We are analyzing https://link.springer.com/article/10.1186/s13059-014-0405-3.

Title:
MBASED: allele-specific expression detection in cancer tissues and cell lines | Genome Biology
Description:
Allele-specific gene expression, ASE, is an important aspect of gene regulation. We developed a novel method MBASED, meta-analysis based allele-specific expression detection for ASE detection using RNA-seq data that aggregates information across multiple single nucleotide variation loci to obtain a gene-level measure of ASE, even when prior phasing information is unavailable. MBASED is capable of one-sample and two-sample analyses and performs well in simulations. We applied MBASED to a panel of cancer cell lines and paired tumor-normal tissue samples, and observed extensive ASE in cancer, but not normal, samples, mainly driven by genomic copy number alterations.
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Keywords {🔍}

ase, genes, samples, mbased, gene, snv, data, snvs, pubmed, cancer, tumor, analysis, allele, expression, article, additional, file, normal, observed, haplotype, maf, google, scholar, sample, allelic, haplotypes, methods, hap, individual, instances, true, information, onesample, cell, rnaseq, counts, number, figure, twosample, tissue, found, cas, read, major, genome, lines, sequencing, estimate, pvalue, tested,

Topics {✒️}

anti-conservative nominal p-values nominal meta-analysis-derived p genome-wide allele-specific analysis excessive inter-loci variability high-throughput transcriptome resequencing multi-mapping rna-seq reads pre-existing allelic bias article download pdf detecting allele-specific expression read count-generating probabilities align reference-supporting read investigating allele-specific expression allele-specific expression assays allele-specific expression detection triple-negative breast cancer variance-stabilizing freeman-tukey allele-specific gene expression pro-apoptotic factor exhibits tumor-specific ase high rna-seq coverage isoform-specific ase occurring isoform-specific ase playing meta-analytic approach adopted paired tumor-normal lung tumor-derived 'minor' haplotype rna-seq data sets assigning snv-level alleles higher rna-seq coverage highest rna-seq coverage matched rna-seq sample tumor-normal allelic imbalance inter-loci variability post-transcriptional suppression resolve snv-level information variant effect predictor variance-stabilizing transformation prior population genetics-based approaches cancer-related genes myh9 true tumor-specific ase na12878 rna-seq data inter-snv variability cancer-specific ase point full size image recurrent normal-specific ase tumor suppressor eaf2[29] small reported p-values recurrent cancer-specific ase paired tissue-normal samples tissue-specific genomic imprinting show tumor-specific ase

Schema {🗺️}

WebPage:
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         headline:MBASED: allele-specific expression detection in cancer tissues and cell lines
         description:Allele-specific gene expression, ASE, is an important aspect of gene regulation. We developed a novel method MBASED, meta-analysis based allele-specific expression detection for ASE detection using RNA-seq data that aggregates information across multiple single nucleotide variation loci to obtain a gene-level measure of ASE, even when prior phasing information is unavailable. MBASED is capable of one-sample and two-sample analyses and performs well in simulations. We applied MBASED to a panel of cancer cell lines and paired tumor-normal tissue samples, and observed extensive ASE in cancer, but not normal, samples, mainly driven by genomic copy number alterations.
         datePublished:2014-08-07T00:00:00Z
         dateModified:2014-08-07T00:00:00Z
         pageStart:1
         pageEnd:21
         license:http://creativecommons.org/licenses/by/4.0/
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            Read Count
            Allelic Imbalance
            Tumor Tissue Sample
            Copy Number Loss
            Variant Effect Predictor
            Animal Genetics and Genomics
            Human Genetics
            Plant Genetics and Genomics
            Microbial Genetics and Genomics
            Bioinformatics
            Evolutionary Biology
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ScholarlyArticle:
      headline:MBASED: allele-specific expression detection in cancer tissues and cell lines
      description:Allele-specific gene expression, ASE, is an important aspect of gene regulation. We developed a novel method MBASED, meta-analysis based allele-specific expression detection for ASE detection using RNA-seq data that aggregates information across multiple single nucleotide variation loci to obtain a gene-level measure of ASE, even when prior phasing information is unavailable. MBASED is capable of one-sample and two-sample analyses and performs well in simulations. We applied MBASED to a panel of cancer cell lines and paired tumor-normal tissue samples, and observed extensive ASE in cancer, but not normal, samples, mainly driven by genomic copy number alterations.
      datePublished:2014-08-07T00:00:00Z
      dateModified:2014-08-07T00:00:00Z
      pageStart:1
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         Read Count
         Allelic Imbalance
         Tumor Tissue Sample
         Copy Number Loss
         Variant Effect Predictor
         Animal Genetics and Genomics
         Human Genetics
         Plant Genetics and Genomics
         Microbial Genetics and Genomics
         Bioinformatics
         Evolutionary Biology
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            address:
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               type:PostalAddress
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               type:PostalAddress
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      name:Colin Watanabe
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      name:Department of Bioinformatics and Computational Biology, Genentech Inc, South San Francisco, USA
      name:Department of Bioinformatics and Computational Biology, Genentech Inc, South San Francisco, USA
      name:Department of Bioinformatics and Computational Biology, Genentech Inc, South San Francisco, USA
      name:Department of Bioinformatics and Computational Biology, Genentech Inc, South San Francisco, USA

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