Homo sapiens
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA223308 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:To understand the role of long non-coding RNAs and interaction with coding RNAs in bladder urothelial cell carcinoma (BUCC), we performed genome-wide screening long non-coding RNAs and coding RNAs expression on primary BUCC tissues and normal tissues using long non-coding RNA array (Agilent plateform (GPL13825). By comparing these two groups, significantly differentially expressed lncRNAs and coding RNAs were identified. We further identifed a subset of long noncoding RNAs and their correlation with neighboring coding genes using bioinformatic tools. This analysis provides foundamental understaning of transcriptomic landscape changing during bladder carcinogenesis. 12 BUCC primary tumors and 3 normal tissues were used for long noncoding RNA array experiments which including long non-coding RNAs and coding RNAs. The differential expression of subset of long noncoding RNAs and their interaction with coding RNAs in BUCC compared with normal tissue will be identified with comtational analysis.
2013-12-31 | E-GEOD-51493 | biostudies-arrayexpress
Project description:To understand the role of long non-coding RNAs and interaction with coding RNAs in bladder urothelial cell carcinoma (BUCC), we performed genome-wide screening long non-coding RNAs and coding RNAs expression on primary BUCC tissues and normal tissues using long non-coding RNA array (Agilent plateform (GPL13825). By comparing these two groups, significantly differentially expressed lncRNAs and coding RNAs were identified. We further identifed a subset of long noncoding RNAs and their correlation with neighboring coding genes using bioinformatic tools. This analysis provides foundamental understaning of transcriptomic landscape changing during bladder carcinogenesis.
2013-12-31 | GSE51493 | GEO
Project description:In order to understand the role of long noncoding RNAs (lncRNAs) and their interaction with coding RNAs in esophageal sqaumous cell cancer (ESCC), we performed genome-wide screening of the expression of lncRNAs and coding RNAs from primary ESCC tissue and adjacent normal tissue using Agilent SurePrint G3 Human GE 8x60K Microarray. By comparing ESCC tissues and matched normal tissues, differentially expressed lncRNAs and coding RNAs were identified and confirmed with PCR and other independent studies. We further identified a subset of co-located and co-expressed lncRNAs and coding RNAs using bioinformatic tools and the analysis suggested that a subset of lncRNAs may influence nearby genes involved in the genesis of ESCC. Four pairs of ESCC primary tumors and adjacent normal tissues were used for genome-scale microarray experiments, which included long noncoding RNAs and coding RNAs. Selected lncRNAs expressed in the experiment were validated on independent matched-pair samples with PCR method.
2013-03-21 | E-GEOD-45350 | biostudies-arrayexpress
Project description:Urine cytologic examination is a widely used primary pathologic screening test in the diagnosis of bladder urothelial carcinoma (BLCA), however the low diagnostic accuracy remains challenging. We conducted high-throughput proteome on ten pairs of BLCA and benign urothelial lesion (BUL) to identify a supportive proteomic marker as an ancillary test in liquid based cytology (LBC).
2018-07-04 | PXD006805 | Pride
Project description:Background: MicroRNAs (miRNAs) are small non-coding RNAs that regulate gene expression. Their abilyty to affect multiple gene pathways by targeting to various mRNAs makes them to an interesting class of regulators. The interplay between miRNA and mRNA has been proposed as an important process in cancer development and progression. In this study, we analyzed miRNA -mRNA interactions in bladder urothelial carcinoma. Methodology/Principal Findings: We have developed a new algorithm which is capable of identifying altered miRNA-mRNA regulation between tissues samples without preexisting stratification of groups. Microarray expression profiling of both miRNA and mRNA from the same sample were performed using a collective of 24 urothelial carcinoma and normal bladder tissue samples. Using our approach, normal and tumor tissue samples as well as different stages of tumor progression were successfully stratified. Also, we were able to analyzed individual miRNA-mRNA interactions from each patient, focusing on different miRNA families. Conclusions: Just recently, the need for tools that allow an integrative analysis of microRNA and mRNA expression data has been addressed. With this study, we provide an algorithm that considers the special nature of miRNA induced regulation and shows good specificities and sensitivities when applied to bladder cancer expression data. mRNA and microRNA expression data were analyzed together to identify bladder cancer specific micoRNA-mRNA interaction
2013-08-24 | E-GEOD-40355 | biostudies-arrayexpress
Project description:Purpose: The goals of this study are to compare 1. The transcription profile in KDM6A wildtype and KDM6A mutated urothelial bladder carcinoma. 2. The transcriptional changes in KDM6A mutated urothelial bladder carcinoma upon EZH2 inhibitor treatment.
2017-03-01 | GSE92723 | GEO
Project description:Expression profiling by arrays Urothelial carcinoma (UC) can arise at any location along the urothelial tract, including the urethra, bladder, ureter or renal pelvis. Although tumors arising in these various locations demonstrate similar morphology, it is unclear whether the gene expression profiles are similar in the upper tract (ureter and renal pelvis) or in the lower tract (bladder and urethra) carcinomas, especially given their different embryologic origins. As differences may facilitate potentially different screening and treatment modalities, we sought to examine the relationship between urothelial carcinoma of the renal pelvis (rUC) and urothelial carcinoma of the bladder (bUC). Fresh tumor tissue was collected from patients with bUC (n=10) and benign mucosa from the bladder (n=7) was collected from individuals undergoing resection for non-UC conditions for comparison. Gene expression profiles from these samples were determined using high-throughput Affymetrix gene expression microarray chips. Bioinformatic approaches were used to compare gene expression profiles of these samples and those of rUC (n= 14) and normal kidney (n=14) that were mostly used in our previous publication. Using unsupervised analytic approaches, rUC and bUC were indistinguishable. When supervised analytic approach was used, a very small number of potentially differentially expressed genes was identified; these differences were most likely to be limited to a single pathway - the chloride ion binding activity pathway -which was more frequently activated in rUC than in bUC. We found that the gene expression profiles of UCs from the upper and lower tract were extremely similar, suggesting that similar pathogenic mechanisms likely function in the development of these tumors. The differential expression of genes in the identified pathway may represent a potential new avenue for detection of upper tract tumors. Tissue samples with urothelial cell carcinoma from lower tract (bladder) as well as normal references were collected and the gene expression profiles were compared with gene expression profiles of samples in our previously published data set . No technical replicates.
2010-12-31 | E-GEOD-24152 | biostudies-arrayexpress
Project description:In order to understand the role of long noncoding RNAs (lncRNAs) and their interaction with coding RNAs in esophageal sqaumous cell cancer (ESCC), we performed genome-wide screening of the expression of lncRNAs and coding RNAs from primary ESCC tissue and adjacent normal tissue using Agilent SurePrint G3 Human GE 8x60K Microarray. By comparing ESCC tissues and matched normal tissues, differentially expressed lncRNAs and coding RNAs were identified and confirmed with PCR and other independent studies. We further identified a subset of co-located and co-expressed lncRNAs and coding RNAs using bioinformatic tools and the analysis suggested that a subset of lncRNAs may influence nearby genes involved in the genesis of ESCC.
2013-03-21 | GSE45350 | GEO
Project description:Inverted papilloma (IP) of the urinary bladder is a relatively rare neoplasm that accounts for < 1% of bladder tumor. Although generally accepted as a benign lesion, occasional reports of IP admixed with urothelial carcinoma (UC) or IP patients with synchronous or metachronous UC have raised a concern in the biologic potential of IP.
2022-05-20 | PXD027602 | Pride