Skin Cutaneous Melanoma: Correlation between copy number variation genes and molecular subtypes<BR>(NF1_Any

Skin Cutaneous Melanoma: Correlation between copy number variation genes and molecular subtypes
(NF1_Any_Mutants cohort)

Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)

Overview

Introduction

This pipeline computes the correlation between significant copy number variation (cnv) genes and molecular subtypes.

Summary

Testing the association between copy number variation of 19 peak regions and 8 molecular subtypes across 31 patients, no significant finding detected with Q value < 0.25.

No gene cnvs related to clinical features.

Results

Overview of the results

Table 1. Get Full Table Overview of the association between significant copy number variation of 19 regions and 8 molecular subtypes. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, no significant finding detected.


		Molecular subtypes	CN CNMF	METHLYATION CNMF	RPPA CNMF	RPPA CHIERARCHICAL	MRNASEQ CNMF	MRNASEQ CHIERARCHICAL	MIRSEQ CNMF	MIRSEQ CHIERARCHICAL
	nCNV (%)	nWild-Type	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Chi-square test
Amp Peak 1(1p12)	10 (32%)	21	0.458 (1.00)	0.441 (1.00)	0.366 (1.00)	1 (1.00)	0.702 (1.00)	0.837 (1.00)	1 (1.00)	0.455 (1.00)
Amp Peak 2(1q44)	19 (61%)	12	0.0659 (1.00)	0.288 (1.00)	1 (1.00)	1 (1.00)	0.37 (1.00)	0.551 (1.00)	0.0659 (1.00)	0.0484 (1.00)
Amp Peak 3(7p22 3)	16 (52%)	15	0.479 (1.00)	1 (1.00)	0.667 (1.00)	0.59 (1.00)	0.815 (1.00)	0.959 (1.00)	0.479 (1.00)	0.628 (1.00)
Amp Peak 4(7q36 1)	18 (58%)	13	0.722 (1.00)	0.717 (1.00)	0.667 (1.00)	1 (1.00)	0.386 (1.00)	0.743 (1.00)	1 (1.00)	0.958 (1.00)
Amp Peak 5(12p12 1)	5 (16%)	26	0.654 (1.00)	0.148 (1.00)	1 (1.00)	0.453 (1.00)	0.394 (1.00)	1 (1.00)	1 (1.00)	0.301 (1.00)
Amp Peak 6(15q26 2)	11 (35%)	20	1 (1.00)	1 (1.00)	0.272 (1.00)	0.539 (1.00)	0.232 (1.00)	0.557 (1.00)	0.716 (1.00)	0.995 (1.00)
Amp Peak 7(17q25 3)	16 (52%)	15	0.156 (1.00)	0.722 (1.00)	1 (1.00)	0.604 (1.00)	0.211 (1.00)	0.755 (1.00)	0.479 (1.00)	0.553 (1.00)
Del Peak 1(1p36 31)	7 (23%)	24	0.0373 (1.00)	0.412 (1.00)	1 (1.00)	0.453 (1.00)	0.0469 (1.00)	0.0483 (1.00)	1 (1.00)	0.0472 (1.00)
Del Peak 2(1p13 2)	9 (29%)	22	0.252 (1.00)	0.456 (1.00)	0.621 (1.00)	0.539 (1.00)	0.329 (1.00)	1 (1.00)	1 (1.00)	0.506 (1.00)
Del Peak 3(2q37 3)	10 (32%)	21	1 (1.00)	1 (1.00)	0.366 (1.00)	0.273 (1.00)	0.702 (1.00)	0.597 (1.00)	0.458 (1.00)	0.506 (1.00)
Del Peak 4(3q23)	4 (13%)	27	1 (1.00)	0.107 (1.00)	0.526 (1.00)	1 (1.00)	1 (1.00)	0.893 (1.00)	1 (1.00)	0.614 (1.00)
Del Peak 5(6q23 2)	14 (45%)	17	0.00385 (0.585)	0.473 (1.00)	0.193 (1.00)	0.317 (1.00)	0.183 (1.00)	0.438 (1.00)	0.479 (1.00)	0.491 (1.00)
Del Peak 6(9p21 3)	20 (65%)	11	0.135 (1.00)	0.153 (1.00)	1 (1.00)	1 (1.00)	0.719 (1.00)	0.845 (1.00)	0.716 (1.00)	0.76 (1.00)
Del Peak 7(10p15 1)	13 (42%)	18	0.722 (1.00)	1 (1.00)	0.0886 (1.00)	0.104 (1.00)	0.0336 (1.00)	0.0571 (1.00)	0.722 (1.00)	0.193 (1.00)
Del Peak 8(10q24 33)	14 (45%)	17	1 (1.00)	0.473 (1.00)	0.0886 (1.00)	0.104 (1.00)	0.224 (1.00)	0.201 (1.00)	1 (1.00)	0.0811 (1.00)
Del Peak 9(11q24 3)	21 (68%)	10	0.252 (1.00)	1 (1.00)	0.621 (1.00)	0.194 (1.00)	1 (1.00)	0.435 (1.00)	0.704 (1.00)	0.984 (1.00)
Del Peak 10(13q34)	8 (26%)	23	0.685 (1.00)	0.412 (1.00)	0.626 (1.00)	1 (1.00)	0.13 (1.00)	0.258 (1.00)	1 (1.00)	0.43 (1.00)
Del Peak 11(14q23 3)	9 (29%)	22	0.433 (1.00)	0.233 (1.00)	1 (1.00)	1 (1.00)	0.116 (1.00)	0.505 (1.00)	0.433 (1.00)	0.717 (1.00)
Del Peak 12(16q12 1)	14 (45%)	17	0.285 (1.00)	1 (1.00)	0.405 (1.00)	0.104 (1.00)	0.0263 (1.00)	0.0311 (1.00)	1 (1.00)	0.612 (1.00)

Methods & Data

Input

Copy number data file = All Lesions File (all_lesions.conf_##.txt, where ## is the confidence level). The all lesions file is from GISTIC pipeline and summarizes the results from the GISTIC run. It contains data about the significant regions of amplification and deletion as well as which samples are amplified or deleted in each of these regions. The identified regions are listed down the first column, and the samples are listed across the first row, starting in column 10.
Molecular subtype file = SKCM-NF1_Any_Mutants.transferedmergedcluster.txt
Number of patients = 31
Number of copy number variation regions = 19
Number of molecular subtypes = 8
Exclude regions that fewer than K tumors have alterations, K = 3

Fisher's exact test

For binary or multi-class clinical features (nominal or ordinal), two-tailed Fisher's exact tests (Fisher 1922) were used to estimate the P values using the 'fisher.test' function in R

Chi-square test

For multi-class clinical features (nominal or ordinal), Chi-square tests (Greenwood and Nikulin 1996) were used to estimate the P values using the 'chisq.test' 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] Fisher, R.A., On the interpretation of chi-square from contingency tables, and the calculation of P, Journal of the Royal Statistical Society 85(1):87-94 (1922)

[2] Greenwood and Nikulin, A guide to chi-squared testing, Wiley, New York. ISBN 047155779X (1996)

[3] 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)

[4] GISTIC_version2

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