This pipeline uses various statistical tests to identify mRNAs whose expression levels correlated to selected clinical features.
Testing the association between 23365 genes and 11 clinical features across 274 samples, statistically thresholded by Q value < 0.05, 7 clinical features related to at least one genes.
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5 genes correlated to 'AGE'.
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CXCL1|2919_CALCULATED , SNORD52|26797_CALCULATED , TMEM240|339453_CALCULATED , PEX7|5191_CALCULATED , TMEM132C|92293_CALCULATED
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121 genes correlated to 'NEOPLASM.DISEASESTAGE'.
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FMO2|2327_CALCULATED , MOXD1|26002_CALCULATED , RSPO3|84870_CALCULATED , SERPING1|710_CALCULATED , PTGER3|5733_CALCULATED , ...
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484 genes correlated to 'PATHOLOGY.T.STAGE'.
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GNB4|59345_CALCULATED , NEXN|91624_CALCULATED , SNTB2|6645_CALCULATED , PPP1R12A|4659_CALCULATED , KCNE4|23704_CALCULATED , ...
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29 genes correlated to 'GENDER'.
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XIST|7503_CALCULATED , TSIX|9383_CALCULATED , PRKY|5616_CALCULATED , DDX3Y|8653_CALCULATED , ZFY|7544_CALCULATED , ...
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480 genes correlated to 'HISTOLOGICAL.TYPE'.
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GEM|2669_CALCULATED , MFAP5|8076_CALCULATED , TCEAL7|56849_CALCULATED , GYPC|2995_CALCULATED , CLMP|79827_CALCULATED , ...
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53 genes correlated to 'RADIATIONS.RADIATION.REGIMENINDICATION'.
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RNU4ATAC|100151683|2OF8_CALCULATED , JA202363|?_CALCULATED , SNORD61|26787_CALCULATED , 5S_RRNA|?|31OF139_CALCULATED , HSA-MIR-3074-5P|?_CALCULATED , ...
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559 genes correlated to 'COMPLETENESS.OF.RESECTION'.
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METAZOA_SRP|?|38OF109_CALCULATED , MIR3648|100500862_CALCULATED , MIR3960|100616250_CALCULATED , METAZOA_SRP|?|35OF109_CALCULATED , RPPH1|85495_CALCULATED , ...
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No genes correlated to 'Time to Death', 'PATHOLOGY.N.STAGE', 'PATHOLOGY.M.STAGE', and 'NUMBER.OF.LYMPH.NODES'.
Complete statistical result table is provided in Supplement Table 1
Clinical feature | Statistical test | Significant genes | Associated with | Associated with | ||
---|---|---|---|---|---|---|
Time to Death | Cox regression test | N=0 | ||||
AGE | Spearman correlation test | N=5 | older | N=3 | younger | N=2 |
NEOPLASM DISEASESTAGE | ANOVA test | N=121 | ||||
PATHOLOGY T STAGE | Spearman correlation test | N=484 | higher stage | N=481 | lower stage | N=3 |
PATHOLOGY N STAGE | Spearman correlation test | N=0 | ||||
PATHOLOGY M STAGE | ANOVA test | N=0 | ||||
GENDER | t test | N=29 | male | N=12 | female | N=17 |
HISTOLOGICAL TYPE | ANOVA test | N=480 | ||||
RADIATIONS RADIATION REGIMENINDICATION | t test | N=53 | yes | N=49 | no | N=4 |
COMPLETENESS OF RESECTION | ANOVA test | N=559 | ||||
NUMBER OF LYMPH NODES | Spearman correlation test | N=0 |
Time to Death | Duration (Months) | 0.1-105.1 (median=10.4) |
censored | N = 187 | |
death | N = 55 | |
Significant markers | N = 0 |
AGE | Mean (SD) | 65.75 (11) |
Significant markers | N = 5 | |
pos. correlated | 3 | |
neg. correlated | 2 |
SpearmanCorr | corrP | Q | |
---|---|---|---|
CXCL1|2919_CALCULATED | 0.3135 | 1.683e-07 | 0.00393 |
SNORD52|26797_CALCULATED | 0.3011 | 6.176e-07 | 0.0144 |
TMEM240|339453_CALCULATED | -0.2972 | 7.558e-07 | 0.0177 |
PEX7|5191_CALCULATED | 0.2938 | 1.03e-06 | 0.0241 |
TMEM132C|92293_CALCULATED | -0.3038 | 1.46e-06 | 0.0341 |
NEOPLASM.DISEASESTAGE | Labels | N |
STAGE I | 2 | |
STAGE IA | 10 | |
STAGE IB | 26 | |
STAGE II | 23 | |
STAGE IIA | 30 | |
STAGE IIB | 42 | |
STAGE III | 3 | |
STAGE IIIA | 40 | |
STAGE IIIB | 32 | |
STAGE IIIC | 24 | |
STAGE IV | 27 | |
Significant markers | N = 121 |
ANOVA_P | Q | |
---|---|---|
FMO2|2327_CALCULATED | 9.614e-15 | 2.25e-10 |
MOXD1|26002_CALCULATED | 7.617e-13 | 1.78e-08 |
RSPO3|84870_CALCULATED | 1.823e-12 | 4.26e-08 |
SERPING1|710_CALCULATED | 3.486e-11 | 8.14e-07 |
PTGER3|5733_CALCULATED | 2.019e-10 | 4.72e-06 |
ST6GALNAC5|81849_CALCULATED | 2.155e-10 | 5.03e-06 |
GREM1|26585_CALCULATED | 2.43e-10 | 5.68e-06 |
GNB4|59345_CALCULATED | 4.947e-10 | 1.16e-05 |
ROR2|4920_CALCULATED | 4.971e-10 | 1.16e-05 |
SFRP4|6424_CALCULATED | 1.285e-09 | 3e-05 |
PATHOLOGY.T.STAGE | Mean (SD) | 2.93 (0.86) |
N | ||
1 | 13 | |
2 | 69 | |
3 | 107 | |
4 | 76 | |
Significant markers | N = 484 | |
pos. correlated | 481 | |
neg. correlated | 3 |
SpearmanCorr | corrP | Q | |
---|---|---|---|
GNB4|59345_CALCULATED | 0.4187 | 1.13e-12 | 2.64e-08 |
NEXN|91624_CALCULATED | 0.4068 | 5.543e-12 | 1.3e-07 |
SNTB2|6645_CALCULATED | 0.4 | 1.329e-11 | 3.1e-07 |
PPP1R12A|4659_CALCULATED | 0.3889 | 5.366e-11 | 1.25e-06 |
KCNE4|23704_CALCULATED | 0.388 | 5.963e-11 | 1.39e-06 |
PLN|5350_CALCULATED | 0.3836 | 1.021e-10 | 2.39e-06 |
SFMBT2|57713_CALCULATED | 0.3822 | 1.204e-10 | 2.81e-06 |
AF268386|?_CALCULATED | 0.3794 | 1.69e-10 | 3.95e-06 |
RYR2|6262_CALCULATED | 0.3756 | 2.649e-10 | 6.19e-06 |
HAND2|9464_CALCULATED | 0.3775 | 2.893e-10 | 6.76e-06 |
PATHOLOGY.N.STAGE | Mean (SD) | 1.21 (1.1) |
N | ||
0 | 90 | |
1 | 77 | |
2 | 46 | |
3 | 49 | |
Significant markers | N = 0 |
PATHOLOGY.M.STAGE | Labels | N |
M0 | 243 | |
M1 | 18 | |
MX | 13 | |
Significant markers | N = 0 |
GENDER | Labels | N |
FEMALE | 105 | |
MALE | 169 | |
Significant markers | N = 29 | |
Higher in MALE | 12 | |
Higher in FEMALE | 17 |
T(pos if higher in 'MALE') | ttestP | Q | AUC | |
---|---|---|---|---|
XIST|7503_CALCULATED | -33.32 | 3.22e-93 | 7.52e-89 | 0.9706 |
TSIX|9383_CALCULATED | -31.68 | 2.155e-89 | 5.04e-85 | 0.9713 |
PRKY|5616_CALCULATED | 27.86 | 1.042e-51 | 2.44e-47 | 0.984 |
DDX3Y|8653_CALCULATED | 31.96 | 1.044e-47 | 2.44e-43 | 0.9781 |
ZFY|7544_CALCULATED | 28.51 | 2.839e-41 | 6.63e-37 | 0.9797 |
KDM5D|8284_CALCULATED | 28.44 | 2.318e-38 | 5.41e-34 | 0.9817 |
EIF1AY|9086_CALCULATED | 26.44 | 7.196e-37 | 1.68e-32 | 0.9798 |
USP9Y|8287_CALCULATED | 23.8 | 1.977e-30 | 4.62e-26 | 0.9739 |
UTY|7404_CALCULATED | 21.48 | 1.872e-26 | 4.37e-22 | 0.972 |
TXLNG2P|246126_CALCULATED | 20.77 | 1.538e-24 | 3.59e-20 | 0.9735 |
HISTOLOGICAL.TYPE | Labels | N |
STOMACH ADENOCARCINOMA DIFFUSE TYPE | 51 | |
STOMACH ADENOCARCINOMA NOT OTHERWISE SPECIFIED (NOS) | 131 | |
STOMACH INTESTINAL ADENOCARCINOMA NOT OTHERWISE SPECIFIED (NOS) | 35 | |
STOMACH INTESTINAL ADENOCARCINOMA TUBULAR TYPE | 36 | |
STOMACH INTESTINAL ADENOCARCINOMA MUCINOUS TYPE | 13 | |
STOMACH INTESTINAL ADENOCARCINOMA PAPILLARY TYPE | 5 | |
STOMACH ADENOCARCINOMA SIGNET RING TYPE | 1 | |
Significant markers | N = 480 |
ANOVA_P | Q | |
---|---|---|
GEM|2669_CALCULATED | 5.504e-12 | 1.29e-07 |
MFAP5|8076_CALCULATED | 5.917e-12 | 1.38e-07 |
TCEAL7|56849_CALCULATED | 1.618e-11 | 3.78e-07 |
GYPC|2995_CALCULATED | 1.777e-11 | 4.15e-07 |
CLMP|79827_CALCULATED | 2.901e-11 | 6.78e-07 |
ZFPM2|23414_CALCULATED | 2.91e-11 | 6.8e-07 |
ARHGAP20|57569_CALCULATED | 3.933e-11 | 9.19e-07 |
DCN|1634_CALCULATED | 4.118e-11 | 9.62e-07 |
FRMD6|122786_CALCULATED | 6.558e-11 | 1.53e-06 |
COLEC12|81035_CALCULATED | 1.234e-10 | 2.88e-06 |
53 genes related to 'RADIATIONS.RADIATION.REGIMENINDICATION'.
RADIATIONS.RADIATION.REGIMENINDICATION | Labels | N |
NO | 7 | |
YES | 267 | |
Significant markers | N = 53 | |
Higher in YES | 49 | |
Higher in NO | 4 |
T(pos if higher in 'YES') | ttestP | Q | AUC | |
---|---|---|---|---|
RNU4ATAC|100151683|2OF8_CALCULATED | 18.43 | 2.784e-42 | 6.25e-38 | 0.9029 |
JA202363|?_CALCULATED | 15.25 | 7.47e-33 | 1.68e-28 | 0.8742 |
SNORD61|26787_CALCULATED | 13.71 | 4.762e-29 | 1.07e-24 | 0.8163 |
5S_RRNA|?|31OF139_CALCULATED | 13.23 | 4.938e-26 | 1.11e-21 | 0.8321 |
HSA-MIR-3074-5P|?_CALCULATED | 12.27 | 7.55e-26 | 1.7e-21 | 0.7632 |
AP1B1P1|23782_CALCULATED | 13.05 | 5.102e-24 | 1.15e-19 | 0.9 |
MIR4326|100422945_CALCULATED | 11.72 | 8.993e-23 | 2.02e-18 | 0.7755 |
DQ586086|?_CALCULATED | 11.7 | 1.6e-22 | 3.59e-18 | 0.7923 |
LOC100507140|100507140_CALCULATED | 11.64 | 2.245e-22 | 5.04e-18 | 0.8169 |
MIR219-1|407002_CALCULATED | 11.3 | 3.363e-22 | 7.55e-18 | 0.7515 |
559 genes related to 'COMPLETENESS.OF.RESECTION'.
COMPLETENESS.OF.RESECTION | Labels | N |
R0 | 217 | |
R1 | 8 | |
R2 | 10 | |
RX | 22 | |
Significant markers | N = 559 |
ANOVA_P | Q | |
---|---|---|
METAZOA_SRP|?|38OF109_CALCULATED | 6.157e-26 | 1.44e-21 |
MIR3648|100500862_CALCULATED | 8.303e-25 | 1.94e-20 |
MIR3960|100616250_CALCULATED | 1.881e-24 | 4.4e-20 |
METAZOA_SRP|?|35OF109_CALCULATED | 2.734e-24 | 6.39e-20 |
RPPH1|85495_CALCULATED | 3.607e-24 | 8.43e-20 |
MIR3687|100500815_CALCULATED | 1.731e-20 | 4.04e-16 |
LOC407835|407835_CALCULATED | 2.683e-20 | 6.27e-16 |
SCARNA2|677766_CALCULATED | 6.407e-20 | 1.5e-15 |
C19ORF68|374920_CALCULATED | 4.928e-19 | 1.15e-14 |
SCARNA17|677769_CALCULATED | 7.93e-19 | 1.85e-14 |
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Expresson data file = STAD-TP.mRNAseq_RPKM_log2.txt
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Clinical data file = STAD-TP.merged_data.txt
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Number of patients = 274
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Number of genes = 23365
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Number of clinical features = 11
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.