GEO DataSets

(Submitter supplied) [original title] Combined gene expression and genomic profiling define two intrinsic molecular subtypes of urothelial carcinoma and gene signatures for molecular grading and outcome. In the present investigation we sought to refine the classification of urothelial carcinoma by combining information on gene expression, genomic, and gene mutation levels. For these purposes we performed gene expression analysis of 144 carcinomas, and whole genome array-CGH analysis and mutation analyses of FGFR3, PIK3CA, KRAS, HRAS, NRAS, TP53, CDKN2A, and TSC1, in 103 of these cases. more...

Organism:

Homo sapiens

Type:

Expression profiling by array; Genome variation profiling by genome tiling array

Platforms:

GPL4723 GPL3883 GPL5186

285 Samples

Download data: GPR, TXT

(Submitter supplied) Even though urothelial cancer (UC) is the fourth common tumor type among males, progress in treatment development has been deficient. Pathological assessment provides the urologists with only a broad classification, complicated by frequent disagreement among pathologist and the co-existence of different grading systems. Consequently, there is a great need for an objective, reproducible and biologically relevant classification system to make treatment more efficient. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL6947

308 Samples

Download data: TXT

(Submitter supplied) Background Clinically useful molecular markers predicting the clinical course of patients diagnosed with non-muscle invasive bladder cancer are needed to improve treatment outcome. Methods We used custom designed oligonucleotide microarrays to validate four previously reported gene expression signatures for molecular diagnosis of disease stage and carcinoma in situ, and for predicting disease recurrence and progression. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL4060

808 Samples

Download data: TXT

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

Organism:

Homo sapiens

Type:

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

Platforms:

GPL96 GPL6984

70 Samples

Download data: CEL, IDAT

(Submitter supplied) This is a comprehensive genomic characterization of 40 urothelial bladder carcinoma (UBC) cell lines including information on origin, mutation status of genes implicated in bladder cancer (FGFR3, PIK3CA, TP53, and RAS), copy number alterations assessed using high density SNP arrays, uniparental disomy (UPD) events, and gene expression. Based on gene mutation patterns and genomic changes we identify lines representative of the FGFR3-driven tumor pathway and of the TP53/RB tumor suppressor-driven pathway. more...

Organism:

Homo sapiens

Type:

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

Platform:

GPL6984

50 Samples

Download data: IDAT, TXT

(Submitter supplied) This is a comprehensive genomic characterization of 40 urothelial bladder carcinoma (UBC) cell lines including information on origin, mutation status of genes implicated in bladder cancer (FGFR3, PIK3CA, TP53, and RAS), copy number alterations assessed using high density SNP arrays, uniparental disomy (UPD) events, and gene expression. Based on gene mutation patterns and genomic changes we identify lines representative of the FGFR3-driven tumor pathway and of the TP53/RB tumor suppressor-driven pathway. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL96

20 Samples

Download data: CEL

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

Organism:

Homo sapiens

Type:

Expression profiling by array; Genome variation profiling by genome tiling array

Platforms:

GPL6947 GPL4723

277 Samples

Download data: GPR

(Submitter supplied) Genomic and gene expression profiling identifies two major gene/genomic circuits operating in urothelial carcinoma

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL6947

131 Samples

Download data: TXT

(Submitter supplied) Genomic and gene expression profiling identifies two major gene/genomic circuits operating in urothelial carcinoma

Organism:

Homo sapiens

Type:

Genome variation profiling by genome tiling array

Platform:

GPL4723

146 Samples

Download data: GPR

(Submitter supplied) The presence of carcinoma in situ (CIS) lesions in the urinary bladder is associated with a high risk of disease progression to a muscle invasive stage. In this study, we used microarray expression profiling to examine the gene expression patterns in superficial transitional cell carcinoma (sTCC) with surrounding CIS (13 patients), without surrounding CIS lesions (15 patients), and in muscle invasive carcinomas (mTCC; 13 patients). more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Dataset:

GDS1479

Platform:

GPL96

60 Samples

Download data: CEL

Analysis of bladder biopsies of superficial transitional cell carcinomas with or without surrounding carcinoma in situ (CIS) lesions and muscle invasive carcinomas (mTCC). CIS is a common mTCC precursor. Results provide insight into which tumors in early stage bladder cancer are likely to progress.

Organism:

Homo sapiens

Type:

Expression profiling by array, count, 6 specimen sets

Platform:

GPL96

Series:

GSE3167

60 Samples

Download data: CEL

(Submitter supplied) 80 bladder tumors of different stages, grades and histologies analyzed on costom made cDNA arrays with 10638 gene elements Keywords: parallel sample

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL1479

80 Samples

Download data

(Submitter supplied) Rhabdomyosarcoma (RMS) is the most common paediatric soft-tissue sarcoma and resembles developing skeletal muscle. Specific genomic alterations including translocations, deletions and amplification events have been associated with the alveolar and embryonal subtypes of RMS. Characterizing these changes has led to increased understanding of the underlying molecular biology. However, further aberrations and their significance remain to be defined. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL570

13 Samples

Download data: CEL, CHP

(Submitter supplied) Bladder tumours used to construct a tumour stage classifier Keywords = bladder cancer, disease stages, classification Keywords: other

Organism:

Homo sapiens

Type:

Expression profiling by array

Dataset:

GDS183

Platform:

GPL80

40 Samples

Download data: CEL

(Submitter supplied) Expression profiling of superficial bladder tumours to delineate the expression pattern differences between non-recurring and recurring tumours. Keywords = bladder cancer, superficial, recurrence, prediction Keywords: other

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL80

31 Samples

Download data: CEL

Identification of clinically relevant subclasses of bladder carcinoma. Three major stages identified, Ta, T1 and T2-4. Ta tumors further classified into subgroups. A 32-gene molecular classifier was built.

Organism:

Homo sapiens

Type:

Expression profiling by array, count, 3 disease state, 4 tissue sets

Platform:

GPL80

Series:

GSE89

40 Samples

Download data: CEL

(Submitter supplied) Purpose HER2 gene amplification or protein overexpression (HER2+) defines a clinically challenging subgroup of breast cancer with variable prognosis and response to therapy. We aimed to investigate the heterogeneous biological appearance and clinical behavior of HER2+ tumors using molecular profiling. Materials and Methods Hierarchical clustering of gene expression data from 58 HER2-amplified tumors of various stage, histological grade and estrogen receptor (ER) status was used to construct a HER2-derived prognostic predictor that was further evaluated in several large independent breast cancer data sets. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL5345

58 Samples

Download data: GPR, TXT

(Submitter supplied) In this study gene expression profiles for 307 cases of advanced bladder cancers were compared to molecular phenotype at the tumor cell level. TUR-B tissue for RNA extraction was macrodissected from the close vicinity of the tissue sampled for immunohistochemistry to ensure high-quality sampling and to minimize the effects of intra-tumor heterogeneity. Despite excellent agreement between gene expression values and IHC-score at the single marker level, broad differences emerge when samples are clustered at the global mRNA versus tumor cell (IHC) levels. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL6244

307 Samples

Download data: CEL, TXT

(Submitter supplied) It is unclear how urothelial carcinoma of the urinary bladder change, genetically and phenotypically, as patients progress from recurrent non muscle-invasive (NMI) to muscle-invasive (MI) disease or disease that require radical cystectomy. This data set contains gene expression data from 200 samples in a longitudinal study of such patients. Overlap with previously GEO-published cohorts from our lab is described in the metadata.

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL6244

200 Samples

Download data: CEL, TXT

(Submitter supplied) This series represents expression profiles of 34 non-seminoma germ cell tumors (NSGCTs) from patients who received cisplatin based chemotherarpy for treatment of their disease for whom full clinical follow-up information was available. These specimens were used as a validation set to test outcome prediction models using a subset of previously profiled GCT specimens (see GEO accession #GSE3218). Keywords: Disease state analysis (good vs. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platforms:

GPL97 GPL96

68 Samples

Download data: CEL, EXP