Journal: BioMed Research International

Article Title: Hypoxia and Human Genome Stability: Downregulation of BRCA2 Expression in Breast Cancer Cell Lines

doi: 10.1155/2013/746858

Figure Lengend Snippet: Heat maps of DEGs involved in DNA damage repair (DDR) pathways deregulated in hypoxia. Clustering of DEGs involved in DNA damage repair (DDR) pathways: mismatch repair (MMR), nucleotide excision repair (NER), nonhomologous end-joining (NHEJ), and homologous recombination repair (HRR). The heat maps were generated from microarray data reflecting gene expression values in MCF-7, MDA-MB-231, and SKBr3 cells exposed to hypoxia (3% O 2 ) for 24 h and 48 h in comparison to control cells cultured under normoxic conditions (16% O 2 , M > |1| and P < 0.05). Each row represents the expression levels for a single gene tested for different experimental conditions. Each column shows the expression levels for the genes tested for a single experimental condition. The absolute expression value (log scale) of each gene is derived from the mean of two biological replicates. The color scale bar on the top represents signal intensity variations ranging from green (poorly expressed genes) to red (highly expressed genes). Black boxes indicate intermediate expression values. N = normoxia; H24 = hypoxia for 24 h; H48 = hypoxia for 48 h.

Article Snippet: Since hypoxia is a condition which during tumor growth influences the expression of several genes involved in angiogenesis, proliferation, cell cycle control, and DNA damage repair (DDR) mechanisms, we first performed a microarray analysis, using Affymetrix platform, in order to compare differential gene expression profiles in MCF-7, MDA-MB-231, and SKBr3 human breast cancer cell lines in response to hypoxic exposure for 24 and 48 hours, respectively.

Techniques: Homologous Recombination, Generated, Microarray, Gene Expression, Comparison, Control, Cell Culture, Expressing, Derivative Assay

Journal: Nucleic Acids Research

Article Title: Implementation of GenePattern within the Stanford Microarray Database

doi: 10.1093/nar/gkn786

Figure Lengend Snippet: Accessing GenePattern microarray data analysis package from a publication record in SMD. Clicking on the red gear icon in a publication record will take the user to the SMD data retrieval pipeline. At any point after the data are retrieved, the user will be able to download the data files or click on the ‘Analyze with GenePattern’ option. GenePattern is launched with the data already loaded into the PCL to GCT conversion module.

Article Snippet: SMD stores data from gene expression as well as array CGH and ChIP–chip experiments, and supports multiple microarray platforms (spotted cDNA or oligonucleotide arrays, Affymetrix, Agilent, Combimatrix and Nimblegen arrays).

Techniques: Microarray