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Series GSE40914 Query DataSets for GSE40914
Status Public on Jan 21, 2014
Title Expression analysis and in silico characterization of intronic long noncoding RNAs in renal cell carcinoma: emerging functional associations
Organism Homo sapiens
Experiment type Non-coding RNA profiling by array
Expression profiling by array
Summary Intronic and intergenic long noncoding RNAs (lncRNAs) are emerging gene expression regulators. The molecular pathogenesis of renal cell carcinoma (RCC) is still poorly understood, and in particular, limited studies are available for intronic lncRNAs expressed in RCC. Microarray experiments were performed with two different custom-designed arrays enriched with probes for lncRNAs mapping to intronic genomic regions. Samples from 18 primary clear cell RCC tumors and 11 nontumor adjacent matched tissues were analyzed with 4k-probes microarrays. Oligoarrays with 44k-probes were used to interrogate 17 RCC samples (14 clear cell, 2 papillary, 1 chromophobe subtypes) split into four pools. Meta-analyses were performed by taking the genomic coordinates of the RCC-expressed lncRNAs, and cross-referencing them with microarray expression data from three additional human tissues (normal liver, prostate tumor and kidney nontumor samples), and with large-scale public data for epigenetic regulatory marks and for evolutionarily conserved sequences. A signature of 29 intronic lncRNAs differentially expressed between RCC and nontumor samples was obtained (false discovery rate (FDR) <5%). An additional signature of 26 intronic lncRNAs significantly correlated with the RCC five-year patient survival outcome was identified (FDR <5%, p-value ≤0.01). We identified 4303 intronic antisense lncRNAs expressed in RCC, of which 25% were cis correlated (r >|0.6|) with the expression of the mRNA in the same locus across three human tissues. Gene Ontology (GO) analysis of those loci pointed to ‘regulation of biological processes’ as the main enriched category. A module map analysis of all expressed protein-coding genes in RCC that had a significant (r ≥|0.8|) trans correlation with the 20% most abundant lncRNAs identified 35 relevant (p <0.05) GO sets. In addition, we determined that 60% of these lncRNAs are evolutionarily conserved. At the genomic loci containing the intronic RCC-expressed lncRNAs, a strong association (p <0.001) was found between their transcription start sites and genomic marks such as CpG islands and histones methylation and acetylation. Intronic antisense lncRNAs are widely expressed in RCC tumors. Some of them are significantly altered in RCC in comparison with nontumor samples. The majority of these lncRNAs is evolutionarily conserved and possibly modulated by epigenetic modifications. Our data suggest that these RCC lncRNAs may contribute to the complex network of regulatory RNAs playing a role in renal cell malignant transformation.
 
Overall design This SuperSeries is composed of the SubSeries listed below.
Refer to individual Series.

Data from the Fachel et al. Mol Cancer 2013 paper comes from two different microarray data sets. The ID_REF column of data table of each sample refers to the ID column of the 4K array (GPL3985) or of the 44K array (GPL4051). The gene name / gene ID are identified at the microarray platform description:
44K array: http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GPL4051 (used for expression set analysis)
4K array: http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GPL3985 (used for malignancy and survival set analysis)
 
Citation(s) 24238219
Submission date Sep 15, 2012
Last update date Apr 21, 2015
Contact name Angela A. Fachel
E-mail(s) [email protected]
Organization name Weill Cornell Medicine
Street address 1300 York Ave
City New York
State/province New York
ZIP/Postal code 10065
Country USA
 
Platforms (2)
GPL3985 IQUSP_Human_intronic_4k_v2.0
GPL4051 IQUSP_human_Intronic44k_v1.0
Samples (80)
GSM1004655 kidney_nontumor_patient3N_replica1 (malignancy set)
GSM1004656 kidney_nontumor_patient3N_replica2 (malignancy set)
GSM1004657 kidney_nontumor_patient5N_replica1 (malignancy set)
This SuperSeries is composed of the following SubSeries:
GSE40911 Expression analysis and in silico characterization of intronic long noncoding RNAs in renal cell carcinoma: emerging functional associations (RCC malignancy)
GSE40912 Expression analysis and in silico characterization of intronic long noncoding RNAs in renal cell carcinoma: emerging functional associations (RCC survival)
GSE40913 Expression analysis and in silico characterization of intronic long noncoding RNAs in renal cell carcinoma: emerging functional associations (RCC expression)
Relations
BioProject PRJNA175339

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE40914_RAW.tar 14.3 Mb (http)(custom) TAR (of TXT)

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