This pipeline uses various statistical tests to identify RPPAs whose expression levels correlated to selected clinical features.

Testing the association between 175 genes and 17 clinical features across 220 samples, statistically thresholded by P value < 0.05 and Q value < 0.3, 12 clinical features related to at least one genes.

• 1 gene correlated to 'Time to Death'.

• CHEK1|CHK1_PS345-R-C

• 24 genes correlated to 'AGE'.

• EGFR|EGFR_PY1068-R-V ,  SNAI2|SNAIL-M-C ,  AKT1 AKT2 AKT3|AKT_PT308-R-V ,  EEF2|EEF2-R-V ,  MAPK8|JNK_PT183_PT185-R-V ,  ...

• 11 genes correlated to 'NEOPLASM.DISEASESTAGE'.

• CDK1|CDK1-R-V ,  MAPK8|JNK_PT183_PT185-R-V ,  CASP3|CASPASE-3_ACTIVE-R-C ,  BECN1|BECLIN-G-V ,  AKT1 AKT2 AKT3|AKT_PS473-R-V ,  ...

• 14 genes correlated to 'PATHOLOGY.T.STAGE'.

• AKT1S1|PRAS40_PT246-R-V ,  CLDN7|CLAUDIN-7-R-V ,  DIABLO|SMAC-M-V ,  AR|AR-R-V ,  C12ORF5|TIGAR-R-V ,  ...

• 35 genes correlated to 'PATHOLOGY.N.STAGE'.

• ANXA1|ANNEXIN_I-R-V ,  PTCH1|PTCH-R-C ,  SRC|SRC_PY527-R-V ,  DVL3|DVL3-R-V ,  ERBB2|HER2_PY1248-R-V ,  ...

• 4 genes correlated to 'PATHOLOGY.M.STAGE'.

• BCL2L1|BCL-XL-R-V ,  BAK1|BAK-R-C ,  ESR1|ER-ALPHA_PS118-R-V ,  DVL3|DVL3-R-V

• 48 genes correlated to 'HISTOLOGICAL.TYPE'.

• ANXA1|ANNEXIN_I-R-V ,  FN1|FIBRONECTIN-R-C ,  PIK3R1|PI3K-P85-R-V ,  CHEK2|CHK2-M-C ,  XIAP|XIAP-R-C ,  ...

• 6 genes correlated to 'RADIATIONS.RADIATION.REGIMENINDICATION'.

• BCL2L1|BCL-XL-R-V ,  DVL3|DVL3-R-V ,  WWTR1|TAZ_PS89-R-C ,  C12ORF5|TIGAR-R-V ,  RAF1|C-RAF-R-V ,  ...

• 13 genes correlated to 'EXTRATHYROIDAL.EXTENSION'.

• BCL2|BCL-2-R-C ,  PIK3CA |PI3K-P110-ALPHA-R-C ,  EIF4EBP1|4E-BP1-R-V ,  PAI-1|PAL-1-M-C ,  EGFR|EGFR_PY1173-R-C ,  ...

• 12 genes correlated to 'NUMBER.OF.LYMPH.NODES'.

• PTCH1|PTCH-R-C ,  MAPK14|P38_MAPK-R-C ,  DVL3|DVL3-R-V ,  ANXA1|ANNEXIN_I-R-V ,  PXN|PAXILLIN-R-V ,  ...

• 2 genes correlated to 'MULTIFOCALITY'.

• CDKN1B|P27_PT157-R-C ,  EIF4EBP1|4E-BP1-R-V

• 2 genes correlated to 'RACE'.

• FOXO3|FOXO3A_PS318_S321-R-C ,  |P-REX1-R-NA

• No genes correlated to 'GENDER', 'RADIATIONEXPOSURE', 'COMPLETENESS.OF.RESECTION', 'TUMOR.SIZE', and 'ETHNICITY'.

• Expresson data file = THCA-TP.rppa.txt

• Clinical data file = THCA-TP.merged_data.txt

• Number of patients = 220

• Number of genes = 175

• Number of clinical features = 17

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.

• Analysis Results (MD5 checksum)

• Auxiliary Data (MD5 checksum)

• MAGE-TAB File (MD5 checksum)