This pipeline uses various statistical tests to identify mRNAs whose log2 expression levels correlated to selected clinical features.
Testing the association between 23512 genes and 9 clinical features across 108 samples, statistically thresholded by P value < 0.05 and Q value < 0.3, 4 clinical features related to at least one genes.
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80 genes correlated to 'AGE'.
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RIPK3|11035_CALCULATED , CBX1|10951_CALCULATED , SIX1|6495_CALCULATED , MCM2|4171_CALCULATED , KIF3C|3797_CALCULATED , ...
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13 genes correlated to 'PATHOLOGY.T.STAGE'.
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R3HDML|140902_CALCULATED , RAP1GAP2|23108_CALCULATED , NHSL1|57224_CALCULATED , TNFRSF11A|8792_CALCULATED , PLEKHG6|55200_CALCULATED , ...
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1 gene correlated to 'GENDER'.
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TXLNG2P|246126_CALCULATED
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1109 genes correlated to 'RACE'.
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RNF217|154214_CALCULATED , TMC5|79838_CALCULATED , HAP1|9001_CALCULATED , TMTC3|160418_CALCULATED , ALOX12P2|245_CALCULATED , ...
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No genes correlated to 'Time to Death', 'NEOPLASM.DISEASESTAGE', 'PATHOLOGY.N.STAGE', 'PATHOLOGY.M.STAGE', and 'NUMBERPACKYEARSSMOKED'.
Complete statistical result table is provided in Supplement Table 1
Clinical feature | Statistical test | Significant genes | Associated with | Associated with | ||
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Time to Death | Cox regression test | N=0 | ||||
AGE | Spearman correlation test | N=80 | older | N=14 | younger | N=66 |
NEOPLASM DISEASESTAGE | Kruskal-Wallis test | N=0 | ||||
PATHOLOGY T STAGE | Spearman correlation test | N=13 | higher stage | N=1 | lower stage | N=12 |
PATHOLOGY N STAGE | Spearman correlation test | N=0 | ||||
PATHOLOGY M STAGE | Kruskal-Wallis test | N=0 | ||||
GENDER | Wilcoxon test | N=1 | male | N=1 | female | N=0 |
NUMBERPACKYEARSSMOKED | Spearman correlation test | N=0 | ||||
RACE | Wilcoxon test | N=1109 | white | N=1109 | asian | N=0 |
Time to Death | Duration (Months) | 0-122.1 (median=4.9) |
censored | N = 67 | |
death | N = 34 | |
Significant markers | N = 0 |
AGE | Mean (SD) | 62.52 (12) |
Significant markers | N = 80 | |
pos. correlated | 14 | |
neg. correlated | 66 |
SpearmanCorr | corrP | Q | |
---|---|---|---|
RIPK3|11035_CALCULATED | 0.4809 | 1.378e-07 | 0.00324 |
CBX1|10951_CALCULATED | -0.4763 | 1.889e-07 | 0.00444 |
SIX1|6495_CALCULATED | -0.4759 | 1.934e-07 | 0.00455 |
MCM2|4171_CALCULATED | -0.4747 | 2.094e-07 | 0.00492 |
KIF3C|3797_CALCULATED | -0.4625 | 4.66e-07 | 0.011 |
TMC5|79838_CALCULATED | 0.4622 | 4.776e-07 | 0.0112 |
CDC7|8317_CALCULATED | -0.4596 | 5.625e-07 | 0.0132 |
HIST1H2BO|8348_CALCULATED | -0.4571 | 7.448e-07 | 0.0175 |
WDHD1|11169_CALCULATED | -0.4519 | 9.16e-07 | 0.0215 |
MCM5|4174_CALCULATED | -0.4517 | 9.282e-07 | 0.0218 |
NEOPLASM.DISEASESTAGE | Labels | N |
STAGE I | 7 | |
STAGE IA | 4 | |
STAGE IB | 4 | |
STAGE II | 1 | |
STAGE IIA | 30 | |
STAGE IIB | 17 | |
STAGE III | 11 | |
STAGE IIIA | 8 | |
STAGE IIIB | 7 | |
STAGE IIIC | 3 | |
STAGE IV | 2 | |
Significant markers | N = 0 |
PATHOLOGY.T.STAGE | Mean (SD) | 2.35 (0.86) |
N | ||
0 | 1 | |
1 | 19 | |
2 | 26 | |
3 | 49 | |
4 | 3 | |
Significant markers | N = 13 | |
pos. correlated | 1 | |
neg. correlated | 12 |
SpearmanCorr | corrP | Q | |
---|---|---|---|
R3HDML|140902_CALCULATED | -0.6038 | 1.342e-06 | 0.0315 |
RAP1GAP2|23108_CALCULATED | -0.4539 | 2.676e-06 | 0.0629 |
NHSL1|57224_CALCULATED | -0.4508 | 3.19e-06 | 0.075 |
TNFRSF11A|8792_CALCULATED | -0.443 | 4.934e-06 | 0.116 |
PLEKHG6|55200_CALCULATED | -0.4417 | 5.293e-06 | 0.124 |
DDIT4L|115265_CALCULATED | 0.4435 | 5.369e-06 | 0.126 |
SEC16B|89866_CALCULATED | -0.4387 | 6.236e-06 | 0.147 |
CPT1A|1374_CALCULATED | -0.4358 | 7.271e-06 | 0.171 |
ACOT11|26027_CALCULATED | -0.4341 | 7.998e-06 | 0.188 |
PLCB3|5331_CALCULATED | -0.4313 | 9.256e-06 | 0.218 |
PATHOLOGY.N.STAGE | Mean (SD) | 0.63 (0.78) |
N | ||
0 | 51 | |
1 | 34 | |
2 | 9 | |
3 | 3 | |
Significant markers | N = 0 |
PATHOLOGY.M.STAGE | Labels | N |
M0 | 77 | |
M1 | 1 | |
M1A | 1 | |
MX | 15 | |
Significant markers | N = 0 |
GENDER | Labels | N |
FEMALE | 16 | |
MALE | 92 | |
Significant markers | N = 1 | |
Higher in MALE | 1 | |
Higher in FEMALE | 0 |
W(pos if higher in 'MALE') | wilcoxontestP | Q | AUC | |
---|---|---|---|---|
TXLNG2P|246126_CALCULATED | 644 | 1.14e-05 | 0.268 | 1 |
NUMBERPACKYEARSSMOKED | Mean (SD) | 35.68 (20) |
Significant markers | N = 0 |
RACE | Labels | N |
ASIAN | 36 | |
WHITE | 68 | |
Significant markers | N = 1109 | |
Higher in WHITE | 1109 | |
Higher in ASIAN | 0 |
W(pos if higher in 'WHITE') | wilcoxontestP | Q | AUC | |
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RNF217|154214_CALCULATED | 259 | 4.394e-11 | 1.03e-06 | 0.8942 |
TMC5|79838_CALCULATED | 2185 | 5.28e-11 | 1.24e-06 | 0.8926 |
HAP1|9001_CALCULATED | 270 | 9.771e-11 | 2.3e-06 | 0.8881 |
TMTC3|160418_CALCULATED | 283 | 1.309e-10 | 3.08e-06 | 0.8844 |
ALOX12P2|245_CALCULATED | 284.5 | 1.399e-10 | 3.29e-06 | 0.8838 |
TSPAN8|7103_CALCULATED | 2081.5 | 1.513e-10 | 3.56e-06 | 0.8876 |
STL|7955_CALCULATED | 288 | 1.635e-10 | 3.84e-06 | 0.8824 |
KLRG2|346689_CALCULATED | 247 | 2.135e-10 | 5.02e-06 | 0.8875 |
LRP12|29967_CALCULATED | 300 | 2.791e-10 | 6.56e-06 | 0.8775 |
CAGE1|285782_CALCULATED | 295 | 2.992e-10 | 7.03e-06 | 0.8777 |
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Expresson data file = ESCA-TP.mRNAseq_RPKM_log2.txt
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Clinical data file = ESCA-TP.merged_data.txt
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Number of patients = 108
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Number of genes = 23512
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Number of clinical features = 9
For survival clinical features, Wald's test in univariate Cox regression analysis with proportional hazards model (Andersen and Gill 1982) was used to estimate the P values using the 'coxph' function in R. Kaplan-Meier survival curves were plot using the four quartile subgroups of patients based on expression levels
For continuous numerical clinical features, Spearman's rank correlation coefficients (Spearman 1904) and two-tailed P values were estimated using 'cor.test' function in R
For multi-class clinical features (ordinal or nominal), one-way analysis of variance (Howell 2002) was applied to compare the log2-expression levels between different clinical classes using 'anova' function in R
For two-class clinical features, two-tailed Student's t test with unequal variance (Lehmann and Romano 2005) was applied to compare the log2-expression levels between the two clinical classes using 't.test' function in R
For multiple hypothesis correction, Q value is the False Discovery Rate (FDR) analogue of the P value (Benjamini and Hochberg 1995), defined as the minimum FDR at which the test may be called significant. We used the 'Benjamini and Hochberg' method of 'p.adjust' function in R to convert P values into Q values.
In addition to the links below, the full results of the analysis summarized in this report can also be downloaded programmatically using firehose_get, or interactively from either the Broad GDAC website or TCGA Data Coordination Center Portal.