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Integrative genomic analyses reveal clinically relevant long noncoding RNAs in human cancer.

Despite growing appreciation of the importance of long noncoding RNAs (lncRNAs) in normal physiology and disease, our knowledge of cancer-related lncRNAs remains limited. By repurposing microarray probes, we constructed expression profiles of 10,207 lncRNA genes in approximately 1,300 tumors over four different cancer types. Through integrative analysis of the lncRNA expression profiles with clinical outcome and somatic copy-number alterations, we identified lncRNAs that are associated with cancer subtypes and clinical prognosis and predicted those that are potential drivers of cancer progression. We validated our predictions by experimentally confirming prostate cancer cell growth dependence on two newly identified lncRNAs. Our analysis provides a resource of clinically relevant lncRNAs for the development of lncRNA biomarkers and the identification of lncRNA therapeutic targets. It also demonstrates the power of integrating publically available genomic data sets and clinical information for discovering disease-associated lncRNAs.

Pubmed ID: 23728290 RIS Download

Mesh terms: Adenocarcinoma | Amino Acid Sequence | Biomarkers, Tumor | Cell Line, Tumor | Conserved Sequence | DNA Probes | DNA, Intergenic | Exons | Gene Dosage | Gene Expression Profiling | Gene Expression Regulation, Neoplastic | Genes, Overlapping | Humans | Introns | Kaplan-Meier Estimate | Male | Models, Molecular | Molecular Sequence Data | Molecular Targeted Therapy | Neoplasms | Oligonucleotide Array Sequence Analysis | Prognosis | Prostatic Neoplasms | Protein Conformation | RNA, Long Noncoding | RNA, Neoplasm | Sequence Alignment | Sequence Homology, Amino Acid

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This is a list of tools and resources that we have found mentioned in this publication.


Ensembl

Collection of genome databases for vertebrates and other eukaryotic species with DNA and protein sequence search capabilities. Used to automatically annotate the genome, integrate this annotation with other available biological data and make the data publicly available via the web. Ensembl tools include BLAST, BLAT, BioMart and the Variant Effect Predictor (VEP) for all supported species.

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UCSC Genome Browser

A collection of genomes which include reference sequences and working draft assemblies, as well as a variety of tools to explore these sequences. The Genome Browser zooms and scrolls over chromosomes, showing the work of annotators worldwide. The Gene Sorter shows expression, homology and other information on groups of genes that can be related in many ways. Blat quickly maps your sequence to the genome. The Table Browser provides access to the underlying database. VisiGene lets you browse through a large collection of in situ mouse and frog images to examine expression patterns. Genome Graphs allows you to upload and display genome-wide data sets. Also provided is a portal to the Encyclopedia of DNA Elements (ENCODE) and Neandertal projects.

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NetAffx

Affymetrix is a partially commercial resource that provides DNA Analysis Arrays, Expression Analysis Arrays, Gene Regulation Analysis, and Microarrays. It also provides reagents and assays, instruments, software, and services for a fee. Information is provided for Rats, Humans, and Mice.

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