Gene Set Analysis

Genes underexpressed in decitabine treated human myeloma cell lines

 Genes overexpressed in decitabine treated HMCLs (Human Myeloma Cell Lines). Five HMCLs were cultured with or without 0.5 μM decitabine for 7 days and gene expression was profiled with Affymetrix U133 plus 2.0. Genes significantly differentially expressed between control and decitabine treated cells were identified using SAM supervised paired analysis with a 5% false discovery rate. When a gene was interrogated by several probe sets, we used the probe set yielding to a maximum variance across control and decitabine treated cells.
 

Genes overexpressed in decitabine treated human myeloma cell lines

 Genes overexpressed in decitabine treated HMCLs (Human Myeloma Cell Lines). Five HMCLs were cultured with or without 0.5 μM decitabine for 7 days and gene expression was profiled with Affymetrix U133 plus 2.0. Genes significantly differentially expressed between control and decitabine treated cells were identified using SAM supervised paired analysis with a 5% false discovery rate. When a gene was interrogated by several probe sets, we used the probe set yielding to a maximum variance across control and decitabine treated cells.

Genes overexpressed in TSA treated human myeloma cell lines

Genes overexpressed in TSA treated HMCLs (Human Myeloma Cell Lines). Five HMCLs were cultured with or without 0.33 μM TSA for 1 day and gene expression was profiled with Affymetrix U133 plus 2.0 microarray. Genes significantly differentially expressed between control and TSA treated cells were identified using SAM supervised paired analysis with a 5% false discovery rate. When a gene was interrogated by several probe sets, we used the probe set yielding to a maximum variance across control and TSA treated cells.

Cancer census genes

The Cancer Gene Census is an ongoing effort to catalogue those genes for which mutations have been causally implicated in cancer.

Spike genes in Multiple Myeloma

Multiple Myeloma (MM) is a heterogeneous disease with recurrent gene translocations, amplifications and deletions in Multiple Myeloma Cells (MMCs). Spiked genes are defined to be low in most of MMCs of MM patients, but are expressed at high levels in a subset of MM cases. Spiked gene expression profile might reflect oncogenic events such as genetic or epigenetic alterations, or the influences of other genes. Thus, the identification of spiked genes will help to find new genes involved in tumor formation and progression.