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Expression data analyzed with LPIA in A549 lung carcinoma cells treated with geldanamycin

ABSTRACT: The statsitcal model, latent pathway identification analysis (LPIA), was implemented for the analysis of A549 lung carcinoma cells treated with geldanamycin. Control and treated samples were assayed with Affymetrix HG_U133_plus_2 arrays and analyzed using LPIA. LPIA looks for statistically signﬁcant evidence of dysregulation in a network of pathways constructed in a manner that explicitly links pathways through their common function in the cell. Geldanamycin (geld) is known to inhibit the molecular chaperone protein, Hsp90, and plays a role in preventing the malignant transformation and proliferation of healthy cells during oncogenesis. LPIA successfully identified pathways specific to geldanamycin effects at the gene transcription level. A549 lung carcinoma cells were allowed to adhere for 24h and further incubated in the presence of geldanamycin at a concentration equivalent to the determined IC50 of 40 nM or IC20 of 10 nM, or with vehicle DMSO (final concentration 0.4%). After 24h and 48 h, cells were harvested and total RNA was purified and processed for Affymetrix HG_U133_Plus_2.0 microarray analysis. Raw probe intensities were RMA-normalized and avereaged for three replicates for each condition. Probe sets for 54,120-annotated open reading frames were included in LPIA analysis.

ORGANISM(S): Homo sapiens

SUBMITTER: Pham L

PROVIDER: S-ECPF-GEOD-26525 | biostudies-other | 2011 Aug

REPOSITORIES: biostudies-other

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Expression data analyzed with LPIA in A549 lung carcinoma cells treated with geldanamycin.

2011-01-11 | GSE26525 | GEO

Expression data analyzed with LPIA in A549 lung carcinoma cells treated with geldanamycin.

Project description:The statsitcal model, latent pathway identification analysis (LPIA), was implemented for the analysis of A549 lung carcinoma cells treated with geldanamycin. Control and treated samples were assayed with Affymetrix HG_U133_plus_2 arrays and analyzed using LPIA. LPIA looks for statistically signï¬cant evidence of dysregulation in a network of pathways constructed in a manner that explicitly links pathways through their common function in the cell. Geldanamycin (geld) is known to inhibit the molecular chaperone protein, Hsp90, and plays a role in preventing the malignant transformation and proliferation of healthy cells during oncogenesis. LPIA successfully identified pathways specific to geldanamycin effects at the gene transcription level. A549 lung carcinoma cells were allowed to adhere for 24h and further incubated in the presence of geldanamycin at a concentration equivalent to the determined IC50 of 40 nM or IC20 of 10 nM, or with vehicle DMSO (final concentration 0.4%). After 24h and 48 h, cells were harvested and total RNA was purified and processed for Affymetrix HG_U133_Plus_2.0 microarray analysis. Raw probe intensities were RMA-normalized and avereaged for three replicates for each condition. Probe sets for 54,120-annotated open reading frames were included in LPIA analysis.

2011-01-11 | E-GEOD-26525 | biostudies-arrayexpress

Expression data from TGFbeta-treated control or aPKC silenced A549 cells

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| S-ECPF-GEOD-26241 | biostudies-other

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Aiolos regulated genes in A549, lung carcinoma cells

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| S-ECPF-GEOD-50812 | biostudies-other

Sodium arsenite induced gene expression changes in A549 human epithelial lung carcinoma cells

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Project description:The major cause of cancer-related deaths in lung cancer patients is commonly attributed to its ability to metastasize to distant organs such as the bone, brain, liver and adrenal glands. The dysregulation in miRNA expression is believed to contribute toward the initiation and progression of metastasis through their capability to regulate target genes. In this study, two NSCLC sub-cell lines possessing opposing migration and invasion properties were established using serial transwell invasion assays, followed by miRNA microarray to obtain the overview of miRNA expression as well as identify important playes in metastasis. High and low invasive A549 sub-cell lines were established from heterogeneous parental population and selected through seven generations. Three replicates were used for RNA extraction and miRNA microarray.

| S-ECPF-GEOD-47056 | biostudies-other

Sodium arsenite induced changes in A549 human epithelial lung carcinoma cells

Project description:This SuperSeries is composed of the SubSeries listed below. Refer to individual Series

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Embelin induced differential gene expression in A549 lung cancer cells

Project description:Embelin (15 uM) induced alterations in the gene expression profile was studied in A549 lung cancer cells during the initial stages of apoptosis (4h following treatment) As embelin (15 uM) induces apoptosis as early as 4h time period, we performed microarray analysis to study embelin-induced differential gene expression as early as 4h to identify the responsible pathways.

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