This pipeline uses various statistical tests to identify mRNAs whose log2 expression levels correlated to selected clinical features.
Testing the association between 17814 genes and 11 clinical features across 88 samples, statistically thresholded by P value < 0.05 and Q value < 0.3, 10 clinical features related to at least one genes.
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1 gene correlated to 'YEARS_TO_BIRTH'.
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OPN4
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30 genes correlated to 'NEOPLASM_DISEASESTAGE'.
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MTFMT , NOP5/NOP58 , BMP5 , TRIM11 , GNL3L , ...
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30 genes correlated to 'PATHOLOGY_T_STAGE'.
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BMP5 , TRIM11 , GNL3L , TARS2 , HIST1H3A , ...
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30 genes correlated to 'PATHOLOGY_N_STAGE'.
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UBIAD1 , WIF1 , SOAT2 , SNAP29 , ISLR , ...
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30 genes correlated to 'PATHOLOGY_M_STAGE'.
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AGXT2L2 , CASP8 , GPRIN1 , STARD3 , B4GALT2 , ...
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16 genes correlated to 'GENDER'.
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CYORF15A , JARID1D , CYORF15B , UTX , CXORF15 , ...
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30 genes correlated to 'HISTOLOGICAL_TYPE'.
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ZFYVE20 , CSNK1A1L , WHDC1L1 , SPATA13 , SOX17 , ...
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1 gene correlated to 'NUMBER_PACK_YEARS_SMOKED'.
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SLCO6A1
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30 genes correlated to 'RACE'.
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PCDH20 , TNNI3 , DUSP1 , FUT8 , CASQ2 , ...
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30 genes correlated to 'ETHNICITY'.
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C14ORF73 , ADPRH , GBAS , VSNL1 , CAMK2B , ...
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No genes correlated to 'DAYS_TO_DEATH_OR_LAST_FUP'
Complete statistical result table is provided in Supplement Table 1
Clinical feature | Statistical test | Significant genes | Associated with | Associated with | ||
---|---|---|---|---|---|---|
DAYS_TO_DEATH_OR_LAST_FUP | Cox regression test | N=0 | ||||
YEARS_TO_BIRTH | Spearman correlation test | N=1 | older | N=1 | younger | N=0 |
NEOPLASM_DISEASESTAGE | Kruskal-Wallis test | N=30 | ||||
PATHOLOGY_T_STAGE | Spearman correlation test | N=30 | higher stage | N=18 | lower stage | N=12 |
PATHOLOGY_N_STAGE | Wilcoxon test | N=30 | n1 | N=28 | n0 | N=0 |
PATHOLOGY_M_STAGE | Wilcoxon test | N=30 | class1 | N=30 | class0 | N=0 |
GENDER | Wilcoxon test | N=16 | male | N=16 | female | N=0 |
HISTOLOGICAL_TYPE | Wilcoxon test | N=30 | kidney papillary renal cell carcinoma | N=29 | kidney clear cell renal carcinoma | N=0 |
NUMBER_PACK_YEARS_SMOKED | Spearman correlation test | N=1 | higher number_pack_years_smoked | N=0 | lower number_pack_years_smoked | N=1 |
RACE | Kruskal-Wallis test | N=30 | ||||
ETHNICITY | Wilcoxon test | N=30 | not hispanic or latino | N=30 | hispanic or latino | N=0 |
DAYS_TO_DEATH_OR_LAST_FUP | Duration (Months) | 0.5-101.1 (median=32.6) |
censored | N = 71 | |
death | N = 16 | |
Significant markers | N = 0 |
YEARS_TO_BIRTH | Mean (SD) | 60.06 (12) |
Significant markers | N = 1 | |
pos. correlated | 1 | |
neg. correlated | 0 |
NEOPLASM_DISEASESTAGE | Labels | N |
STAGE I | 45 | |
STAGE II | 16 | |
STAGE III | 15 | |
STAGE IV | 6 | |
Significant markers | N = 30 |
PATHOLOGY_T_STAGE | Mean (SD) | 1.67 (0.81) |
N | ||
T1 | 48 | |
T2 | 21 | |
T3 | 19 | |
Significant markers | N = 30 | |
pos. correlated | 18 | |
neg. correlated | 12 |
SpearmanCorr | corrP | Q | |
---|---|---|---|
BMP5 | -0.4491 | 1.141e-05 | 0.104 |
TRIM11 | 0.4486 | 1.17e-05 | 0.104 |
GNL3L | 0.4289 | 3.05e-05 | 0.136 |
TARS2 | 0.4222 | 4.181e-05 | 0.136 |
HIST1H3A | 0.4218 | 4.255e-05 | 0.136 |
OAT | -0.4153 | 5.744e-05 | 0.136 |
PCBP2 | -0.4145 | 5.944e-05 | 0.136 |
FAM89A | 0.4139 | 6.122e-05 | 0.136 |
RNF125 | 0.4033 | 9.789e-05 | 0.176 |
ZNF233 | -0.403 | 9.905e-05 | 0.176 |
PATHOLOGY_N_STAGE | Labels | N |
N0 | 37 | |
N1 | 4 | |
Significant markers | N = 30 | |
Higher in N1 | 28 | |
Higher in N0 | 0 |
W(pos if higher in 'N1') | wilcoxontestP | Q | AUC | |
---|---|---|---|---|
UBIAD1 | 0 | 0.001239 | 0.233 | 1 |
WIF1 | 148 | 0.00124 | 0.233 | 1 |
SOAT2 | 148 | 0.00124 | 0.233 | 1 |
SNAP29 | 0 | 0.00124 | 0.233 | 1 |
ISLR | 148 | 0.00124 | 0.233 | 1 |
FLJ40869 | 148 | 0.00124 | 0.233 | 1 |
LEPRE1 | 147 | 0.001445 | 0.233 | 0.9932 |
RPS27L | 1 | 0.001445 | 0.233 | 0.9932 |
SPEG | 147 | 0.001445 | 0.233 | 0.9932 |
OR1J1 | 147 | 0.001445 | 0.233 | 0.9932 |
PATHOLOGY_M_STAGE | Labels | N |
class0 | 77 | |
class1 | 6 | |
Significant markers | N = 30 | |
Higher in class1 | 30 | |
Higher in class0 | 0 |
W(pos if higher in 'class1') | wilcoxontestP | Q | AUC | |
---|---|---|---|---|
AGXT2L2 | 452 | 0.0001056 | 0.131 | 0.9784 |
CASP8 | 449 | 0.000131 | 0.131 | 0.9719 |
GPRIN1 | 447 | 0.000151 | 0.131 | 0.9675 |
STARD3 | 445 | 0.0001738 | 0.131 | 0.9632 |
B4GALT2 | 445 | 0.0001738 | 0.131 | 0.9632 |
MCM4 | 444 | 0.0001864 | 0.131 | 0.961 |
TRIM41 | 441 | 0.0002296 | 0.131 | 0.9545 |
BTF3 | 21 | 0.0002296 | 0.131 | 0.9545 |
KIAA1737 | 21 | 0.0002296 | 0.131 | 0.9545 |
C17ORF56 | 440 | 0.000246 | 0.131 | 0.9524 |
GENDER | Labels | N |
FEMALE | 33 | |
MALE | 55 | |
Significant markers | N = 16 | |
Higher in MALE | 16 | |
Higher in FEMALE | 0 |
W(pos if higher in 'MALE') | wilcoxontestP | Q | AUC | |
---|---|---|---|---|
CYORF15A | 1746 | 5.095e-13 | 3.03e-09 | 0.962 |
JARID1D | 1735 | 1.019e-12 | 3.22e-09 | 0.9559 |
CYORF15B | 1714 | 3.733e-12 | 8.31e-09 | 0.9444 |
UTX | 402 | 1.345e-05 | 0.0141 | 0.7785 |
CXORF15 | 426 | 3.387e-05 | 0.0335 | 0.7653 |
CBLN3 | 431 | 4.084e-05 | 0.0383 | 0.7625 |
PRPF39 | 1381 | 4.566e-05 | 0.0402 | 0.7609 |
JARID1C | 435 | 4.738e-05 | 0.0402 | 0.7603 |
PCDH21 | 1374 | 5.908e-05 | 0.0478 | 0.757 |
UCHL5IP | 1368 | 7.347e-05 | 0.0565 | 0.7537 |
HISTOLOGICAL_TYPE | Labels | N |
KIDNEY CLEAR CELL RENAL CARCINOMA | 72 | |
KIDNEY PAPILLARY RENAL CELL CARCINOMA | 16 | |
Significant markers | N = 30 | |
Higher in KIDNEY PAPILLARY RENAL CELL CARCINOMA | 29 | |
Higher in KIDNEY CLEAR CELL RENAL CARCINOMA | 0 |
W(pos if higher in 'KIDNEY PAPILLARY RENAL CELL CARCINOMA') | wilcoxontestP | Q | AUC | |
---|---|---|---|---|
ZFYVE20 | c("1152", "4.78e-10") | c("1152", "4.78e-10") | 1.37e-06 | 1 |
CSNK1A1L | c("0", "4.782e-10") | c("0", "4.782e-10") | 1.37e-06 | 1 |
WHDC1L1 | c("3", "5.88e-10") | c("3", "5.88e-10") | 1.37e-06 | 0.9974 |
SPATA13 | c("4", "6.297e-10") | c("4", "6.297e-10") | 1.37e-06 | 0.9965 |
SOX17 | c("5", "6.744e-10") | c("5", "6.744e-10") | 1.37e-06 | 0.9957 |
SFRS2IP | c("7", "7.731e-10") | c("7", "7.731e-10") | 1.37e-06 | 0.9939 |
RBM22 | c("10", "9.482e-10") | c("10", "9.482e-10") | 1.37e-06 | 0.9913 |
PLDN | c("14", "1.243e-09") | c("14", "1.243e-09") | 1.37e-06 | 0.9878 |
ODC1 | c("1137", "1.329e-09") | c("1137", "1.329e-09") | 1.37e-06 | 0.987 |
SCLT1 | c("16", "1.422e-09") | c("16", "1.422e-09") | 1.37e-06 | 0.9861 |
NUMBER_PACK_YEARS_SMOKED | Mean (SD) | 12 (3.6) |
Value | N | |
8 | 1 | |
10 | 1 | |
15 | 2 | |
Significant markers | N = 1 | |
pos. correlated | 0 | |
neg. correlated | 1 |
RACE | Labels | N |
ASIAN | 1 | |
BLACK OR AFRICAN AMERICAN | 12 | |
WHITE | 71 | |
Significant markers | N = 30 |
ETHNICITY | Labels | N |
HISPANIC OR LATINO | 7 | |
NOT HISPANIC OR LATINO | 58 | |
Significant markers | N = 30 | |
Higher in NOT HISPANIC OR LATINO | 30 | |
Higher in HISPANIC OR LATINO | 0 |
W(pos if higher in 'NOT HISPANIC OR LATINO') | wilcoxontestP | Q | AUC | |
---|---|---|---|---|
C14ORF73 | c("18", "9.447e-05") | c("18", "9.447e-05") | 0.148 | 0.9557 |
ADPRH | c("19", "0.0001031") | c("19", "0.0001031") | 0.148 | 0.9532 |
GBAS | c("384", "0.0001336") | c("384", "0.0001336") | 0.148 | 0.9458 |
VSNL1 | c("378", "0.0002218") | c("378", "0.0002218") | 0.148 | 0.931 |
CAMK2B | c("377", "0.000241") | c("377", "0.000241") | 0.148 | 0.9286 |
POLR2J | c("375", "0.0002842") | c("375", "0.0002842") | 0.148 | 0.9236 |
RIN3 | c("31", "0.0002842") | c("31", "0.0002842") | 0.148 | 0.9236 |
SRCRB4D | c("374", "0.0003083") | c("374", "0.0003083") | 0.148 | 0.9212 |
ZNF366 | c("32", "0.0003084") | c("32", "0.0003084") | 0.148 | 0.9212 |
CDH5 | c("33", "0.0003345") | c("33", "0.0003345") | 0.148 | 0.9187 |
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Expresson data file = KIPAN-TP.medianexp.txt
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Clinical data file = KIPAN-TP.merged_data.txt
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Number of patients = 88
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Number of genes = 17814
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Number of clinical features = 11
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For clinical features selected for this analysis and their value conozzle.versions, please find a documentation on selected CDEs .
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Survival time data
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Survival time data is a combined value of days_to_death and days_to_last_followup. For each patient, it creates a combined value 'days_to_death_or_last_fup' using conversion process below.
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if 'vital_status'==1(dead), 'days_to_last_followup' is always NA. Thus, uses 'days_to_death' value for 'days_to_death_or_fup'
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if 'vital_status'==0(alive),
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if 'days_to_death'==NA & 'days_to_last_followup'!=NA, uses 'days_to_last_followup' value for 'days_to_death_or_fup'
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if 'days_to_death'!=NA, excludes this case in survival analysis and report the case.
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if 'vital_status'==NA,excludes this case in survival analysis and report the case.
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cf. In certain diesase types such as SKCM, days_to_death parameter is replaced with time_from_specimen_dx or time_from_specimen_procurement_to_death .
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This analysis excluded clinical variables that has only NA values.
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 two groups (mutant or wild-type) of continuous type of clinical data, wilcoxon rank sum test (Mann and Whitney, 1947) was applied to compare their mean difference using 'wilcox.test(continuous.clinical ~ as.factor(group), exact=FALSE)' function in R. This test is equivalent to the Mann-Whitney test.
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.