Open Access Highly Accessed Research article

Global analysis of gene expression changes during retinoic acid-induced growth arrest and differentiation of melanoma: comparison to differentially expressed genes in melanocytes vs melanoma

Mary Estler, Goran Boskovic, James Denvir, Sarah Miles, Donald A Primerano and Richard M Niles*

Author Affiliations

Department of Biochemistry and Microbiology, Joan C. Edwards School of Medicine, Marshall University, One John Marshall Drive – BBSC, Huntington, WV 25755, USA

For all author emails, please log on.

BMC Genomics 2008, 9:478  doi:10.1186/1471-2164-9-478

Published: 11 October 2008

Additional files

Additional file 1:

List of genes whose expression is significantly regulated by RA treatment at one or more time point. Statistical significance is determined by SAM with a false discovery rate of 10%, and a minimum fold change of 1.5. Average fold changes across six replicates are reported for significant changes only. Gene IDs (first column) are linked to search pages at the National Center for Biotechnology Information.

Format: HTM Size: 449KB Download file

Open Data

Additional file 2:

List of genes whose expression is significantly different between the melan-a and B16 cell lines. Statistical significance is determined by SAM with a false discovery rate of 10% and a minimum fold change of 1.5. Average fold changes across six replicates are reported. Gene IDs (first column) are linked to search pages at the National Center for Biotechnology Information.

Format: HTM Size: 849KB Download file

Open Data

Additional file 3:

Members of the 203 gene set, fold change at 48 h of RA treatment and relative expression in melan-a vs. B16 cells.

Format: PDF Size: 60KB Download file

This file can be viewed with: Adobe Acrobat Reader

Open Data

Additional file 4:

Classification of 203 Gene Set Members According to Gene Ontology Biological Processes. Processes were ranked by p-value which is the Holm-Bonferroni adjusted probability of a random set of 203 genes containing at least the stated representation in the Pathway Studio database. The number of members within each process that are expressed lower in melan-a, higher in melan-a and the total number of members are provided in columns 2, 3 and 4 respectively.

Format: PDF Size: 14KB Download file

This file can be viewed with: Adobe Acrobat Reader

Open Data

Additional file 5:

Members of 203 gene set which are components of the major biological processes. Using Pathway Studio, we identified biological processes which were enriched for members of the 203 gene set. Members of the five processes that are most significantly enriched according to Fisher's Exact Test are given.

Format: PDF Size: 17KB Download file

This file can be viewed with: Adobe Acrobat Reader

Open Data