B
49 years, male, black or african american, dead, 29 days
143.9
TCGA-06-1804-01A
81 years, female, white, dead, 414 days
143.2
TCGA-06-0649-01B
73 years, female, black or african american, dead, 64 days
143.0
TCGA-06-2567-01A
65 years, male, white, dead, 133 days
143.0
TCGA-06-0878-01A
74 years, male, white, alive, 218 days
142.0
TCGA-06-0130-01A
54 years, male, white, dead, 394 days
140.9
TCGA-27-1834-01A
56 years, male, white, dead, 1233 days
139.4
TCGA-14-2554-01A
52 years, female, white, dead, 532 days
136.0
TCGA-19-4065-01A
36 years, male, white, alive, 214 days
132.7
TCGA-06-0141-01A
62 years, male, white, dead, 313 days
131.0
TCGA-06-2569-01A
24 years, female, black or african american, alive, 13 days
130.5
TCGA-16-1045-01B
49 years, female, white, dead, 883 days
125.2
TCGA-14-1829-01A
57 years, male, black or african american, alive, 218 days
124.8
TCGA-28-5213-01A
72 years, male, white, alive, 951 days
116.0
TCGA-06-0168-01A
59 years, female, white, dead, 598 days
115.9
TCGA-28-2513-01A
69 years, female, white, alive, 222 days
108.1
TCGA-27-1831-01A
66 years, male, white, dead, 505 days
107.7
TCGA-06-2561-01A
53 years, female, white, dead, 537 days
106.5
TCGA-27-1832-01A
59 years, female, white, dead, 300 days
104.2
TCGA-32-2615-01A
62 years, male, white, dead, 485 days
103.8
TCGA-06-0139-01A
40 years, male, white, dead, 362 days
98.7
TCGA-41-4097-01A
63 years, female, white, dead, 6 days
97.2
TCGA-06-0644-01A
71 years, male, black or african american, dead, 384 days
94.8
TCGA-28-2499-01A
59 years, male, white, dead, 95 days
94.0
TCGA-06-5418-01A
75 years, female, white, dead, 83 days
91.8
TCGA-06-2562-01A
81 years, male, white, dead, 382 days
91.0
TCGA-06-5412-01A
78 years, female, white, dead, 138 days
90.5
TCGA-06-5859-01A
63 years, male, white, alive, 139 days
82.1
TCGA-14-0789-01A
54 years, male, white, dead, 342 days
72.6
TCGA-14-1823-01A
58 years, female, white, dead, 543 days
51.7
TCGA-02-2486-01A
64 years, male, white, dead, 618 days
47.5
TCGA-02-0055-01A
62 years, female, white, dead, 76 days
39.7
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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
