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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.
SAA2 is not prognostic in Skin Cuteneous Melanoma (TCGA)
Stage:
Survival analysis
Current cut offi
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 TPM
3.0
Number of samples
99
Samples
Sample
Description
TPM
TCGA-EB-A550-01A
0 years, female, white, stage:Stage IIC, dead, 264 days
56.4
TCGA-EB-A57M-01A
0 years, male, asian, stage:Stage IIIB, dead, 472 days
31.2
TCGA-BF-AAOU-01A
0 years, female, white, stage:Stage IIC, alive, 476 days
27.2
TCGA-EB-A299-01A
0 years, male, white, stage:Stage IIA, alive, 378 days
17.5
TCGA-GF-A769-01A
0 years, male, white, stage:Stage IIC, dead, 1070 days
17.3
TCGA-BF-A3DJ-01A
0 years, female, white, stage:Stage IIIB, alive, 464 days
13.1
TCGA-EB-A553-01A
0 years, male, white, stage:Stage IIC, alive, 226 days
10.4
TCGA-BF-AAP8-01A
0 years, male, white, stage:Stage IIC, alive, 447 days
10.4
TCGA-XV-AAZY-01A
0 years, female, white, stage:Stage IIIC, alive, 405 days
9.2
TCGA-EB-A3XD-01A
0 years, female, white, stage:Stage IIC, alive, 1160 days
8.2
TCGA-BF-A1PU-01A
0 years, female, white, stage:Stage IIC, alive, 387 days
7.9
TCGA-BF-AAP7-01A
0 years, female, white, stage:Stage IIC, alive, 318 days
7.5
TCGA-D9-A3Z4-01A
0 years, male, white, stage:Stage IIIC, dead, 519 days
7.4
TCGA-BF-A1PV-01A
0 years, female, white, stage:Stage IIC, alive, 14 days
7.4
TCGA-EB-A3Y7-01A
0 years, female, white, stage:Stage IIIB, dead, 326 days
5.6
TCGA-XV-A9W2-01A
0 years, male, white, stage:Stage I, alive, 417 days
4.7
TCGA-BF-AAP2-01A
0 years, male, white, stage:Stage IIB, alive, 405 days
4.5
TCGA-EB-A3XC-01A
0 years, male, white, stage:Stage IIC, alive, 650 days
3.3
TCGA-EB-A82B-01A
0 years, female, asian, stage:Stage III, alive, 390 days
3.1
TCGA-BF-A5EO-01A
0 years, male, white, stage:Stage IIC, alive, 703 days
2.7
TCGA-BF-AAP4-01A
0 years, male, white, stage:Stage IIC, alive, 335 days
2.5
TCGA-IH-A3EA-01A
0 years, male, white, stage:Stage IIC, alive, 524 days
2.4
TCGA-EB-A5UM-01A
0 years, female, white, stage:Stage IIC, alive, 779 days
2.4
TCGA-EB-A3XF-01A
0 years, male, white, stage:Stage IIC, alive, 278 days
1.9
TCGA-EB-A3XB-01A
0 years, male, white, stage:Stage II, alive, 796 days
1.9
TCGA-BF-AAP6-01A
0 years, male, white, stage:Stage III, alive, 325 days
1.8
TCGA-ER-A196-01A
0 years, female, white, stage:Stage IIC, alive, 1785 days
1.8
TCGA-EB-A4IQ-01A
0 years, female, asian, stage:Stage IIIB, dead, 636 days
1.7
TCGA-FS-A1ZN-01A
0 years, male, white, stage:Stage IIIA, dead, 730 days
1.5
TCGA-XV-AAZV-01A
0 years, female, white, stage:Stage II, alive, 412 days
1.3
TCGA-EB-A85I-01A
0 years, male, white, stage:Stage IIC, alive, 362 days
1.1
TCGA-EB-A3XE-01A
0 years, female, white, stage:Stage IIA, alive, 180 days
1.1
TCGA-EB-A4IS-01A
0 years, male, white, stage:Stage IIB, alive, 774 days
1.1
TCGA-XV-A9W5-01A
0 years, male, white, stage:Not Reported, alive, 392 days
1.1
TCGA-GF-A2C7-01A
0 years, male, white, stage:Stage IIC, alive, 21 days
1.0
TCGA-EB-A41B-01A
0 years, female, white, stage:Stage IIC, alive, 291 days
1.0
TCGA-BF-A3DN-01A
0 years, female, white, stage:Stage IIIC, alive, 717 days
1.0
TCGA-GN-A263-01A
0 years, male, white, stage:Stage IV, dead, 467 days
0.9
TCGA-BF-A5EQ-01A
0 years, male, white, stage:Stage IIC, alive, 323 days
0.8
TCGA-BF-AAOX-01A
0 years, male, white, stage:Stage IIC, alive, 444 days
0.8
TCGA-XV-AAZW-01A
0 years, female, white, stage:Stage II, dead, 393 days
0.8
TCGA-GN-A4U5-01A
0 years, female, white, stage:Stage IB, alive, 1156 days
0.7
TCGA-EB-A5SE-01A
0 years, male, white, stage:Stage IIB, dead, 401 days
0.7
TCGA-FW-A5DX-01A
0 years, male, white, stage:Stage IIIC, alive, 640 days
0.7
TCGA-BF-A9VF-01A
0 years, male, white, stage:Stage IIC, alive, 440 days
0.7
TCGA-EB-A85J-01A
0 years, female, white, stage:Stage IIB, alive, 360 days
0.7
TCGA-EB-A24D-01A
0 years, male, white, stage:Stage IIIB, alive, 645 days
0.5
TCGA-BF-AAP1-01A
0 years, male, white, stage:Stage IIC, alive, 409 days
0.5
TCGA-BF-A1PZ-01A
0 years, female, white, stage:Stage IIB, alive, 853 days
0.5
TCGA-EB-A4OZ-01A
0 years, female, white, stage:Stage IIIC, alive, 620 days
0.4
TCGA-BF-A5ES-01A
0 years, female, white, stage:Stage IIC, alive, 490 days
0.4
TCGA-EB-A5VU-01A
0 years, male, asian, stage:Stage IIIB, dead, 321 days
0.4
TCGA-ER-A2NB-01A
0 years, male, white, stage:Stage IIIB, dead, 857 days
0.4
TCGA-ER-A2NF-01A
0 years, male, white, stage:Stage IIIB, dead, 877 days
0.4
TCGA-ER-A42H-01A
0 years, male, white, stage:'--, dead, 426 days
0.4
TCGA-EB-A551-01A
0 years, female, white, stage:Stage IIIC, alive, 590 days
0.3
TCGA-EB-A6R0-01A
0 years, female, white, stage:Stage IIC, dead, 608 days
0.3
TCGA-FR-A728-01A
0 years, female, white, stage:Stage IIIB, alive, 583 days
0.3
TCGA-FR-A3R1-01A
0 years, male, white, stage:Stage IIC, alive, 685 days
0.3
TCGA-ER-A19K-01A
0 years, female, white, stage:Stage IIC, dead, 469 days
0.3
TCGA-EB-A6QZ-01A
0 years, female, white, stage:Stage IIA, dead, 352 days
0.3
TCGA-BF-A3DL-01A
0 years, female, white, stage:Stage IIIB, alive, 769 days
0.3
TCGA-EB-A82C-01A
0 years, female, asian, stage:Stage IIC, alive, 17 days
0.2
TCGA-EB-A44P-01A
0 years, female, white, stage:Stage IIC, alive, 741 days
0.2
TCGA-D9-A4Z3-01A
0 years, female, white, stage:Stage IIIC, alive, 505 days
0.2
TCGA-EB-A42Y-01A
0 years, female, asian, stage:Stage IIC, dead, 721 days
0.2
TCGA-D3-A5GT-01A
0 years, male, white, stage:Stage IIIC, alive, 487 days
0.2
TCGA-EB-A1NK-01A
0 years, male, white, stage:Stage IIC, alive, 1039 days
0.2
TCGA-EB-A5FP-01A
0 years, female, white, stage:Stage IV, dead, 454 days
0.1
TCGA-EB-A4XL-01A
0 years, female, white, stage:Stage IIC, alive, 777 days
0.1
TCGA-EB-A431-01A
0 years, male, white, stage:Stage IIC, alive, 568 days
0.1
TCGA-BF-A1PX-01A
0 years, male, white, stage:Stage IIIB, dead, 282 days
0.1
TCGA-EB-A4P0-01A
0 years, male, white, stage:Stage IIC, dead, 326 days
0.1
TCGA-D9-A4Z5-01A
0 years, male, white, stage:Stage IIB, alive, 218 days
0.1
TCGA-DA-A960-01A
0 years, male, white, stage:Stage IIB, alive, 804 days
0.1
TCGA-EB-A44O-01A
0 years, male, white, stage:Stage IIB, alive, 81 days
0.0
TCGA-EB-A3HV-01A
0 years, male, white, stage:Stage IIC, alive, 39 days
0.0
TCGA-EB-A4OY-01A
0 years, female, white, stage:Stage IIIB, alive, 977 days
0.0
TCGA-EB-A51B-01A
0 years, male, white, stage:Stage IIC, alive, 931 days
0.0
TCGA-BF-A1Q0-01A
0 years, male, white, stage:Stage IIC, alive, 831 days
0.0
TCGA-EB-A5SF-01A
0 years, female, white, stage:Stage IIC, dead, 369 days
0.0
TCGA-EB-A6QY-01A
0 years, male, white, stage:Stage IIC, alive, 382 days
0.0
TCGA-BF-A5EP-01A
0 years, female, white, stage:Stage IIIC, alive, 335 days
0.0
TCGA-FR-A2OS-01A
0 years, female, white, stage:Stage IIC, dead, 368 days
0.0
TCGA-ER-A194-01A
0 years, male, white, stage:'--, dead, 1354 days
0.0
TCGA-EB-A24C-01A
0 years, male, white, stage:'--, alive, 632 days
0.0
TCGA-GN-A26C-01A
0 years, male, white, stage:Stage IIIC, dead, 821 days
0.0
TCGA-BF-A5ER-01A
0 years, male, white, stage:Stage IIC, alive, 327 days
0.0
TCGA-GN-A8LN-01A
0 years, male, white, stage:Stage IIC, alive, 772 days
0.0
TCGA-EB-A44N-01A
0 years, male, white, stage:Stage IIC, dead, 205 days
0.0
TCGA-ER-A19T-01A
0 years, male, white, stage:Stage IV, dead, 270 days
0.0
TCGA-EB-A97M-01A
0 years, male, white, stage:Stage IIC, alive, 414 days
0.0
TCGA-EB-A42Z-01A
0 years, male, asian, stage:Stage IIIC, alive, 441 days
0.0
TCGA-BF-A3DM-01A
0 years, male, white, stage:Stage IIA, alive, 601 days
0.0
TCGA-D9-A4Z2-01A
0 years, male, white, stage:Stage IIIC, dead, 190 days
0.0
TCGA-YG-AA3N-01A
0 years, male, stage:Stage IIC, alive, 306 days
0.0
TCGA-WE-A8K4-01A
0 years, male, white, stage:Stage IIB, alive, 614 days
0.0
TCGA-EB-A3Y6-01A
0 years, female, white, stage:Stage IIC, alive, 126 days
0.0
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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.
The Human Protein Atlas project is funded
