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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
5-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
5-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
1.8
Number of samples
64
Samples
Sample
Description
FPKM
TCGA-KL-8333-01A
69 years, male, white, stage:ii, alive, 2991 days
3.8
TCGA-KL-8343-01A
72 years, male, white, stage:iii, dead, 2172 days
3.6
TCGA-KO-8404-01A
78 years, male, white, stage:iv, dead, 325 days
3.5
TCGA-KN-8435-01A
59 years, male, white, stage:ii, alive, 3498 days
3.4
TCGA-KL-8341-01A
41 years, male, asian, stage:iv, dead, 754 days
3.2
TCGA-KL-8325-01A
56 years, female, white, stage:ii, dead, 725 days
2.9
TCGA-KO-8411-01A
58 years, male, white, stage:i, alive, 3958 days
2.8
TCGA-KN-8425-01A
53 years, male, white, stage:i, alive, 3179 days
2.7
TCGA-KN-8423-01A
44 years, male, white, stage:i, alive, 788 days
2.7
TCGA-KN-8419-01A
43 years, male, black or african american, stage:ii, alive, 714 days
2.6
TCGA-KO-8410-01A
74 years, female, white, stage:i, alive, 3136 days
2.6
TCGA-KN-8432-01A
86 years, female, white, stage:ii, alive, 76 days
2.6
TCGA-KL-8323-01A
57 years, female, white, stage:iii, dead, 1158 days
2.5
TCGA-KL-8334-01A
37 years, female, white, stage:iii, alive, 2949 days
2.4
TCGA-KL-8336-01A
51 years, female, white, stage:iv, dead, 920 days
2.4
TCGA-KN-8421-01A
48 years, female, white, stage:ii, alive, 2674 days
2.3
TCGA-KL-8344-01A
51 years, male, white, stage:iii, alive, 876 days
2.2
TCGA-KO-8417-01A
30 years, female, white, stage:i, alive, 2815 days
2.2
TCGA-KM-8440-01A
37 years, male, black or african american, stage:iii, alive, 1366 days
2.2
TCGA-KN-8429-01A
38 years, female, white, stage:iii, alive, 2650 days
2.2
TCGA-KM-8639-01A
67 years, male, white, stage:i, alive, 953 days
2.1
TCGA-KO-8406-01A
17 years, female, white, stage:i, alive, 3145 days
2.1
TCGA-KN-8418-01A
41 years, female, white, stage:ii, alive, 3935 days
2.1
TCGA-KN-8427-01A
54 years, male, white, stage:iv, alive, 30 days
2.1
TCGA-KN-8424-01A
42 years, female, white, stage:i, alive, 1983 days
2.0
TCGA-KM-8441-01A
61 years, female, white, stage:i, alive, 876 days
1.9
TCGA-KO-8413-01A
46 years, male, white, stage:i, alive, 3038 days
1.9
TCGA-KL-8339-01A
67 years, male, white, stage:iv, dead, 855 days
1.8
TCGA-KN-8436-01A
63 years, male, white, stage:ii, alive, 1288 days
1.8
TCGA-KN-8437-01A
42 years, female, white, stage:i, alive, 3068 days
1.8
TCGA-KN-8426-01A
50 years, male, white, stage:iv, alive, 108 days
1.8
TCGA-KN-8428-01A
71 years, male, white, stage:ii, dead, 1590 days
1.8
TCGA-KL-8340-01A
34 years, male, white, stage:ii, alive, 2024 days
1.8
TCGA-KM-8438-01A
45 years, female, white, stage:ii, alive, 4622 days
1.7
TCGA-KM-8442-01A
38 years, male, stage:ii, alive, 1437 days
1.7
TCGA-KO-8408-01A
47 years, male, white, stage:iii, dead, 507 days
1.7
TCGA-KL-8330-01A
44 years, female, black or african american, stage:ii, alive, 3304 days
1.7
TCGA-KL-8345-01A
75 years, male, white, stage:iii, alive, 1665 days
1.7
TCGA-KL-8329-01A
57 years, female, asian, stage:i, alive, 2752 days
1.6
TCGA-KN-8431-01A
35 years, female, stage:ii, alive, 588 days
1.6
TCGA-KO-8414-01A
50 years, female, white, stage:ii, alive, 3212 days
1.6
TCGA-KM-8477-01A
56 years, male, white, stage:i, alive, 1553 days
1.5
TCGA-KL-8337-01A
26 years, male, black or african american, stage:ii, alive, 1364 days
1.5
TCGA-KN-8434-01A
65 years, female, white, stage:ii, alive, 1797 days
1.4
TCGA-KO-8415-01A
44 years, female, white, stage:i, alive, 2939 days
1.4
TCGA-KM-8439-01A
30 years, male, white, stage:i, alive, 708 days
1.4
TCGA-KO-8407-01A
42 years, male, white, stage:ii, alive, 2820 days
1.4
TCGA-KO-8416-01A
41 years, male, white, stage:iii, alive, 2752 days
1.3
TCGA-KN-8433-01A
46 years, female, white, stage:iii, alive, 341 days
1.2
TCGA-KO-8403-01A
49 years, male, white, stage:i, alive, 3208 days
1.2
TCGA-KL-8332-01A
55 years, male, white, stage:i, alive, 2582 days
1.1
TCGA-KL-8335-01A
68 years, male, white, stage:iii, alive, 2815 days
1.1
TCGA-KL-8328-01A
60 years, male, white, stage:ii, alive, 3127 days
1.0
TCGA-KL-8331-01A
48 years, female, white, stage:ii, alive, 3010 days
1.0
TCGA-KM-8443-01A
58 years, male, white, stage:ii, alive, 1520 days
1.0
TCGA-KL-8338-01A
51 years, male, white, stage:iii, alive, 2633 days
1.0
TCGA-KL-8342-01A
45 years, female, white, stage:ii, alive, 2248 days
0.9
TCGA-KO-8405-01A
29 years, male, white, stage:iii, alive, 3056 days
0.9
TCGA-KM-8476-01A
47 years, male, white, stage:i, alive, 3745 days
0.9
TCGA-KL-8326-01A
69 years, male, white, stage:iii, alive, 3322 days
0.9
TCGA-KL-8324-01A
67 years, female, white, stage:ii, alive, 4676 days
0.8
TCGA-KO-8409-01A
69 years, male, white, stage:ii, alive, 3180 days
0.8
TCGA-KL-8346-01A
62 years, male, white, stage:ii, alive, 1897 days
0.7
TCGA-KL-8327-01A
46 years, female, white, stage:i, alive, 4169 days
The Human Protein Atlas project is funded
