Abstract:
BACKGROUND:Cancer is a complex disease driven by somatic genomic alterations (SGAs) that perturb signaling pathways and consequently cellular function. Identifying patterns of pathway perturbations would provide insights into common disease mechanisms shared among tumors, which is important for guiding treatment and predicting outcome. However, identifying perturbed pathways is challenging, because different tumors can have the same perturbed pathways that are perturbed by different SGAs. Here, we designed novel semantic representations that capture the functional similarity of distinct SGAs perturbing a common pathway in different tumors. Combining this representation with topic modeling would allow us to identify patterns in altered signaling pathways. RESULTS:We represented each gene with a vector of words describing its function, and we represented the SGAs of a tumor as a text document by pooling the words representing individual SGAs. We applied the nested hierarchical Dirichlet process (nHDP) model to a collection of tumors of 5 cancer types from TCGA. We identified topics (consisting of co-occurring words) representing the common functional themes of different SGAs. Tumors were clustered based on their topic associations, such that each cluster consists of tumors sharing common functional themes. The resulting clusters contained mixtures of cancer types, which indicates that different cancer types can share disease mechanisms. Survival analysis based on the clusters revealed significant differences in survival among the tumors of the same cancer type that were assigned to different clusters. CONCLUSIONS:The results indicate that applying topic modeling to semantic representations of tumors identifies patterns in the combinations of altered functional pathways in cancer.
journal_name
BMC Genomicsjournal_title
BMC genomicsauthors
Chen V,Paisley J,Lu Xdoi
10.1186/s12864-017-3494-zsubject
Has Abstractpub_date
2017-03-14 00:00:00pages
105issue
Suppl 2issn
1471-2164pii
10.1186/s12864-017-3494-zjournal_volume
18pub_type
杂志文章相关文献
BMC GENOMICS文献大全abstract:BACKGROUND:Sugarcane (Saccharum spp.) is predominantly an autopolyploid plant with a variable ploidy level, frequent aneuploidy and a large genome that hampers investigation of its organization. Genetic architecture studies are important for identifying genomic regions associated with traits of interest. However, due t...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-016-3383-x
更新日期:2017-01-11 00:00:00
abstract:BACKGROUND:Pseudogenes are ubiquitous genetic elements that derive from functional genes after mutational inactivation. Characterization of pseudogenes is important to understand genome dynamics and evolution, and its significance increases when several genomes of related organisms can be compared. Among yeasts, only t...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-11-260
更新日期:2010-04-22 00:00:00
abstract:BACKGROUND:BCG is the most widely used vaccine of all time and remains the only licensed vaccine for use against tuberculosis in humans. BCG also protects other species such as cattle against tuberculosis, but due to its incompatibility with current tuberculin testing regimens remains unlicensed. BCG's efficacy relates...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-019-5791-1
更新日期:2019-05-28 00:00:00
abstract:BACKGROUND:Insect mitochondrial genomes (mitogenomes) are the most extensively used genetic marker for evolutionary and population genetics studies of insects. The Pentatomoidea superfamily is economically important and the largest superfamily within Pentatomomorpha with over 7,000 species. To better understand the div...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-015-1679-x
更新日期:2015-06-16 00:00:00
abstract:BACKGROUND:Leishmania (L) are intracellular protozoan parasites that are able to survive and replicate within the harsh and potentially hostile phagolysosomal environment of mammalian mononuclear phagocytes. A complex interplay then takes place between the macrophage (MPhi) striving to eliminate the pathogen and the pa...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-9-238
更新日期:2008-05-21 00:00:00
abstract:BACKGROUND:Starches are the main storage polysaccharides in plants and are distributed widely throughout plants including seeds, roots, tubers, leaves, stems and so on. Currently, microscopic observation is one of the most important ways to investigate and analyze the structure of starches. The position, shape, and siz...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-11-S2-S13
更新日期:2010-11-02 00:00:00
abstract::We describe an emerging initiative - the 'Functional Annotation of All Salmonid Genomes' (FAASG), which will leverage the extensive trait diversity that has evolved since a whole genome duplication event in the salmonid ancestor, to develop an integrative understanding of the functional genomic basis of phenotypic var...
journal_title:BMC genomics
pub_type: 社论
doi:10.1186/s12864-017-3862-8
更新日期:2017-06-27 00:00:00
abstract:BACKGROUND:Aedes aegypti is the principle vector of many arboviruses, including dengue virus and Zika virus, which are transmitted when an infected female mosquito takes a blood meal in order to initiate vitellogenesis. During blood digestion, ~ 10 mM heme-iron is ingested into the midgut lumen. While heme acts as both...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-020-06981-5
更新日期:2020-08-31 00:00:00
abstract:BACKGROUND:Understanding how and why genetic variation is partitioned across geographic space is of fundamental importance to understanding the nature of biological species. How geographical isolation and local adaptation contribute to the formation of ecotypically differentiated groups of plants is just beginning to b...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-018-5179-7
更新日期:2018-11-01 00:00:00
abstract:BACKGROUND:In recent years, the number of human infections caused by opportunistic pathogens has increased dramatically. Plant rhizospheres are one of the most typical natural reservoirs for these pathogens but they also represent a great source for beneficial microbes with potential for biotechnological applications. ...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-15-482
更新日期:2014-06-18 00:00:00
abstract:BACKGROUND:Transcription factors (TFs) play essential roles during plant development and response to environmental stresses. However, the relationships among transcription factors, cis-acting elements and target gene expression under endo- and exogenous stimuli have not been systematically characterized. RESULTS:Here,...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-018-4469-4
更新日期:2018-05-09 00:00:00
abstract:BACKGROUND:During the evolution of mammalian sex chromosomes, the degeneration of Y-linked homologs has led to a dosage imbalance between X-linked and autosomal genes. The evolutionary resolution to such dosage imbalance, as hypothesized by Susumu Ohno fifty years ago, should be doubling the expression of X-linked gene...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-019-5432-8
更新日期:2019-01-14 00:00:00
abstract:BACKGROUND:Genome-wide association studies show that most human traits and diseases are caused by a combination of environmental and genetic causes, with each one of these having a relatively small effect. In contrast, most therapies based on macromolecules like antibodies, antisense oligonucleotides or peptides focus ...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-015-1727-6
更新日期:2015-07-18 00:00:00
abstract:BACKGROUND:Maternal effects contribute to adaptive significance for shaping various phenotypes of many traits. Potential implications of maternal effects are the cause of expression diversity, but these effects on mRNA expression and alternative splicing (AS) have not been fully elucidated in hybrid animals. RESULTS:T...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-020-06866-7
更新日期:2020-07-02 00:00:00
abstract:BACKGROUND:Taraxacum kok-saghyz R. (Tks) is a promising alternative species to Hevea brasiliensis for production of high quality natural rubber (NR). A comparative transcriptome analysis of plants with differential production of NR will contribute to elucidate which genes are involved in the synthesis, regulation and a...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-018-5287-4
更新日期:2018-12-04 00:00:00
abstract:BACKGROUND:Pseudomonas aeruginosa is an opportunistic pathogen with a high incidence of hospital infections that represents a threat to immune compromised patients. Genomic studies have shown that, in contrast to other pathogenic bacteria, clinical and environmental isolates do not show particular genomic differences. ...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-15-318
更新日期:2014-04-28 00:00:00
abstract:BACKGROUND:The mosquito Anopheles gambiae is a major vector of human malaria. Increasing evidence indicates that blood cells (hemocytes) comprise an essential arm of the mosquito innate immune response against both bacteria and malaria parasites. To further characterize the role of hemocytes in mosquito immunity, we un...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-10-257
更新日期:2009-06-05 00:00:00
abstract:BACKGROUND:Improving fiber quality is a major challenge in cotton breeding, since the molecular basis of fiber quality traits is poorly understood. Fine mapping and candidate gene prediction of quantitative trait loci (QTL) controlling cotton fiber quality traits can help to elucidate the molecular basis of fiber quali...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-016-2605-6
更新日期:2016-04-19 00:00:00
abstract:BACKGROUND:Adult neurogenesis, which is the continual production of new neurons in the mature brain, demonstrates the strikingly plastic nature of the nervous system. Adult neural stem cells and their neural precursors, collectively referred to as neural progenitor cells (NPCs), are present in the subgranular zone (SGZ...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-15-206
更新日期:2014-03-19 00:00:00
abstract:BACKGROUND:Prediction methods are increasingly used in biosciences to forecast diverse features and characteristics. Binary two-state classifiers are the most common applications. They are usually based on machine learning approaches. For the end user it is often problematic to evaluate the true performance and applica...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-13-S4-S2
更新日期:2012-06-18 00:00:00
abstract:BACKGROUND:Marek's disease (MD) is a lymphoproliferative disease in chickens caused by Marek's disease virus (MDV) and characterized by T cell lymphoma and infiltration of lymphoid cells into various organs such as liver, spleen, peripheral nerves and muscle. Resistance to MD and disease risk have long been thought to ...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-12-501
更新日期:2011-10-12 00:00:00
abstract:BACKGROUND:Determination of genome-wide DNA methylation is significant for both basic research and drug development. As a key epigenetic modification, this biochemical process can modulate gene expression to influence the cell differentiation which can possibly lead to cancer. Due to the involuted biochemical mechanism...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-019-5488-5
更新日期:2019-04-04 00:00:00
abstract:BACKGROUND:The Gram-negative bacterium Chlamydia pneumoniae (Cpn) is the leading intracellular human pathogen responsible for respiratory infections such as pneumonia and bronchitis. Basic and applied research in pathogen biology, especially the elaboration of new mechanism-based anti-pathogen strategies, target discov...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-13-632
更新日期:2012-11-16 00:00:00
abstract:BACKGROUND:Understanding the basis for volatile organic compound (VOC) biosynthesis and regulation is of great importance for the genetic improvement of fruit flavor. Lactones constitute an essential group of fatty acid-derived VOCs conferring peach-like aroma to a number of fruits including peach, plum, pineapple and ...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-15-218
更新日期:2014-04-17 00:00:00
abstract:BACKGROUND:The nutritional value of soybean oil is largely influenced by the proportions of unsaturated fatty acids (FAs), including oleic acid (OA, 18:1), linoleic acid (LLA, 18:2), and linolenic acid (LNA, 18:3). Genome-wide association (GWAS) studies along with gene expression studies in soybean [Glycine max (L.) Me...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-019-5449-z
更新日期:2019-01-21 00:00:00
abstract:BACKGROUND:Helicobacter pylori is presumed to be co-evolved with its human host and is a highly diverse gastric pathogen at genetic levels. Ancient origins of H. pylori in the New World are still debatable. It is not clear how different waves of human migrations in South America contributed to the evolution of strain d...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-7-191
更新日期:2006-07-27 00:00:00
abstract:BACKGROUND:Cottonseed is one of the most important raw materials for plant protein, oil and alternative biofuel for diesel engines. Understanding the complex genetic basis of cottonseed traits is requisite for achieving efficient genetic improvement of the traits. However, it is not yet clear about their genetic archit...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-018-4837-0
更新日期:2018-06-13 00:00:00
abstract:BACKGROUND:Abnormalities of pre-mRNA splicing are increasingly recognized as an important mechanism through which gene mutations cause disease. However, apart from the mutations in the donor and acceptor sites, the effects on splicing of other sequence variations are difficult to predict. Loosely defined exonic and int...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-7-243
更新日期:2006-09-22 00:00:00
abstract:BACKGROUND:Ashbya gossypii is a filamentous Saccharomycete used for the industrial production of riboflavin that has been recently explored as a host system for recombinant protein production. To gain insight into the protein secretory pathway of this biotechnologically relevant fungus, we undertook genome-wide analyse...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-15-1137
更新日期:2014-12-18 00:00:00
abstract:BACKGROUND:Starch and protein are two major components of polished rice, and the amylose and protein contents affect eating and cooking qualities (ECQs). In the present study, genome-wide association study with high-quality re-sequencing data was performed for 10 ECQs in a panel of 227 non-glutinous rice accessions and...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-016-3000-z
更新日期:2016-08-20 00:00:00