GEO DataSets

(Submitter supplied) Gene expression signatures were measured in logarithmic growing cultures Affymetrix HG-U133AV2 expression arrays were performed according to the manufacturer's directions using RNA extracted by Qiagen RNeasy from engineered human melanoma cells

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL571

6 Samples

Download data: CEL

(Submitter supplied) Multiple BRAF inhibitor resistance mechanisms have been described, however their relative frequency, clinical correlates, and effect on subsequent therapy have not been assessed in patients with metastatic melanoma. Excised progressing BRAFV600 mutant melanoma metastases (Prog) from patients treated with dabrafenib (n=22) or vemurafenib (n=8) were analyzed for known resistance mechanisms. Oncogenic signaling in Prog and matched pre-treatment tumors was examined using gene expression analysis. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL10558

61 Samples

Download data: TXT

(Submitter supplied) PGC1a is a transcriptional coactivator that regulates energy metabolism. PGC1a is highly expressed in a subset of melanoma tumors and cell lines. We generated gene-expression profile of control and PGC1alpha depleted A375P melanoma cells, a melanoma cell line that expresses very high levels of PGC1a to investigate the role of this gene in melanoma.

Organism:

Homo sapiens

Type:

Expression profiling by array

Dataset:

GDS4989

Platform:

GPL571

8 Samples

Download data: CEL

Analysis of A375P melanoma cells depleted for PGC1alpha. PGC1alpha is a transcriptional coactivator that promotes mitochondrial biogenesis and respiration. A375P is a cell line that overexpresses PGC1alpha. Results provide insight into the role of PGC1alpha in melanoma.

Organism:

Homo sapiens

Type:

Expression profiling by array, count, 2 protocol sets

Platform:

GPL571

Series:

GSE36879

8 Samples

Download data: CEL

(Submitter supplied) A panel of 29 melanoma cell lines were gene expression profiled by RNA-Seq.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL11154

29 Samples

Download data: TXT

(Submitter supplied) Increased MITF expression contributes to melanoma progression and resistance to BRAF pathway inhibition. We show that, unexpectedly, lack of MITF is associated with more severe resistance to a range of inhibitors. Indeed, the presence of endogenous MITF was essential for robust drug responses. Both in primary and acquired resistance, MITF levels inversely correlated with expression of several activated receptor tyrosine kinases, most commonly AXL. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL11154

14 Samples

Download data: TXT

(Submitter supplied) Metastasis is the deadliest phase of cancer progression. Experimental models using immunodeficient mice have been used to gain insights into the mechanisms of metastasis. We report here the identification of a “metastasis aggressiveness gene expression signature” derived using human melanoma cells selected based on their metastatic potentials in a xenotransplant metastasis model. Comparison with expression data from human melanoma patients shows that this metastasis gene signature correlates with the aggressiveness of melanoma metastases in human patients. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Dataset:

GDS3966

Platform:

GPL96

83 Samples

Download data: CEL

Analysis of melanoma clinical samples representing 31 primary melanomas and 52 melanoma metastases. These results, together with results from tumor samples from highly-metastatic derivatives of an A375 (ATCC) melanoma cell line, provide insight into the molecular basis of metastasis.

Organism:

Homo sapiens

Type:

Expression profiling by array, count, 2 disease state sets

Platform:

GPL96

Series:

GSE8401

83 Samples

Download data: CEL

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Homo sapiens

Type:

Expression profiling by array; Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL6244 GPL11154

12 Samples

Download data: CEL

(Submitter supplied) Thousands of enhancers are characterized in the human genome, yet few have been shown important in cancer. Inhibiting oncokinases, such as EGFR, ALK, HER2, and BRAF, is a mainstay of current cancer therapy but is hindered by innate drug resistance mediated by upregulation of the HGF receptor, MET. The mechanisms mediating such genomic responses to targeted therapy are unknown. Here, we identify lineage-specific MET enhancers for multiple common tumor types, including a melanoma lineage-specific MET enhancer that displays inducible chromatin looping and MET gene induction upon BRAF inhibition. more...

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL11154

4 Samples

Download data: TXT

(Submitter supplied) Thousands of enhancers are characterized in the human genome, yet few have been shown important in cancer. Inhibiting oncokinases, such as EGFR, ALK, HER2, and BRAF, is a mainstay of current cancer therapy but is hindered by innate drug resistance mediated by upregulation of the HGF receptor, MET. The mechanisms mediating such genomic responses to targeted therapy are unknown. Here, we identify lineage-specific MET enhancers for multiple common tumor types, including a melanoma lineage-specific MET enhancer that displays inducible chromatin looping and MET gene induction upon BRAF inhibition. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL6244

8 Samples

Download data: CEL

(Submitter supplied) Colon cancer cell lines with partial sensitivity to the BRAF inhibitor PLX4720 were grown in increasing concentration of the drug to develop acquired resistance. Gene expression was performed for comparison of the resistant clones to the parental lines.

Organism:

Homo sapiens

Type:

Expression profiling by array

Dataset:

GDS4700

Platform:

GPL570

4 Samples

Download data: CEL

Analysis of HT29 and Colo205 parental colorectal cancer (CRC) cell lines and HT29 and Colo205 clones with acquired resistance to BRAF inhibitor PLX4720. BRAF is a protein kinase in the RAS/RAF/MEK/ERK pathway. Results provide insight into mechanisms of acquired resistance to BRAF inhibitors in CRC.

Organism:

Homo sapiens

Type:

Expression profiling by array, transformed count, 4 cell line sets

Platform:

GPL570

Series:

GSE34299

4 Samples

Download data: CEL

(Submitter supplied) H3K27 acetylation statuses were analyzed in four colon cancer cell lines (RKO, Caco2, SW48, and SW620), and colorectal cancer-specific super-enhancers were identified.

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL20301

8 Samples

Download data: WIG

(Submitter supplied) Illumina HumanExon510S-DUO bead arrays (Illumina Inc) were performed according to the manufacturer's protocol.

Organism:

Homo sapiens

Type:

Genome variation profiling by SNP array; SNP genotyping by SNP array

Platform:

GPL6988

4 Samples

Download data: TXT

(Submitter supplied) Differential gene expression analysis of parental and resistant sub-lines of melanoma cell lines treated or untreated with PLX4032 Using microarray we sought to obtain a genome-wide profile of differentially expressed genes in parental melanoma cell lines and resistant sub-lines in response to PLX4032 vs DMSO control treatment.

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL6244

24 Samples

Download data: CEL, TXT

(Submitter supplied) Microarray expression analysis to identify global changes in transcription in response to RAF inhibition. Genes under RAF control were identified in a panel of BRAFV600E tumor cells, following the short-term inhibition of RAF using a pan-RAF kinase inhibitor, PLX4032 (Plexxikon). For comparison with changes in gene expression in response to MEK inhibition using PD0325901 (Pfizer), the following array data was referenced: (http://www.ncbi.nlm.nih.gov/geo/ (accession no. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL571

12 Samples

Download data: CEL

(Submitter supplied) These studies demonstrate multiple pro-tumorigenic functions for BPTF, and identify it as a novel target for anti-cancer therapy. They also suggest the combination of BPTF targeting with BRAF inhibitors as a novel therapeutic strategy for melanomas with mutant BRAF.

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL19556

10 Samples

Download data: GPR

(Submitter supplied) The combination of JQ1 and Vemurafenib acted synergistically in BRAF-mutant cell lines, resulting in marked apoptosis in vitro, with up-regulation of pro-apoptotic proteins. In vivo, combination treatment suppressed tumor growth and significantly improved survival compared to either drug alone. RNA sequencing of tumor tissues revealed almost four thousand genes that were uniquely modulated by the combination, with several anti-apoptotic genes significantly down-regulated.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL11154

16 Samples

Download data: TXT

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Homo sapiens

Type:

Expression profiling by array; SNP genotyping by SNP array; Genome variation profiling by SNP array

Platforms:

GPL570 GPL13135

126 Samples

Download data: CEL, IDAT