Thyroid Adenocarcinoma: Correlation between miRseq expression and clinical features
(primary solid tumor cohort)
Maintained by Juok Cho (Broad Institute)
Overview
Introduction

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

Summary

Testing the association between 511 genes and 13 clinical features across 302 samples, statistically thresholded by Q value < 0.05, 11 clinical features related to at least one genes.

  • 4 genes correlated to 'AGE'.

    • HSA-MIR-362 ,  HSA-MIR-874 ,  HSA-MIR-1229 ,  HSA-MIR-500A

  • 1 gene correlated to 'GENDER'.

    • HSA-MIR-651

  • 173 genes correlated to 'HISTOLOGICAL.TYPE'.

    • HSA-MIR-21 ,  HSA-MIR-146B ,  HSA-MIR-7-2 ,  HSA-MIR-31 ,  HSA-MIR-511-2 ,  ...

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

    • HSA-MIR-888 ,  HSA-MIR-374A ,  HSA-MIR-660 ,  HSA-MIR-324 ,  HSA-MIR-20B ,  ...

  • 2 genes correlated to 'DISTANT.METASTASIS'.

    • HSA-MIR-1274B ,  HSA-MIR-151

  • 12 genes correlated to 'EXTRATHYROIDAL.EXTENSION'.

    • HSA-MIR-21 ,  HSA-MIR-204 ,  HSA-MIR-7-2 ,  HSA-MIR-363 ,  HSA-MIR-148B ,  ...

  • 28 genes correlated to 'LYMPH.NODE.METASTASIS'.

    • HSA-MIR-146B ,  HSA-MIR-7-2 ,  HSA-MIR-31 ,  HSA-MIR-21 ,  HSA-MIR-1179 ,  ...

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

    • HSA-MIR-7-2 ,  HSA-MIR-1179 ,  HSA-MIR-31 ,  HSA-MIR-146B ,  HSA-MIR-152 ,  ...

  • 6 genes correlated to 'NEOPLASM.DISEASESTAGE'.

    • HSA-MIR-31 ,  HSA-MIR-146B ,  HSA-MIR-139 ,  HSA-MIR-375 ,  HSA-MIR-183 ,  ...

  • 1 gene correlated to 'MULTIFOCALITY'.

    • HSA-MIR-132

  • 8 genes correlated to 'TUMOR.SIZE'.

    • HSA-MIR-182 ,  HSA-MIR-183 ,  HSA-MIR-136 ,  HSA-MIR-199A-1 ,  HSA-MIR-96 ,  ...

  • No genes correlated to 'RADIATIONEXPOSURE', and 'COMPLETENESS.OF.RESECTION'.

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 Q value < 0.05.

Clinical feature Statistical test Significant genes Associated with                 Associated with
AGE Spearman correlation test N=4 older N=4 younger N=0
GENDER t test N=1 male N=0 female N=1
HISTOLOGICAL TYPE ANOVA test N=173        
RADIATIONS RADIATION REGIMENINDICATION t test N=7 yes N=5 no N=2
RADIATIONEXPOSURE t test   N=0        
DISTANT METASTASIS ANOVA test N=2        
EXTRATHYROIDAL EXTENSION ANOVA test N=12        
LYMPH NODE METASTASIS ANOVA test N=28        
COMPLETENESS OF RESECTION ANOVA test   N=0        
NUMBER OF LYMPH NODES Spearman correlation test N=20 higher number.of.lymph.nodes N=11 lower number.of.lymph.nodes N=9
NEOPLASM DISEASESTAGE ANOVA test N=6        
MULTIFOCALITY t test N=1 unifocal N=0 multifocal N=1
TUMOR SIZE Spearman correlation test N=8 higher tumor.size N=3 lower tumor.size N=5
Clinical variable #1: 'AGE'

4 genes related to 'AGE'.

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

AGE Mean (SD) 46.47 (15)
  Significant markers N = 4
  pos. correlated 4
  neg. correlated 0
List of 4 genes significantly correlated to 'AGE' by Spearman correlation test

Table S2.  Get Full Table List of 4 genes significantly correlated to 'AGE' by Spearman correlation test

SpearmanCorr corrP Q
HSA-MIR-362 0.2528 8.666e-06 0.00443
HSA-MIR-874 0.2512 9.948e-06 0.00507
HSA-MIR-1229 0.2664 3.01e-05 0.0153
HSA-MIR-500A 0.2234 8.982e-05 0.0456

Figure S1.  Get High-res Image As an example, this figure shows the association of HSA-MIR-362 to 'AGE'. P value = 8.67e-06 with Spearman correlation analysis. The straight line presents the best linear regression.

Clinical variable #2: 'GENDER'

One gene related to 'GENDER'.

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

GENDER Labels N
  FEMALE 226
  MALE 76
     
  Significant markers N = 1
  Higher in MALE 0
  Higher in FEMALE 1
List of one gene differentially expressed by 'GENDER'

Table S4.  Get Full Table List of one gene differentially expressed by 'GENDER'

T(pos if higher in 'MALE') ttestP Q AUC
HSA-MIR-651 -5.56 1.666e-07 8.51e-05 0.7084

Figure S2.  Get High-res Image As an example, this figure shows the association of HSA-MIR-651 to 'GENDER'. P value = 1.67e-07 with T-test analysis.

Clinical variable #3: 'HISTOLOGICAL.TYPE'

173 genes related to 'HISTOLOGICAL.TYPE'.

Table S5.  Basic characteristics of clinical feature: 'HISTOLOGICAL.TYPE'

HISTOLOGICAL.TYPE Labels N
  OTHER 20
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL 174
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED) 78
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES) 30
     
  Significant markers N = 173
List of top 10 genes differentially expressed by 'HISTOLOGICAL.TYPE'

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

ANOVA_P Q
HSA-MIR-21 5.247e-41 2.68e-38
HSA-MIR-146B 3.65e-28 1.86e-25
HSA-MIR-7-2 2.527e-22 1.29e-19
HSA-MIR-31 7.399e-20 3.76e-17
HSA-MIR-511-2 1.77e-19 8.97e-17
HSA-MIR-1179 7.694e-18 3.89e-15
HSA-MIR-345 1.148e-17 5.8e-15
HSA-MIR-511-1 3.016e-17 1.52e-14
HSA-MIR-30C-2 5.48e-17 2.76e-14
HSA-MIR-204 5.562e-17 2.79e-14

Figure S3.  Get High-res Image As an example, this figure shows the association of HSA-MIR-21 to 'HISTOLOGICAL.TYPE'. P value = 5.25e-41 with ANOVA analysis.

Clinical variable #4: 'RADIATIONS.RADIATION.REGIMENINDICATION'

7 genes related to 'RADIATIONS.RADIATION.REGIMENINDICATION'.

Table S7.  Basic characteristics of clinical feature: 'RADIATIONS.RADIATION.REGIMENINDICATION'

RADIATIONS.RADIATION.REGIMENINDICATION Labels N
  NO 14
  YES 288
     
  Significant markers N = 7
  Higher in YES 5
  Higher in NO 2
List of 7 genes differentially expressed by 'RADIATIONS.RADIATION.REGIMENINDICATION'

Table S8.  Get Full Table List of 7 genes differentially expressed by 'RADIATIONS.RADIATION.REGIMENINDICATION'

T(pos if higher in 'YES') ttestP Q AUC
HSA-MIR-888 7.97 2.253e-10 1.12e-07 0.8582
HSA-MIR-374A -7.55 1.023e-06 0.000509 0.8829
HSA-MIR-660 6.48 7.108e-06 0.00353 0.8495
HSA-MIR-324 6.2 1.131e-05 0.0056 0.8304
HSA-MIR-20B 6 1.719e-05 0.00849 0.8285
HSA-MIR-3130-1 -5.28 3.207e-05 0.0158 0.728
HSA-MIR-1976 5.57 3.678e-05 0.0181 0.7969

Figure S4.  Get High-res Image As an example, this figure shows the association of HSA-MIR-888 to 'RADIATIONS.RADIATION.REGIMENINDICATION'. P value = 2.25e-10 with T-test analysis.

Clinical variable #5: 'RADIATIONEXPOSURE'

No gene related to 'RADIATIONEXPOSURE'.

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

RADIATIONEXPOSURE Labels N
  NO 254
  YES 13
     
  Significant markers N = 0
Clinical variable #6: 'DISTANT.METASTASIS'

2 genes related to 'DISTANT.METASTASIS'.

Table S10.  Basic characteristics of clinical feature: 'DISTANT.METASTASIS'

DISTANT.METASTASIS Labels N
  M0 140
  M1 4
  MX 157
     
  Significant markers N = 2
List of 2 genes differentially expressed by 'DISTANT.METASTASIS'

Table S11.  Get Full Table List of 2 genes differentially expressed by 'DISTANT.METASTASIS'

ANOVA_P Q
HSA-MIR-1274B 9.971e-07 0.00051
HSA-MIR-151 9.592e-05 0.0489

Figure S5.  Get High-res Image As an example, this figure shows the association of HSA-MIR-1274B to 'DISTANT.METASTASIS'. P value = 9.97e-07 with ANOVA analysis.

Clinical variable #7: 'EXTRATHYROIDAL.EXTENSION'

12 genes related to 'EXTRATHYROIDAL.EXTENSION'.

Table S12.  Basic characteristics of clinical feature: 'EXTRATHYROIDAL.EXTENSION'

EXTRATHYROIDAL.EXTENSION Labels N
  MINIMAL (T3) 68
  MODERATE/ADVANCED (T4A) 6
  NONE 214
     
  Significant markers N = 12
List of top 10 genes differentially expressed by 'EXTRATHYROIDAL.EXTENSION'

Table S13.  Get Full Table List of top 10 genes differentially expressed by 'EXTRATHYROIDAL.EXTENSION'

ANOVA_P Q
HSA-MIR-21 1.065e-06 0.000544
HSA-MIR-204 5.819e-06 0.00297
HSA-MIR-7-2 8.783e-06 0.00447
HSA-MIR-363 8.941e-06 0.00454
HSA-MIR-148B 1.05e-05 0.00532
HSA-MIR-1180 2.88e-05 0.0146
HSA-MIR-514-2 3.244e-05 0.0164
HSA-MIR-652 3.905e-05 0.0197
HSA-MIR-146B 4.64e-05 0.0233
HSA-MIR-139 7.211e-05 0.0362

Figure S6.  Get High-res Image As an example, this figure shows the association of HSA-MIR-21 to 'EXTRATHYROIDAL.EXTENSION'. P value = 1.06e-06 with ANOVA analysis.

Clinical variable #8: 'LYMPH.NODE.METASTASIS'

28 genes related to 'LYMPH.NODE.METASTASIS'.

Table S14.  Basic characteristics of clinical feature: 'LYMPH.NODE.METASTASIS'

LYMPH.NODE.METASTASIS Labels N
  N0 151
  N1 17
  N1A 63
  N1B 41
  NX 30
     
  Significant markers N = 28
List of top 10 genes differentially expressed by 'LYMPH.NODE.METASTASIS'

Table S15.  Get Full Table List of top 10 genes differentially expressed by 'LYMPH.NODE.METASTASIS'

ANOVA_P Q
HSA-MIR-146B 1.199e-09 6.13e-07
HSA-MIR-7-2 2.282e-08 1.16e-05
HSA-MIR-31 5.92e-08 3.01e-05
HSA-MIR-21 1.038e-07 5.27e-05
HSA-MIR-1179 5.068e-07 0.000257
HSA-MIR-152 5.509e-07 0.000279
HSA-MIR-551B 1.43e-06 0.000722
HSA-MIR-204 1.766e-06 0.00089
HSA-MIR-511-2 3.28e-06 0.00165
HSA-MIR-142 5.36e-06 0.00269

Figure S7.  Get High-res Image As an example, this figure shows the association of HSA-MIR-146B to 'LYMPH.NODE.METASTASIS'. P value = 1.2e-09 with ANOVA analysis.

Clinical variable #9: 'COMPLETENESS.OF.RESECTION'

No gene related to 'COMPLETENESS.OF.RESECTION'.

Table S16.  Basic characteristics of clinical feature: 'COMPLETENESS.OF.RESECTION'

COMPLETENESS.OF.RESECTION Labels N
  R0 240
  R1 21
  R2 1
  RX 19
     
  Significant markers N = 0
Clinical variable #10: 'NUMBER.OF.LYMPH.NODES'

20 genes related to 'NUMBER.OF.LYMPH.NODES'.

Table S17.  Basic characteristics of clinical feature: 'NUMBER.OF.LYMPH.NODES'

NUMBER.OF.LYMPH.NODES Mean (SD) 2.74 (5.1)
  Significant markers N = 20
  pos. correlated 11
  neg. correlated 9
List of top 10 genes significantly correlated to 'NUMBER.OF.LYMPH.NODES' by Spearman correlation test

Table S18.  Get Full Table List of top 10 genes significantly correlated to 'NUMBER.OF.LYMPH.NODES' by Spearman correlation test

SpearmanCorr corrP Q
HSA-MIR-7-2 -0.4053 1.152e-10 5.88e-08
HSA-MIR-1179 -0.3596 3.051e-08 1.56e-05
HSA-MIR-31 0.3223 3.534e-07 0.00018
HSA-MIR-146B 0.3117 8.332e-07 0.000423
HSA-MIR-152 -0.3055 1.411e-06 0.000715
HSA-MIR-19B-1 0.2973 2.751e-06 0.00139
HSA-MIR-21 0.2916 4.348e-06 0.0022
HSA-MIR-765 -0.3352 4.8e-06 0.00242
HSA-MIR-204 -0.2862 6.632e-06 0.00334
HSA-MIR-139 -0.28 1.064e-05 0.00534

Figure S8.  Get High-res Image As an example, this figure shows the association of HSA-MIR-7-2 to 'NUMBER.OF.LYMPH.NODES'. P value = 1.15e-10 with Spearman correlation analysis. The straight line presents the best linear regression.

Clinical variable #11: 'NEOPLASM.DISEASESTAGE'

6 genes related to 'NEOPLASM.DISEASESTAGE'.

Table S19.  Basic characteristics of clinical feature: 'NEOPLASM.DISEASESTAGE'

NEOPLASM.DISEASESTAGE Labels N
  STAGE I 171
  STAGE II 35
  STAGE III 66
  STAGE IVA 26
  STAGE IVC 3
     
  Significant markers N = 6
List of 6 genes differentially expressed by 'NEOPLASM.DISEASESTAGE'

Table S20.  Get Full Table List of 6 genes differentially expressed by 'NEOPLASM.DISEASESTAGE'

ANOVA_P Q
HSA-MIR-31 1.685e-07 8.61e-05
HSA-MIR-146B 4.361e-06 0.00222
HSA-MIR-139 1.257e-05 0.0064
HSA-MIR-375 1.423e-05 0.00723
HSA-MIR-183 1.762e-05 0.00893
HSA-MIR-376C 2.307e-05 0.0117

Figure S9.  Get High-res Image As an example, this figure shows the association of HSA-MIR-31 to 'NEOPLASM.DISEASESTAGE'. P value = 1.68e-07 with ANOVA analysis.

Clinical variable #12: 'MULTIFOCALITY'

One gene related to 'MULTIFOCALITY'.

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

MULTIFOCALITY Labels N
  MULTIFOCAL 148
  UNIFOCAL 145
     
  Significant markers N = 1
  Higher in UNIFOCAL 0
  Higher in MULTIFOCAL 1
List of one gene differentially expressed by 'MULTIFOCALITY'

Table S22.  Get Full Table List of one gene differentially expressed by 'MULTIFOCALITY'

T(pos if higher in 'UNIFOCAL') ttestP Q AUC
HSA-MIR-132 -4.09 5.66e-05 0.0289 0.6371

Figure S10.  Get High-res Image As an example, this figure shows the association of HSA-MIR-132 to 'MULTIFOCALITY'. P value = 5.66e-05 with T-test analysis.

Clinical variable #13: 'TUMOR.SIZE'

8 genes related to 'TUMOR.SIZE'.

Table S23.  Basic characteristics of clinical feature: 'TUMOR.SIZE'

TUMOR.SIZE Mean (SD) 2.68 (1.5)
  Significant markers N = 8
  pos. correlated 3
  neg. correlated 5
List of 8 genes significantly correlated to 'TUMOR.SIZE' by Spearman correlation test

Table S24.  Get Full Table List of 8 genes significantly correlated to 'TUMOR.SIZE' by Spearman correlation test

SpearmanCorr corrP Q
HSA-MIR-182 0.352 4.406e-08 2.25e-05
HSA-MIR-183 0.3363 1.851e-07 9.44e-05
HSA-MIR-136 -0.3277 5.284e-07 0.000269
HSA-MIR-199A-1 -0.304 2.78e-06 0.00141
HSA-MIR-96 0.3011 3.483e-06 0.00177
HSA-MIR-199A-2 -0.2988 4.173e-06 0.00211
HSA-MIR-199B -0.2957 5.288e-06 0.00267
HSA-MIR-1247 -0.2933 1.293e-05 0.00652

Figure S11.  Get High-res Image As an example, this figure shows the association of HSA-MIR-182 to 'TUMOR.SIZE'. P value = 4.41e-08 with Spearman correlation analysis. The straight line presents the best linear regression.

Methods & Data
Input

  • Expresson data file = THCA-TP.miRseq_RPKM_log2.txt

  • Clinical data file = THCA-TP.clin.merged.picked.txt

  • Number of patients = 302

  • Number of genes = 511

  • Number of clinical features = 13

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

Student's t-test analysis

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

ANOVA analysis

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

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

This is an experimental feature. The full results of the analysis summarized in this report can be downloaded from the TCGA Data Coordination Center.

References
[1] Spearman, C, The proof and measurement of association between two things, Amer. J. Psychol 15:72-101 (1904)
[2] Lehmann and Romano, Testing Statistical Hypotheses (3E ed.), New York: Springer. ISBN 0387988645 (2005)
[3] Howell, D, Statistical Methods for Psychology. (5th ed.), Duxbury Press:324-5 (2002)
[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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