We are analyzing https://link.springer.com/article/10.1186/gb-2013-14-9-r106.

Title:
The mutational landscape of chromatin regulatory factors across 4,623 tumor samples | Genome Biology
Description:
Background Chromatin regulatory factors are emerging as important genes in cancer development and are regarded as interesting candidates for novel targets for cancer treatment. However, we lack a comprehensive understanding of the role of this group of genes in different cancer types. Results We have analyzed 4,623 tumor samples from thirteen anatomical sites to determine which chromatin regulatory factors are candidate drivers in these different sites. We identify 34 chromatin regulatory factors that are likely drivers in tumors from at least one site, all with relatively low mutational frequency. We also analyze the relative importance of mutations in this group of genes for the development of tumorigenesis in each site, and in different tumor types from the same site. Conclusions We find that, although tumors from all thirteen sites show mutations in likely driver chromatin regulatory factors, these are more prevalent in tumors arising from certain tissues. With the exception of hematopoietic, liver and kidney tumors, as a median, the mutated factors are less than one fifth of all mutated drivers across all sites analyzed. We also show that mutations in two of these genes, MLL and EP300, correlate with broad expression changes across cancer cell lines, thus presenting at least one mechanism through which these mutations could contribute to tumorigenesis in cells of the corresponding tissues.
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Keywords {🔍}

pubmed, cancer, google, scholar, mutations, cas, crfs, genes, central, cell, gene, samples, tumor, tumors, chromatin, genome, figure, sites, analysis, driver, drivers, expression, histone, human, lines, file, table, regulatory, tumorigenesis, site, datasets, pams, nature, nat, factors, functional, additional, bias, somatic, data, anatomical, genet, mutational, obtained, network, research, mutated, mutation, sequencing, genomic,

Topics {✒️}

atp-dependent chromatin-remodeling complexes wilcoxon-mann–whitney test nuria lopez-bigas biomolecular interaction networks acute monocytic leukemia cell line-based platforms article download pdf cr rev oncol-hem array-based genomic resequencing article gonzalez-perez cell cycle-related modules small-cell lung cancer skin pre-malignant lesions candidate tumor-suppressor gene abel gonzalez-perez atypical teratoid/rhabdoid tumors trx/mll gene family fm-biased crf bearing article number r106 full size image identifies key genes direct structural remodeling chromatin regulatory factors acute myeloid leukemia jene-sanz left heat-map shows privacy choices/manage cookies cancer genetics cancer genome atlas z-score enrichment values clust-biased genes tend references papamichos-chronakis large gene sets endometrial carcinomas stand small sample size functional elements chronic lymphocytic leukemia full access tcga research network cancer cell lines broad gene sets swi/snf family comprehensive molecular characterization cancer data analysis chromatin remodelling factors cell lines originated chromatin remodeling genes high-resolution profiling noncoding regulatory mutations maintain cellular identity

Questions {❓}

You JS, Jones PA: Cancer genetics and epigenetics: two sides of the same coin?

Schema {🗺️}

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         description:Chromatin regulatory factors are emerging as important genes in cancer development and are regarded as interesting candidates for novel targets for cancer treatment. However, we lack a comprehensive understanding of the role of this group of genes in different cancer types. We have analyzed 4,623 tumor samples from thirteen anatomical sites to determine which chromatin regulatory factors are candidate drivers in these different sites. We identify 34 chromatin regulatory factors that are likely drivers in tumors from at least one site, all with relatively low mutational frequency. We also analyze the relative importance of mutations in this group of genes for the development of tumorigenesis in each site, and in different tumor types from the same site. We find that, although tumors from all thirteen sites show mutations in likely driver chromatin regulatory factors, these are more prevalent in tumors arising from certain tissues. With the exception of hematopoietic, liver and kidney tumors, as a median, the mutated factors are less than one fifth of all mutated drivers across all sites analyzed. We also show that mutations in two of these genes, MLL and EP300, correlate with broad expression changes across cancer cell lines, thus presenting at least one mechanism through which these mutations could contribute to tumorigenesis in cells of the corresponding tissues.
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         Anatomical Site
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         Plant Genetics and Genomics
         Microbial Genetics and Genomics
         Bioinformatics
         Evolutionary Biology
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