This pipeline uses various statistical tests to identify mRNAs whose log2 expression levels correlated to selected clinical features.
Testing the association between 18035 genes and 13 clinical features across 601 samples, statistically thresholded by P value < 0.05 and Q value < 0.3, 11 clinical features related to at least one genes.
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37 genes correlated to 'AGE'.
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MTERF|7978 , AMH|268 , MGA|23269 , CNTD2|79935 , MRE11A|4361 , ...
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184 genes correlated to 'PRIMARY.SITE.OF.DISEASE'.
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HOXB13|10481 , ZNF528|84436 , ELAVL2|1993 , ZNF530|348327 , ZNF662|389114 , ...
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105 genes correlated to 'NEOPLASM.DISEASESTAGE'.
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RGL2|5863 , C5ORF23|79614 , C2CD4A|145741 , GSR|2936 , BEND3|57673 , ...
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188 genes correlated to 'PATHOLOGY.T.STAGE'.
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SCG2|7857 , C5ORF23|79614 , SPP1|6696 , SOX11|6664 , CSRP2|1466 , ...
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353 genes correlated to 'PATHOLOGY.N.STAGE'.
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GSR|2936 , TEAD3|7005 , RGL2|5863 , C5ORF23|79614 , AGPAT5|55326 , ...
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514 genes correlated to 'PATHOLOGY.M.STAGE'.
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FUNDC2P2|388965 , POTEE|445582 , MCART2|147407 , LOC344967|344967 , SPIN2A|54466 , ...
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10 genes correlated to 'GENDER'.
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CYORF15A|246126 , CYORF15B|84663 , HDHD1A|8226 , NCRNA00183|554203 , SPESP1|246777 , ...
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1380 genes correlated to 'HISTOLOGICAL.TYPE'.
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PLAGL2|5326 , POFUT1|23509 , SLC19A3|80704 , SLC5A6|8884 , MUC2|4583 , ...
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628 genes correlated to 'COMPLETENESS.OF.RESECTION'.
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RRN3P2|653390 , LOC150776|150776 , PMS2CL|441194 , POLR2J4|84820 , SCXB|642658 , ...
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237 genes correlated to 'NUMBER.OF.LYMPH.NODES'.
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GSR|2936 , TEAD3|7005 , CASP1|834 , C5ORF23|79614 , NPR3|4883 , ...
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19 genes correlated to 'RACE'.
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ULK4|54986 , LOC441455|441455 , C14ORF167|55449 , NOTCH2NL|388677 , PPIL3|53938 , ...
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No genes correlated to 'Time to Death', and 'RADIATIONS.RADIATION.REGIMENINDICATION'.
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=37 | older | N=13 | younger | N=24 |
PRIMARY SITE OF DISEASE | Wilcoxon test | N=184 | rectum | N=184 | colon | N=0 |
NEOPLASM DISEASESTAGE | Kruskal-Wallis test | N=105 | ||||
PATHOLOGY T STAGE | Spearman correlation test | N=188 | higher stage | N=172 | lower stage | N=16 |
PATHOLOGY N STAGE | Spearman correlation test | N=353 | higher stage | N=240 | lower stage | N=113 |
PATHOLOGY M STAGE | Kruskal-Wallis test | N=514 | ||||
GENDER | Wilcoxon test | N=10 | male | N=10 | female | N=0 |
HISTOLOGICAL TYPE | Kruskal-Wallis test | N=1380 | ||||
RADIATIONS RADIATION REGIMENINDICATION | Wilcoxon test | N=0 | ||||
COMPLETENESS OF RESECTION | Kruskal-Wallis test | N=628 | ||||
NUMBER OF LYMPH NODES | Spearman correlation test | N=237 | higher number.of.lymph.nodes | N=153 | lower number.of.lymph.nodes | N=84 |
RACE | Kruskal-Wallis test | N=19 |
Time to Death | Duration (Months) | 0.1-140.4 (median=18) |
censored | N = 463 | |
death | N = 109 | |
Significant markers | N = 0 |
AGE | Mean (SD) | 66.49 (13) |
Significant markers | N = 37 | |
pos. correlated | 13 | |
neg. correlated | 24 |
SpearmanCorr | corrP | Q | |
---|---|---|---|
MTERF|7978 | -0.2408 | 2.518e-09 | 4.54e-05 |
AMH|268 | 0.2328 | 1.444e-08 | 0.00026 |
MGA|23269 | -0.2251 | 2.493e-08 | 0.00045 |
CNTD2|79935 | 0.2088 | 2.563e-07 | 0.00462 |
MRE11A|4361 | -0.2008 | 7.278e-07 | 0.0131 |
TGFBR2|7048 | -0.197 | 1.155e-06 | 0.0208 |
ZNF134|7693 | -0.1958 | 1.404e-06 | 0.0253 |
LOC154761|154761 | 0.1955 | 1.427e-06 | 0.0257 |
ZNF518B|85460 | -0.1911 | 2.526e-06 | 0.0455 |
ZNF75A|7627 | -0.1882 | 3.572e-06 | 0.0644 |
PRIMARY.SITE.OF.DISEASE | Labels | N |
COLON | 437 | |
RECTUM | 160 | |
Significant markers | N = 184 | |
Higher in RECTUM | 184 | |
Higher in COLON | 0 |
W(pos if higher in 'RECTUM') | wilcoxontestP | Q | AUC | |
---|---|---|---|---|
HOXB13|10481 | 48933 | 4.587e-14 | 8.27e-10 | 0.7014 |
ZNF528|84436 | 46390.5 | 4.555e-10 | 8.21e-06 | 0.6665 |
ELAVL2|1993 | 37834 | 6.841e-10 | 1.23e-05 | 0.6712 |
ZNF530|348327 | 46262 | 7.067e-10 | 1.27e-05 | 0.6647 |
ZNF662|389114 | 46004 | 8.447e-10 | 1.52e-05 | 0.664 |
HOXC4|3221 | 18471.5 | 1.376e-09 | 2.48e-05 | 0.6718 |
HOXC6|3223 | 15520 | 1.845e-09 | 3.33e-05 | 0.6791 |
ZNF813|126017 | 45746 | 2.01e-09 | 3.62e-05 | 0.6603 |
ZNF141|7700 | 45516 | 3.07e-09 | 5.53e-05 | 0.6585 |
ELAC1|55520 | 24090 | 5.779e-09 | 0.000104 | 0.6555 |
NEOPLASM.DISEASESTAGE | Labels | N |
STAGE I | 102 | |
STAGE IA | 1 | |
STAGE II | 35 | |
STAGE IIA | 171 | |
STAGE IIB | 11 | |
STAGE IIC | 3 | |
STAGE III | 27 | |
STAGE IIIA | 21 | |
STAGE IIIB | 78 | |
STAGE IIIC | 52 | |
STAGE IV | 59 | |
STAGE IVA | 26 | |
STAGE IVB | 1 | |
Significant markers | N = 105 |
ANOVA_P | Q | |
---|---|---|
RGL2|5863 | 2.816e-09 | 5.08e-05 |
C5ORF23|79614 | 5.722e-09 | 0.000103 |
C2CD4A|145741 | 1.46e-08 | 0.000263 |
GSR|2936 | 2.41e-08 | 0.000435 |
BEND3|57673 | 4.06e-08 | 0.000732 |
C13ORF15|28984 | 5.17e-08 | 0.000932 |
NPR3|4883 | 1.046e-07 | 0.00189 |
IRF1|3659 | 1.451e-07 | 0.00262 |
CDRT1|374286 | 2.159e-07 | 0.00389 |
LAP3|51056 | 2.43e-07 | 0.00438 |
PATHOLOGY.T.STAGE | Mean (SD) | 2.87 (0.63) |
N | ||
1 | 20 | |
2 | 105 | |
3 | 409 | |
4 | 65 | |
Significant markers | N = 188 | |
pos. correlated | 172 | |
neg. correlated | 16 |
SpearmanCorr | corrP | Q | |
---|---|---|---|
SCG2|7857 | 0.2513 | 5.226e-10 | 9.43e-06 |
C5ORF23|79614 | 0.2503 | 1.193e-09 | 2.15e-05 |
SPP1|6696 | 0.2364 | 4.738e-09 | 8.54e-05 |
SOX11|6664 | 0.239 | 5.586e-09 | 0.000101 |
CSRP2|1466 | 0.233 | 7.888e-09 | 0.000142 |
OLR1|4973 | 0.234 | 8.301e-09 | 0.00015 |
HTR2B|3357 | 0.2384 | 8.594e-09 | 0.000155 |
LOC100126784|100126784 | 0.2456 | 9.854e-09 | 0.000178 |
NALCN|259232 | 0.244 | 1.393e-08 | 0.000251 |
S1PR3|1903 | 0.2248 | 2.662e-08 | 0.00048 |
PATHOLOGY.N.STAGE | Mean (SD) | 0.61 (0.78) |
N | ||
0 | 341 | |
1 | 147 | |
2 | 109 | |
Significant markers | N = 353 | |
pos. correlated | 240 | |
neg. correlated | 113 |
SpearmanCorr | corrP | Q | |
---|---|---|---|
GSR|2936 | -0.2831 | 1.838e-12 | 3.32e-08 |
TEAD3|7005 | 0.2792 | 3.77e-12 | 6.8e-08 |
RGL2|5863 | 0.2546 | 2.735e-10 | 4.93e-06 |
C5ORF23|79614 | 0.2568 | 4.555e-10 | 8.21e-06 |
AGPAT5|55326 | -0.2512 | 4.818e-10 | 8.69e-06 |
COQ2|27235 | -0.2485 | 7.433e-10 | 1.34e-05 |
NAT1|9 | -0.2482 | 7.782e-10 | 1.4e-05 |
CASP1|834 | -0.2481 | 7.958e-10 | 1.43e-05 |
TCHH|7062 | 0.2466 | 2.831e-09 | 5.1e-05 |
NPR3|4883 | 0.2582 | 3.292e-09 | 5.93e-05 |
PATHOLOGY.M.STAGE | Labels | N |
M0 | 449 | |
M1 | 71 | |
M1A | 10 | |
M1B | 1 | |
MX | 61 | |
Significant markers | N = 514 |
ANOVA_P | Q | |
---|---|---|
FUNDC2P2|388965 | 3.695e-12 | 6.66e-08 |
POTEE|445582 | 7.385e-12 | 1.33e-07 |
MCART2|147407 | 1.952e-11 | 3.52e-07 |
LOC344967|344967 | 2.104e-11 | 3.79e-07 |
SPIN2A|54466 | 2.692e-11 | 4.85e-07 |
NBPF15|284565 | 2.797e-11 | 5.04e-07 |
EDARADD|128178 | 3.505e-11 | 6.32e-07 |
UBE2NL|389898 | 6.395e-11 | 1.15e-06 |
C14ORF19|280655 | 1.225e-10 | 2.21e-06 |
PPIAL4D|645142 | 1.562e-10 | 2.82e-06 |
GENDER | Labels | N |
FEMALE | 279 | |
MALE | 322 | |
Significant markers | N = 10 | |
Higher in MALE | 10 | |
Higher in FEMALE | 0 |
W(pos if higher in 'MALE') | wilcoxontestP | Q | AUC | |
---|---|---|---|---|
CYORF15A|246126 | 23504 | 6.095e-39 | 1.1e-34 | 0.9864 |
CYORF15B|84663 | 20075 | 7.111e-34 | 1.28e-29 | 0.9802 |
HDHD1A|8226 | 20735 | 4.609e-30 | 8.31e-26 | 0.7692 |
NCRNA00183|554203 | 24022 | 7.335e-23 | 1.32e-18 | 0.7326 |
SPESP1|246777 | 47584 | 6.593e-08 | 0.00119 | 0.6337 |
FRG1B|284802 | 56159 | 7.274e-08 | 0.00131 | 0.6274 |
CD207|50489 | 30189 | 6.212e-07 | 0.0112 | 0.6214 |
C2ORF84|653140 | 30515.5 | 6.245e-06 | 0.112 | 0.6249 |
ZNF578|147660 | 34946.5 | 6.339e-06 | 0.114 | 0.607 |
CXORF38|159013 | 35450 | 8.193e-06 | 0.147 | 0.6054 |
HISTOLOGICAL.TYPE | Labels | N |
COLON ADENOCARCINOMA | 379 | |
COLON MUCINOUS ADENOCARCINOMA | 57 | |
RECTAL ADENOCARCINOMA | 144 | |
RECTAL MUCINOUS ADENOCARCINOMA | 13 | |
Significant markers | N = 1380 |
ANOVA_P | Q | |
---|---|---|
PLAGL2|5326 | 8.155e-20 | 1.47e-15 |
POFUT1|23509 | 9.17e-19 | 1.65e-14 |
SLC19A3|80704 | 6.011e-18 | 1.08e-13 |
SLC5A6|8884 | 3.367e-17 | 6.07e-13 |
MUC2|4583 | 3.633e-17 | 6.55e-13 |
SNHG11|128439 | 5.008e-17 | 9.03e-13 |
ACTR5|79913 | 6.127e-17 | 1.1e-12 |
AQP3|360 | 1.893e-16 | 3.41e-12 |
TM9SF4|9777 | 2.135e-16 | 3.85e-12 |
HNF4A|3172 | 2.204e-16 | 3.97e-12 |
No gene related to 'RADIATIONS.RADIATION.REGIMENINDICATION'.
RADIATIONS.RADIATION.REGIMENINDICATION | Labels | N |
NO | 9 | |
YES | 592 | |
Significant markers | N = 0 |
628 genes related to 'COMPLETENESS.OF.RESECTION'.
COMPLETENESS.OF.RESECTION | Labels | N |
R0 | 434 | |
R1 | 5 | |
R2 | 35 | |
RX | 28 | |
Significant markers | N = 628 |
ANOVA_P | Q | |
---|---|---|
RRN3P2|653390 | 8.363e-12 | 1.51e-07 |
LOC150776|150776 | 1.26e-11 | 2.27e-07 |
PMS2CL|441194 | 1.774e-11 | 3.2e-07 |
POLR2J4|84820 | 3.249e-11 | 5.86e-07 |
SCXB|642658 | 4.247e-11 | 7.66e-07 |
GUSBL2|375513 | 6.601e-11 | 1.19e-06 |
NSUN5P1|155400 | 6.66e-11 | 1.2e-06 |
AGAP11|119385 | 7.776e-11 | 1.4e-06 |
CCDC85B|11007 | 8.55e-11 | 1.54e-06 |
PMS2L2|5380 | 9.867e-11 | 1.78e-06 |
NUMBER.OF.LYMPH.NODES | Mean (SD) | 2.2 (4.7) |
Significant markers | N = 237 | |
pos. correlated | 153 | |
neg. correlated | 84 |
SpearmanCorr | corrP | Q | |
---|---|---|---|
GSR|2936 | -0.277 | 1.971e-11 | 3.56e-07 |
TEAD3|7005 | 0.2622 | 2.378e-10 | 4.29e-06 |
CASP1|834 | -0.2595 | 3.654e-10 | 6.59e-06 |
C5ORF23|79614 | 0.261 | 7.14e-10 | 1.29e-05 |
NPR3|4883 | 0.2689 | 1.977e-09 | 3.57e-05 |
SHC1|6464 | 0.2479 | 2.252e-09 | 4.06e-05 |
C2CD4A|145741 | -0.2467 | 2.714e-09 | 4.89e-05 |
CXCL2|2920 | -0.2467 | 2.722e-09 | 4.91e-05 |
RGL2|5863 | 0.2426 | 4.988e-09 | 8.99e-05 |
AGPAT5|55326 | -0.2417 | 5.711e-09 | 0.000103 |
RACE | Labels | N |
AMERICAN INDIAN OR ALASKA NATIVE | 1 | |
ASIAN | 12 | |
BLACK OR AFRICAN AMERICAN | 47 | |
WHITE | 294 | |
Significant markers | N = 19 |
ANOVA_P | Q | |
---|---|---|
ULK4|54986 | 5.725e-11 | 1.03e-06 |
LOC441455|441455 | 1.14e-10 | 2.06e-06 |
C14ORF167|55449 | 1.419e-10 | 2.56e-06 |
NOTCH2NL|388677 | 1.461e-09 | 2.63e-05 |
PPIL3|53938 | 1.185e-08 | 0.000214 |
CROCCL1|84809 | 3.382e-08 | 0.00061 |
CYP3A5|1577 | 5.327e-08 | 0.00096 |
SPDYE1|285955 | 4.084e-07 | 0.00736 |
RPS26|6231 | 9.27e-07 | 0.0167 |
LOC90784|90784 | 1.166e-06 | 0.021 |
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Expresson data file = COADREAD-TP.uncv2.mRNAseq_RSEM_normalized_log2.txt
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Clinical data file = COADREAD-TP.merged_data.txt
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Number of patients = 601
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Number of genes = 18035
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Number of clinical features = 13
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-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 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 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.