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Gene expression profiling reveals different pathways related to Abl and other genes that cooperate with c-Myc in a model of plasma cell neoplasia

Eun Sung Park14, John D Shaughnessy2, Shalu Gupta1, Hongyang Wang15, Ju-Seog Lee34, Hyun Goo Woo3, Fenghuang Zhan2, James D Owens1, Michael Potter1, Siegfried Janz16 and J Frederic Mushinski1*

Author Affiliations

1 Laboratory of Cancer Biology and Genetics, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892 USA

2 Donna and Donald Lambert Laboratory of Myeloma Genetics, Myeloma Institute for Research and Therapy, University of Arkansas for Medical Sciences, AR 72205 USA

3 Laboratory of Experimental Carcinogenesis, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892 USA

4 Molecular Therapeutics, University of Texas M. D. Anderson Cancer Center, Houston, TX 77030 USA

5 Department of Medicine, University of Virginia, Charlottesville, VA 22908

6 Department of Pathology, University of Iowa Roy J. and Lucille A. Carver College of Medicine, Iowa City, IA 52242 USA

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BMC Genomics 2007, 8:302  doi:10.1186/1471-2164-8-302

Published: 31 August 2007

Additional files

Additional file 1:

Supplementary Tables 1. Functional enrichment analysis of genes that showed significant differences in expression between plasma cell tumors and B-cell lymphomas. Supplementary Table 1A. Functional enrichment analysis according to GO Molecular Function category. Supplementary Table 1B. Functional enrichment analysis by GO Cellular Component category. Supplementary Table 1C. Functional enrichment analysis by GO Biological Process category. Supplementary Table 1D. Genes present in nine GO Molecular Function categories that were shown to be functionally enriched (see Supplementary Table 1A, above). Four tables showing lists of genes that showed significant (p < 0.005) differences in expression between plasma cell tumors and B-cell lymphomas characterized by their functional enrichment according to biological processes defined by the Gene Ontology Consortium. The enrichment of gene set was estimated by calculating the cumulated hypergeometric p values of the each biological process defined by the Gene Ontology Consortium http://www.geneontology.org webcite. In Table 1D, 9 components from the Molecular Function GO category were selected to show the actual genes involved.

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Additional file 2:

Supplementary Tables 2. Genes that showed significant (p < 0.001) differences in expression between rapid-forming plasma cell tumors (ABPC and ABLMYCPC) and slow-forming plasma cell tumors (TEPC, IL6PC and KiPC). Supplementary Table 2A. Genes that showed more than 2-fold higher expression in rapid-forming plasma cell tumors than in slow-forming plasma cell tumors. Supplementary Table 2B. Genes that showed more than 2-fold higher expression in slow-forming plasma cell tumors than in rapid-forming plasma cell tumors. Two tables showing lists of genes that showed significant (p < 0.001) differences in expression between rapid- and slow-forming plasma cell tumors.

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Additional file 3:

Supplementary Figure 1. Quantitative RT-PCR of relative mRNA content in 13 mouse B-cell lymphomas and plasma cell tumors for 9 key genes. Results of quantitative RT-PCR validation of relative mRNA content in 13 mouse B-cell lymphomas and plasma cell tumors for 9 key genes: c-Myc, Socs1, Socs2, Abl1, Jak1, Xbp1, Sdc1, Irf4, Pax5 (BSAP) and the "housekeeping" gene, GAPDH.

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Additional file 4:

Supplementary Tables 3. Genes with significant (p < 0.001) differences in gene expression associated with site of chromosomal translocation in two sample t-tests. Supplementary Table 3A. Genes that showed significant differences in expression between ABPCs with T(12;15) and ABPCs with T(6;15). Supplementary Table 3B. Genes that showed significant differences in expression between TEPCs with T(12;15 class I) and TEPC T(12;15 class II) chromosome translocations. Two tables showing lists of genes that showed significant (p < 0.001) differences in expression between similar subclasses of plasma cell tumors that differ in site of Myc-activating chromosomal translocation.

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Additional file 5:

Supplementary Figure 2. Meta-analysis of global gene expression of 67 mouse samples (including 5 different subgroups of plasma cell tumors and B-cell lymphomas) combined with 123 human samples (including 5 different subgroups of multiple myelomas and tonsilar B cells). Heat map derived from a meta-analysis of a combination of expression data from human and mouse plasma cell dyscrasias.

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