Correlation between mRNAseq expression and clinical features
Thyroid Adenocarcinoma (Primary solid tumor)
28 January 2016  |  analyses__2016_01_28
Maintainer Information
Citation Information
doi:10.7908/C1HD7V4N
Maintained by Juok Cho (Broad Institute)
Cite as Broad Institute TCGA Genome Data Analysis Center (2016): Correlation between mRNAseq expression and clinical features. Broad Institute of MIT and Harvard. doi:10.7908/C1HD7V4N
Overview
Introduction

This pipeline uses various statistical tests to identify mRNAs whose log2 expression levels correlated to selected clinical features. The input file "THCA-TP.uncv2.mRNAseq_RSEM_normalized_log2.txt" is generated in the pipeline mRNAseq_Preprocess in the stddata run.

Summary

Testing the association between 17991 genes and 17 clinical features across 501 samples, statistically thresholded by P value < 0.05 and Q value < 0.3, 15 clinical features related to at least one genes.

  • 15 genes correlated to 'DAYS_TO_DEATH_OR_LAST_FUP'.

    • FLJ44635|392490 ,  HECTD3|79654 ,  MSX2|4488 ,  SNAI1|6615 ,  RFPL2|10739 ,  ...

  • 30 genes correlated to 'YEARS_TO_BIRTH'.

    • ZNF518B|85460 ,  RANBP17|64901 ,  MSL3L2|151507 ,  HCG11|493812 ,  ASB13|79754 ,  ...

  • 30 genes correlated to 'PATHOLOGIC_STAGE'.

    • SLC10A4|201780 ,  WISP2|8839 ,  SYT1|6857 ,  ALOX5|240 ,  EXOC3L2|90332 ,  ...

  • 30 genes correlated to 'PATHOLOGY_T_STAGE'.

    • FBXO9|26268 ,  SPCS3|60559 ,  VIPR1|7433 ,  LTF|4057 ,  GNG7|2788 ,  ...

  • 30 genes correlated to 'PATHOLOGY_N_STAGE'.

    • CBFB|865 ,  CREB5|9586 ,  CLCNKA|1187 ,  PELI1|57162 ,  ZNF346|23567 ,  ...

  • 5 genes correlated to 'GENDER'.

    • HDHD1A|8226 ,  NCRNA00183|554203 ,  CA5BP|340591 ,  CYORF15A|246126 ,  CYORF15B|84663

  • 30 genes correlated to 'RADIATION_THERAPY'.

    • ZC3HAV1|56829 ,  IPO8|10526 ,  ANUBL1|93550 ,  PHACTR2|9749 ,  MUTED|63915 ,  ...

  • 30 genes correlated to 'HISTOLOGICAL_TYPE'.

    • SFTPB|6439 ,  ITGA3|3675 ,  FN1|2335 ,  ANXA2P2|304 ,  AHNAK2|113146 ,  ...

  • 30 genes correlated to 'EXTRATHYROIDAL_EXTENSION'.

    • SLC10A4|201780 ,  SLC25A42|284439 ,  SRPX2|27286 ,  FLRT1|23769 ,  FOXJ1|2302 ,  ...

  • 30 genes correlated to 'RESIDUAL_TUMOR'.

    • SHOX2|6474 ,  LGR5|8549 ,  APCDD1L|164284 ,  SLC10A4|201780 ,  WNT2|7472 ,  ...

  • 30 genes correlated to 'NUMBER_OF_LYMPH_NODES'.

    • CBFB|865 ,  FAM60A|58516 ,  PELI1|57162 ,  CLCNKA|1187 ,  CREB5|9586 ,  ...

  • 30 genes correlated to 'MULTIFOCALITY'.

    • AVPI1|60370 ,  SCD5|79966 ,  CXCL3|2921 ,  AMDHD2|51005 ,  A2BP1|54715 ,  ...

  • 30 genes correlated to 'TUMOR_SIZE'.

    • C3ORF32|51066 ,  ISLR2|57611 ,  ZC3H10|84872 ,  CXCL12|6387 ,  FOXI2|399823 ,  ...

  • 30 genes correlated to 'RACE'.

    • XKR9|389668 ,  LRRC37A2|474170 ,  SEC1|653677 ,  RPS26|6231 ,  UTS2|10911 ,  ...

  • 30 genes correlated to 'ETHNICITY'.

    • SNAPC3|6619 ,  ZFP36L1|677 ,  ATG12|9140 ,  TEC|7006 ,  MCF2L2|23101 ,  ...

  • No genes correlated to 'PATHOLOGY_M_STAGE', and 'RADIATION_EXPOSURE'.

Results
Overview of the results

Complete statistical result table is provided in Supplement Table 1

Table 1.  Get Full Table This table shows the clinical features, statistical methods used, and the number of genes that are significantly associated with each clinical feature at P value < 0.05 and Q value < 0.3.

Clinical feature Statistical test Significant genes Associated with                 Associated with
DAYS_TO_DEATH_OR_LAST_FUP Cox regression test N=15   N=NA   N=NA
YEARS_TO_BIRTH Spearman correlation test N=30 older N=11 younger N=19
PATHOLOGIC_STAGE Kruskal-Wallis test N=30        
PATHOLOGY_T_STAGE Spearman correlation test N=30 higher stage N=2 lower stage N=28
PATHOLOGY_N_STAGE Wilcoxon test N=30 n1 N=30 n0 N=0
PATHOLOGY_M_STAGE Wilcoxon test   N=0        
GENDER Wilcoxon test N=5 male N=5 female N=0
RADIATION_THERAPY Wilcoxon test N=30 yes N=30 no N=0
HISTOLOGICAL_TYPE Kruskal-Wallis test N=30        
RADIATION_EXPOSURE Wilcoxon test   N=0        
EXTRATHYROIDAL_EXTENSION Kruskal-Wallis test N=30        
RESIDUAL_TUMOR Kruskal-Wallis test N=30        
NUMBER_OF_LYMPH_NODES Spearman correlation test N=30 higher number_of_lymph_nodes N=17 lower number_of_lymph_nodes N=13
MULTIFOCALITY Wilcoxon test N=30 unifocal N=30 multifocal N=0
TUMOR_SIZE Spearman correlation test N=30 higher tumor_size N=2 lower tumor_size N=28
RACE Kruskal-Wallis test N=30        
ETHNICITY Wilcoxon test N=30 not hispanic or latino N=30 hispanic or latino N=0
Clinical variable #1: 'DAYS_TO_DEATH_OR_LAST_FUP'

15 genes related to 'DAYS_TO_DEATH_OR_LAST_FUP'.

Table S1.  Basic characteristics of clinical feature: 'DAYS_TO_DEATH_OR_LAST_FUP'

DAYS_TO_DEATH_OR_LAST_FUP Duration (Months) 0.2-178.3 (median=31)
  censored N = 484
  death N = 16
     
  Significant markers N = 15
  associated with shorter survival NA
  associated with longer survival NA
List of top 10 genes differentially expressed by 'DAYS_TO_DEATH_OR_LAST_FUP'

Table S2.  Get Full Table List of top 10 genes significantly associated with 'Time to Death' by Cox regression test. For the survival curves, it compared quantile intervals at c(0, 0.25, 0.50, 0.75, 1) and did not try survival analysis if there is only one interval.

logrank_P Q C_index
FLJ44635|392490 3.39e-06 0.061 0.211
HECTD3|79654 2.54e-05 0.17 0.265
MSX2|4488 4.06e-05 0.17 0.774
SNAI1|6615 4.53e-05 0.17 0.831
RFPL2|10739 4.82e-05 0.17 0.718
ROR2|4920 8e-05 0.24 0.767
CLTA|1211 0.000131 0.27 0.396
TMEM90B|79953 0.000132 0.27 0.816
ANTXR1|84168 0.000134 0.27 0.797
SIX2|10736 0.000169 0.28 0.803
Clinical variable #2: 'YEARS_TO_BIRTH'

30 genes related to 'YEARS_TO_BIRTH'.

Table S3.  Basic characteristics of clinical feature: 'YEARS_TO_BIRTH'

YEARS_TO_BIRTH Mean (SD) 47.26 (16)
  Significant markers N = 30
  pos. correlated 11
  neg. correlated 19
List of top 10 genes differentially expressed by 'YEARS_TO_BIRTH'

Table S4.  Get Full Table List of top 10 genes significantly correlated to 'YEARS_TO_BIRTH' by Spearman correlation test

SpearmanCorr corrP Q
ZNF518B|85460 -0.3443 2.193e-15 3.94e-11
RANBP17|64901 -0.3301 4.016e-14 3.61e-10
MSL3L2|151507 -0.3241 1.025e-13 6.15e-10
HCG11|493812 -0.2935 2.076e-11 9.34e-08
ASB13|79754 0.2843 9.117e-11 3.28e-07
C12ORF52|84934 0.2816 1.387e-10 4.16e-07
ST3GAL1|6482 -0.2757 3.46e-10 8.89e-07
LHFPL4|375323 0.2841 5.955e-10 1.27e-06
C1ORF59|113802 -0.2717 6.335e-10 1.27e-06
DDIT4L|115265 0.2634 2.211e-09 3.98e-06
Clinical variable #3: 'PATHOLOGIC_STAGE'

30 genes related to 'PATHOLOGIC_STAGE'.

Table S5.  Basic characteristics of clinical feature: 'PATHOLOGIC_STAGE'

PATHOLOGIC_STAGE Labels N
  STAGE I 283
  STAGE II 51
  STAGE III 110
  STAGE IV 2
  STAGE IVA 47
  STAGE IVC 6
     
  Significant markers N = 30
List of top 10 genes differentially expressed by 'PATHOLOGIC_STAGE'

Table S6.  Get Full Table List of top 10 genes differentially expressed by 'PATHOLOGIC_STAGE'

kruskal_wallis_P Q
SLC10A4|201780 4.445e-10 4.8e-06
WISP2|8839 8.846e-10 4.8e-06
SYT1|6857 1.476e-09 4.8e-06
ALOX5|240 2.846e-09 4.8e-06
EXOC3L2|90332 2.96e-09 4.8e-06
PRDM16|63976 3.154e-09 4.8e-06
PEG3|5178 3.273e-09 4.8e-06
CHI3L1|1116 3.31e-09 4.8e-06
UNC5CL|222643 3.333e-09 4.8e-06
CCL22|6367 3.627e-09 4.8e-06
Clinical variable #4: 'PATHOLOGY_T_STAGE'

30 genes related to 'PATHOLOGY_T_STAGE'.

Table S7.  Basic characteristics of clinical feature: 'PATHOLOGY_T_STAGE'

PATHOLOGY_T_STAGE Mean (SD) 2.15 (0.89)
  N
  T1 142
  T2 165
  T3 169
  T4 23
     
  Significant markers N = 30
  pos. correlated 2
  neg. correlated 28
List of top 10 genes differentially expressed by 'PATHOLOGY_T_STAGE'

Table S8.  Get Full Table List of top 10 genes significantly correlated to 'PATHOLOGY_T_STAGE' by Spearman correlation test

SpearmanCorr corrP Q
FBXO9|26268 -0.2919 2.937e-11 2.65e-07
SPCS3|60559 -0.2894 4.4e-11 2.65e-07
VIPR1|7433 -0.2885 5.093e-11 2.65e-07
LTF|4057 -0.2876 5.902e-11 2.65e-07
GNG7|2788 -0.2741 4.718e-10 1.33e-06
SYT15|83849 -0.2733 5.383e-10 1.33e-06
KCNJ16|3773 -0.2728 5.785e-10 1.33e-06
LOC653566|653566 -0.2726 5.935e-10 1.33e-06
LRRC4|64101 -0.2716 7.205e-10 1.37e-06
PLEKHA2|59339 -0.2703 8.348e-10 1.37e-06
Clinical variable #5: 'PATHOLOGY_N_STAGE'

30 genes related to 'PATHOLOGY_N_STAGE'.

Table S9.  Basic characteristics of clinical feature: 'PATHOLOGY_N_STAGE'

PATHOLOGY_N_STAGE Labels N
  N0 226
  N1 225
     
  Significant markers N = 30
  Higher in N1 30
  Higher in N0 0
List of top 10 genes differentially expressed by 'PATHOLOGY_N_STAGE'

Table S10.  Get Full Table List of top 10 genes differentially expressed by 'PATHOLOGY_N_STAGE'

W(pos if higher in 'N1') wilcoxontestP Q AUC
CBFB|865 37843 2.9e-19 5.22e-15 0.7442
CREB5|9586 37124 2.841e-17 1.77e-13 0.7301
CLCNKA|1187 13658 2.95e-17 1.77e-13 0.7302
PELI1|57162 36915 1.025e-16 4.61e-13 0.726
ZNF346|23567 14109 2.93e-16 1.05e-12 0.7225
MLEC|9761 14141 3.549e-16 1.06e-12 0.7219
TFAP2C|7022 36658 4.81e-16 1.2e-12 0.7209
TMEM117|84216 36641 5.322e-16 1.2e-12 0.7206
GPER|2852 14330 1.088e-15 2.15e-12 0.7182
FN1|2335 36504 1.195e-15 2.15e-12 0.7179
Clinical variable #6: 'PATHOLOGY_M_STAGE'

No gene related to 'PATHOLOGY_M_STAGE'.

Table S11.  Basic characteristics of clinical feature: 'PATHOLOGY_M_STAGE'

PATHOLOGY_M_STAGE Labels N
  class0 279
  class1 9
     
  Significant markers N = 0
Clinical variable #7: 'GENDER'

5 genes related to 'GENDER'.

Table S12.  Basic characteristics of clinical feature: 'GENDER'

GENDER Labels N
  FEMALE 366
  MALE 135
     
  Significant markers N = 5
  Higher in MALE 5
  Higher in FEMALE 0
List of 5 genes differentially expressed by 'GENDER'

Table S13.  Get Full Table List of 5 genes differentially expressed by 'GENDER'. 25 significant gene(s) located in sex chromosomes is(are) filtered out.

W(pos if higher in 'MALE') wilcoxontestP Q AUC
HDHD1A|8226 4097 1.349e-46 4.04e-43 0.9171
NCRNA00183|554203 5206.5 6.734e-42 1.35e-38 0.8946
CA5BP|340591 9709 1.805e-25 1.55e-22 0.8035
CYORF15A|246126 5762 6.663e-23 5.45e-20 1
CYORF15B|84663 3752 9.755e-17 6.5e-14 1
Clinical variable #8: 'RADIATION_THERAPY'

30 genes related to 'RADIATION_THERAPY'.

Table S14.  Basic characteristics of clinical feature: 'RADIATION_THERAPY'

RADIATION_THERAPY Labels N
  NO 180
  YES 305
     
  Significant markers N = 30
  Higher in YES 30
  Higher in NO 0
List of top 10 genes differentially expressed by 'RADIATION_THERAPY'

Table S15.  Get Full Table List of top 10 genes differentially expressed by 'RADIATION_THERAPY'

W(pos if higher in 'YES') wilcoxontestP Q AUC
ZC3HAV1|56829 20011 6.084e-07 0.00749 0.6355
IPO8|10526 20102 8.329e-07 0.00749 0.6338
ANUBL1|93550 20554.5 3.764e-06 0.0188 0.6256
PHACTR2|9749 20751 7.047e-06 0.0188 0.622
MUTED|63915 20808 8.428e-06 0.0188 0.621
MRPS36|92259 34069 9.055e-06 0.0188 0.6206
NEK1|4750 20876 1.041e-05 0.0188 0.6197
FAM120B|84498 20916 1.178e-05 0.0188 0.619
NR3C1|2908 20918 1.185e-05 0.0188 0.619
FAM114A2|10827 20945 1.288e-05 0.0188 0.6185
Clinical variable #9: 'HISTOLOGICAL_TYPE'

30 genes related to 'HISTOLOGICAL_TYPE'.

Table S16.  Basic characteristics of clinical feature: 'HISTOLOGICAL_TYPE'

HISTOLOGICAL_TYPE Labels N
  OTHER, SPECIFY 7
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL 357
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED) 102
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES) 35
     
  Significant markers N = 30
List of top 10 genes differentially expressed by 'HISTOLOGICAL_TYPE'

Table S17.  Get Full Table List of top 10 genes differentially expressed by 'HISTOLOGICAL_TYPE'

kruskal_wallis_P Q
SFTPB|6439 7.67e-35 7.07e-31
ITGA3|3675 7.856e-35 7.07e-31
FN1|2335 4.297e-33 2.19e-29
ANXA2P2|304 5.019e-33 2.19e-29
AHNAK2|113146 6.093e-33 2.19e-29
SERPINA1|5265 1.538e-32 4.61e-29
CYP2S1|29785 5.956e-32 1.53e-28
UNC5CL|222643 9.881e-32 2.22e-28
ERBB3|2065 1.213e-31 2.42e-28
KCNN4|3783 1.679e-31 3.02e-28
Clinical variable #10: 'RADIATION_EXPOSURE'

No gene related to 'RADIATION_EXPOSURE'.

Table S18.  Basic characteristics of clinical feature: 'RADIATION_EXPOSURE'

RADIATION_EXPOSURE Labels N
  NO 421
  YES 17
     
  Significant markers N = 0
Clinical variable #11: 'EXTRATHYROIDAL_EXTENSION'

30 genes related to 'EXTRATHYROIDAL_EXTENSION'.

Table S19.  Basic characteristics of clinical feature: 'EXTRATHYROIDAL_EXTENSION'

EXTRATHYROIDAL_EXTENSION Labels N
  MINIMAL (T3) 133
  MODERATE/ADVANCED (T4A) 18
  NONE 331
  VERY ADVANCED (T4B) 1
     
  Significant markers N = 30
List of top 10 genes differentially expressed by 'EXTRATHYROIDAL_EXTENSION'

Table S20.  Get Full Table List of top 10 genes differentially expressed by 'EXTRATHYROIDAL_EXTENSION'

kruskal_wallis_P Q
SLC10A4|201780 1.021e-14 1.84e-10
SLC25A42|284439 4.332e-14 3.9e-10
SRPX2|27286 1.611e-13 9.66e-10
FLRT1|23769 5.523e-13 2.48e-09
FOXJ1|2302 8.375e-13 2.93e-09
FAM69C|125704 1.081e-12 2.93e-09
COL1A1|1277 1.404e-12 2.93e-09
FN1|2335 1.464e-12 2.93e-09
BAG3|9531 1.465e-12 2.93e-09
KDM4B|23030 1.851e-12 3.29e-09
Clinical variable #12: 'RESIDUAL_TUMOR'

30 genes related to 'RESIDUAL_TUMOR'.

Table S21.  Basic characteristics of clinical feature: 'RESIDUAL_TUMOR'

RESIDUAL_TUMOR Labels N
  R0 383
  R1 52
  R2 4
  RX 30
     
  Significant markers N = 30
List of top 10 genes differentially expressed by 'RESIDUAL_TUMOR'

Table S22.  Get Full Table List of top 10 genes differentially expressed by 'RESIDUAL_TUMOR'

kruskal_wallis_P Q
SHOX2|6474 2.142e-06 0.0288
LGR5|8549 5.695e-06 0.0288
APCDD1L|164284 6.099e-06 0.0288
SLC10A4|201780 6.402e-06 0.0288
WNT2|7472 8.024e-06 0.0289
RCBTB2|1102 2.822e-05 0.0823
COL12A1|1303 4.184e-05 0.0823
CYP26A1|1592 4.199e-05 0.0823
COL5A1|1289 4.459e-05 0.0823
CA4|762 4.574e-05 0.0823
Clinical variable #13: 'NUMBER_OF_LYMPH_NODES'

30 genes related to 'NUMBER_OF_LYMPH_NODES'.

Table S23.  Basic characteristics of clinical feature: 'NUMBER_OF_LYMPH_NODES'

NUMBER_OF_LYMPH_NODES Mean (SD) 3.66 (6.2)
  Significant markers N = 30
  pos. correlated 17
  neg. correlated 13
List of top 10 genes differentially expressed by 'NUMBER_OF_LYMPH_NODES'

Table S24.  Get Full Table List of top 10 genes significantly correlated to 'NUMBER_OF_LYMPH_NODES' by Spearman correlation test

SpearmanCorr corrP Q
CBFB|865 0.366 1.04e-13 1.87e-09
FAM60A|58516 0.359 3.268e-13 2.5e-09
PELI1|57162 0.3574 4.167e-13 2.5e-09
CLCNKA|1187 -0.3524 9.969e-13 4.04e-09
CREB5|9586 0.3512 1.121e-12 4.04e-09
TAGLN2|8407 0.3411 5.338e-12 1.45e-08
FECH|2235 -0.3392 7.103e-12 1.45e-08
MLEC|9761 -0.3379 8.656e-12 1.45e-08
FAM178B|51252 0.3412 8.662e-12 1.45e-08
WFS1|7466 -0.3377 8.915e-12 1.45e-08
Clinical variable #14: 'MULTIFOCALITY'

30 genes related to 'MULTIFOCALITY'.

Table S25.  Basic characteristics of clinical feature: 'MULTIFOCALITY'

MULTIFOCALITY Labels N
  MULTIFOCAL 226
  UNIFOCAL 265
     
  Significant markers N = 30
  Higher in UNIFOCAL 30
  Higher in MULTIFOCAL 0
List of top 10 genes differentially expressed by 'MULTIFOCALITY'

Table S26.  Get Full Table List of top 10 genes differentially expressed by 'MULTIFOCALITY'

W(pos if higher in 'UNIFOCAL') wilcoxontestP Q AUC
AVPI1|60370 37326 2.478e-06 0.0446 0.6232
SCD5|79966 23013 9.715e-06 0.0874 0.6157
CXCL3|2921 33143 2.524e-05 0.107 0.613
AMDHD2|51005 36541 2.565e-05 0.107 0.6101
A2BP1|54715 18490.5 2.968e-05 0.107 0.6153
ARHGAP31|57514 23624 5.495e-05 0.147 0.6055
SLC35F1|222553 23677 8.182e-05 0.147 0.6032
TMTC1|83857 23794 8.672e-05 0.147 0.6027
ATXN2L|11273 36075 9.168e-05 0.147 0.6024
C18ORF1|753 23861 0.0001035 0.147 0.6016
Clinical variable #15: 'TUMOR_SIZE'

30 genes related to 'TUMOR_SIZE'.

Table S27.  Basic characteristics of clinical feature: 'TUMOR_SIZE'

TUMOR_SIZE Mean (SD) 2.98 (1.6)
  Significant markers N = 30
  pos. correlated 2
  neg. correlated 28
List of top 10 genes differentially expressed by 'TUMOR_SIZE'

Table S28.  Get Full Table List of top 10 genes significantly correlated to 'TUMOR_SIZE' by Spearman correlation test

SpearmanCorr corrP Q
C3ORF32|51066 -0.2812 1.549e-08 0.000279
ISLR2|57611 -0.2649 6.954e-08 0.000558
ZC3H10|84872 -0.2625 9.303e-08 0.000558
CXCL12|6387 -0.2583 1.505e-07 0.000677
FOXI2|399823 -0.2558 2.46e-07 0.000791
LRRC55|219527 -0.2546 2.64e-07 0.000791
SLC14A1|6563 -0.2466 5.55e-07 0.0013
CLDN2|9075 -0.2468 6.16e-07 0.0013
GPR34|2857 -0.2452 6.482e-07 0.0013
PI16|221476 -0.2438 9.042e-07 0.00163
Clinical variable #16: 'RACE'

30 genes related to 'RACE'.

Table S29.  Basic characteristics of clinical feature: 'RACE'

RACE Labels N
  AMERICAN INDIAN OR ALASKA NATIVE 1
  ASIAN 51
  BLACK OR AFRICAN AMERICAN 27
  WHITE 331
     
  Significant markers N = 30
List of top 10 genes differentially expressed by 'RACE'

Table S30.  Get Full Table List of top 10 genes differentially expressed by 'RACE'

kruskal_wallis_P Q
XKR9|389668 6.716e-12 1.21e-07
LRRC37A2|474170 1.059e-10 9.53e-07
SEC1|653677 4.066e-10 2.44e-06
RPS26|6231 9.813e-10 4.41e-06
UTS2|10911 1.184e-08 3.75e-05
ATAD3C|219293 1.25e-08 3.75e-05
DDX11L2|84771 2.737e-08 7.04e-05
LRRC19|64922 4.019e-08 8.12e-05
TMX4|56255 4.06e-08 8.12e-05
MKX|283078 5.607e-08 0.000101
Clinical variable #17: 'ETHNICITY'

30 genes related to 'ETHNICITY'.

Table S31.  Basic characteristics of clinical feature: 'ETHNICITY'

ETHNICITY Labels N
  HISPANIC OR LATINO 38
  NOT HISPANIC OR LATINO 360
     
  Significant markers N = 30
  Higher in NOT HISPANIC OR LATINO 30
  Higher in HISPANIC OR LATINO 0
List of top 10 genes differentially expressed by 'ETHNICITY'

Methods & Data
Input

  • Expresson data file = THCA-TP.uncv2.mRNAseq_RSEM_normalized_log2.txt

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

  • Number of patients = 501

  • Number of genes = 17991

  • Number of clinical features = 17

Selected clinical features

  • Further details on clinical features selected for this analysis, please find a documentation on selected CDEs (Clinical Data Elements). The first column of the file is a formula to convert values and the second column is a clinical parameter name.

  • Survival time data

    • 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.

      • if 'vital_status'==1(dead), 'days_to_last_followup' is always NA. Thus, uses 'days_to_death' value for 'days_to_death_or_fup'

      • if 'vital_status'==0(alive),

        • if 'days_to_death'==NA & 'days_to_last_followup'!=NA, uses 'days_to_last_followup' value for 'days_to_death_or_fup'

        • if 'days_to_death'!=NA, excludes this case in survival analysis and report the case.

      • if 'vital_status'==NA,excludes this case in survival analysis and report the case.

    • 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 .

  • This analysis excluded clinical variables that has only NA values.

Survival analysis

For survival clinical features, logrank test in univariate Cox regression analysis with proportional hazards model (Andersen and Gill 1982) was used to estimate the P values comparing quantile intervals using the 'coxph' function in R. Kaplan-Meier survival curves were plotted using quantile intervals at c(0, 0.25, 0.50, 0.75, 1). If there is only one interval group, it will not try survival analysis.

Correlation analysis

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

Wilcoxon rank sum test (Mann-Whitney U test)

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.

Q value calculation

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.

Download Results

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.

References
[1] Andersen and Gill, Cox's regression model for counting processes, a large sample study, Annals of Statistics 10(4):1100-1120 (1982)
[2] Spearman, C, The proof and measurement of association between two things, Amer. J. Psychol 15:72-101 (1904)
[3] Mann and Whitney, On a Test of Whether one of Two Random Variables is Stochastically Larger than the Other, Annals of Mathematical Statistics 18 (1), 50-60 (1947)
[4] Benjamini and Hochberg, Controlling the false discovery rate: a practical and powerful approach to multiple testing, Journal of the Royal Statistical Society Series B 59:289-300 (1995)
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