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We began analyzing https://genomebiology.biomedcentral.com/articles/10.1186/s13059-014-0429-8, but it redirected us to https://genomebiology.biomedcentral.com/articles/10.1186/s13059-014-0429-8. The analysis below is for the second page.

Title[redir]:
Transcriptome sequencing reveals altered long intergenic non-coding RNAs in lung cancer | Genome Biology | Full Text
Description:
Background Long intergenic non-coding RNAs (lncRNAs) represent an emerging and under-studied class of transcripts that play a significant role in human cancers. Due to the tissue- and cancer-specific expression patterns observed for many lncRNAs it is believed that they could serve as ideal diagnostic biomarkers. However, until each tumor type is examined more closely, many of these lncRNAs will remain elusive. Results Here we characterize the lncRNA landscape in lung cancer using publicly available transcriptome sequencing data from a cohort of 567 adenocarcinoma and squamous cell carcinoma tumors. Through this compendium we identify over 3,000 unannotated intergenic transcripts representing novel lncRNAs. Through comparison of both adenocarcinoma and squamous cell carcinomas with matched controls we discover 111 differentially expressed lncRNAs, which we term lung cancer-associated lncRNAs (LCALs). A pan-cancer analysis of 324 additional tumor and adjacent normal pairs enable us to identify a subset of lncRNAs that display enriched expression specific to lung cancer as well as a subset that appear to be broadly deregulated across human cancers. Integration of exome sequencing data reveals that expression levels of many LCALs have significant associations with the mutational status of key oncogenes in lung cancer. Functional validation, using both knockdown and overexpression, shows that the most differentially expressed lncRNA, LCAL1, plays a role in cellular proliferation. Conclusions Our systematic characterization of publicly available transcriptome data provides the foundation for future efforts to understand the role of LCALs, develop novel biomarkers, and improve knowledge of lung tumor biology.

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Keywords {πŸ”}

lncrnas, cancer, lung, pubmed, lcal, cell, expression, article, figure, lcals, google, scholar, additional, expressed, transcripts, cas, human, file, central, noncoding, carcinoma, tumor, differentially, rna, gene, lncrna, normal, adenocarcinoma, genes, transcript, data, cells, squamous, genome, cohort, tumors, luad, nature, long, rnas, cancers, proteincoding, cohorts, analysis, altered, levels, lusc, sirna, unannotated, rnaseq,

Topics {βœ’οΈ}

org/packages/devel/bioc/html/sigfuge /partners_programs/programs/developer/tools/powertools h3k4me3 histone modification h3k4me3 histone modifications death-inducing signaling complex quantitative real-time pcr beas-2b overexpressing clones coding-potential assessment tool annotating high-confidence candidates cellular flice-inhibitory protein protein-coding gene annotations stem cell-specific class raw cel files scrambled-matched %gc oligo normal beas-2b cells linc-ubc1 physically associates purified rna-seq data beas-2b cells seeded observed rna-seq coverage authors scientific editing squamous cell carcinoma tissue-specific expression profiles pdf 3 mb privacy choices/manage cookies observing h3k4me3 marks designed gene-specific primers affymetrix exon arrays comprehensive probe coverage pre-malignant human tissues bmc comprehensive molecular characterization including single-exon transcripts chromatin signature reveals squamous cell carcinomas existing gene annotation beas-2b control protein-coding genes annotated lung cancer research ucsc browser tracks cabili mn gene expression omnibus pan-cancer analysis decreased cell growth cancer cell lines rna-seq data human body map beas-2b cells extensive studies characterizing gene racer kit transcriptome sequencing data

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External Links {πŸ”—}(350)

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