GEO DataSets

Comparison of chromophobe renal cell carcinoma (RCC) and benign oncocytoma tumor samples. Malignant chromophobe RCC and benign oncocytoma share morphologic features. Results provide insight into the molecular differences between the two types of tumors.

Organism:

Homo sapiens

Type:

Expression profiling by array, transformed count, 2 disease state sets

Platform:

GPL570

Series:

GSE12090

18 Samples

Download data: CEL

(Submitter supplied) This study aims to compare gene expression profiles of chromophobe renal cell carcinoma (RCC) and benign oncocytoma, aiming at identifying differentially expressed genes.

Organism:

Homo sapiens

Type:

Expression profiling by array

Dataset:

GDS3274

Platform:

GPL570

18 Samples

Download data: CEL

(Submitter supplied) [original title] Genomic expression and single-nucleotide polymorphism profiling discriminates chromophobe renal cell carcinoma and oncocytoma. Background : Chromophobe renal cell carcinoma (chRCC) and renal oncocytoma are two distinct but closely related entities with strong morphologic and genetic similarities. While chRCC is a malignant tumor, oncocytoma is usually regarded as a benign entity. The overlapping characteristics are best explained by a common cellular origin, and the biologic differences between chRCC and oncocytoma are therefore of considerable interest in terms of carcinogenesis, diagnosis and clinical management. Previous studies have been relatively limited in terms of examining the differences between oncocytoma and chromophobe RCC. Methods : Gene expression profiling using the Affymetrix HGU133Plus2 platform was applied on chRCC (n=15) and oncocytoma specimens (n=15). Supervised analysis was applied to identify a discriminatory gene signature, as well as differentially expressed genes. Immunohistochemical validation was performed in an independent set of tumors. Results : A novel 14 probe-set signature was developed to classify the tumors internally with 93% accuracy, and this was successfully validated on an external data-set with 94% accuracy. Parafibromin, aquaporin 6, and synaptogyrin 3 were novel immunohistochemical markers effectively discriminating the two pathologic entities. Conclusion : Gene expression profiles and pathway analysis effectively distinguish chRCC from oncocytoma. We have generated a novel transcript predictor that is able to discriminate between the two entities accurately, and which has been validated both in an internal and an independent data-set, implying generalizability. We have identified a series of immunohistochemical markers that are clinically useful in discriminating chRCC and oncocytoma.

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL570

30 Samples

Download data: CEL

(Submitter supplied) Identification and evaluation of specific molecular markers is of great importance for reliable diagnostics and outcome prediction of renal neoplasms Using the Affymetrix microarray, we established the gene expression signatures of normal kidneys and different types of renal tumors. Keywords: Several different biological groups, several samples per group

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL570

67 Samples

Download data: CEL

(Submitter supplied) End stage renal disease (ESRD) is associated with hyperplastic-cystic remodelling of the kidneys (ARCD) and increased rate of kidney tumours. Using the Affymetrix oligoarray, we have established the gene expression signature of ESRD/ARCD kidneys and compared to those of normal kidneys and of distinct types of renal tumours. Keywords: normal and different tumor tissues

Organism:

Homo sapiens

Type:

Expression profiling by array

Platforms:

GPL96 GPL97

40 Samples

Download data: CEL

(Submitter supplied) We profiled DNA methylation in fresh-frozen oncocytoma and chRCC tumors and tumor-adjacent adjacent normal tissue to identify a signature of differentially methylated CpG sites that robustly distinguish oncocytoma from chRCC. DNA methylation profiles were generated for renal oncocytomas (n=12), primary kidney chromophobes (chRCC) (n=8) and primary kidney clear cell carcinomas (ccRCC) (n=2). Also profiled were three oncocytic neoplasms of unclear pathological diagnosis, including two masses described as hybrid oncocytic/chromophobe type (n=2), and one mass described as hybrid oncocytic renal neoplasm. more...

Organism:

Homo sapiens

Type:

Methylation profiling by genome tiling array

Platform:

GPL13534

40 Samples

Download data: IDAT

(Submitter supplied) Background: Renal cell carcinoma (RCC) is characterized by a number of diverse molecular aberrations that differ among individuals. Recent approaches to molecularly classify RCC were based on clinical, pathological as well as on single molecular parameters. As a consequence, gene expression patterns reflecting the sum of genetic aberrations in individual tumors may not have been recognized. In an attempt to uncover such molecular features in RCC, we used a novel, unbiased and integrative approach. more...

Organism:

Homo sapiens

Type:

Expression profiling by array; Genome variation profiling by SNP array

Platforms:

GPL6801 GPL3921

261 Samples

Download data: CEL, CSV

(Submitter supplied) Chromosomal abnormalities, such as structural and numerical abnormalities, are a common occurrence in cancer. The close association of homologous chromosomes during interphase, a phenomenon termed somatic chromosome pairing, has been observed in cancerous cells, but the functional consequences of somatic pairing have not been established. Gene expression profiling studies revealed that somatic pairing of chromosome 19 is a recurrent chromosomal abnormality in renal oncocytoma, a neoplasia of the adult kidney. more...

Organism:

Homo sapiens

Type:

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

Platforms:

GPL4866 GPL2005 GPL2004

34 Samples

Download data: CEL, CHP

(Submitter supplied) We investigated the changes in gene expression accompanying the development and progression of kidney cancer using 31,500 element complementary DNA arrays. We measured expression profiles for paired neoplastic and non-cancerous renal epithelium samples from 37 individuals. Using an experimental design optimized for factoring out technological and biological noise, and an adapted statistical test, we find 1738 differentially expressed cDNAs with an expected number of 6 false positives. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platforms:

GPL10 GPL9

342 Samples

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(Submitter supplied) Epilepsy is a common cause of morbidity affecting approximately one third of patients with primary brain tumors. However, the molecular mechanism underlying the tumor induced epileptogenesis is poorly understood. The alteration in peritumoral microenvironments is believed to play a significant role in inducing epileptogenesis. We hypothesize that the change of gene expression in neighboring astrocytes and neurons may contribute to the increased neuronal excitability and epileptogenesis.

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL570

10 Samples

Download data: CEL

(Submitter supplied) Gene expression microarrays are the most widely used technique for genome-wide expression profiling. However, microarrays do not perform well on formalin fixed paraffin embedded tissue (FFPET). Consequently, microarrays cannot be effectively utilized to perform gene expression profiling on the vast majority of archival tumor samples. To address this limitation of gene expression microarrays, we designed a novel procedure (3'-end sequencing for expression quantification (3SEQ)) for gene expression profiling from FFPET using next-generation sequencing. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

4 related Platforms

31 Samples

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