Abstract：
:mRNA-Seq is a precise and highly reproducible technique for measurement of transcripts levels and yields sequence information of a transcriptome at a single nucleotide base-level thus enabling us to determine splice junctions and alternative splicing events with high confidence. Often analysis of mRNA-Seq data does not attempt to quantify the expressions at isoform level. In this paper our objective would be use the mRNA-Seq data to infer expression at isoform level, where splicing patterns of a gene is assumed to be known. A Bayesian latent variable based modeling framework is proposed here, where the parameterization enables us to infer at various levels. For example, expression variability of an isoform across different conditions; the model parameterization also allows us to carry out two-sample comparisons, e.g., using a Bayesian t-test, in addition simple presence or absence of an isoform can also be estimated by the use of the latent variables present in the model. In this paper we would carry out inference on isoform expression under different normalization techniques, since it has been recently shown that one of the most prominent sources of variation in differential call using mRNA-Seq data is the normalization method used. The statistical framework is developed for multiple isoforms and easily extends to reads mapping to multiple genes. This could be achieved by slight conceptual modifications in definitions of what we consider as a gene and what as an exon. Additionally proposed framework can be extended by appropriate modeling of the design matrix to infer about yet unknown novel transcripts. However such attempts should be made judiciously since the input date used in the proposed model does not use reads from splice junctions.
journal_name
Front Genetjournal_title
Frontiers in geneticsauthors
Bhattacharjee M,Gupta R,Davuluri RVdoi
10.3389/fgene.2012.00239subject
Has Abstractpub_date
2012-11-27 00:00:00pages
239issn
1664-8021journal_volume
3pub_type
杂志文章abstract：:Most proteins are regulated by posttranslational modifications and changes in these modifications contribute to evolutionary changes as well as to human diseases. Phosphorylation of serines, threonines, and tyrosines are the most common modifications identified to date in eukaryotic proteomes. While the mode of action...
journal_title：Frontiers in genetics
pub_type： 杂志文章,评审
doi：10.3389/fgene.2014.00245
更新日期：2014-07-23 00:00:00
abstract：:MicroRNAs (miRNAs) are small RNAs repressing gene expression. They contribute to many physiological processes and pathologies. Consequently, strategies for manipulation of the miRNA pathway are of interest as they could provide tools for experimental or therapeutic interventions. One of such tools could be small chemi...
journal_title：Frontiers in genetics
pub_type： 杂志文章
doi：10.3389/fgene.2018.00045
更新日期：2018-02-27 00:00:00
abstract：:Trauma is a leading cause of morbidity and mortality. It is unclear why some trauma victims follow a complicated clinical course and die, while others, with apparently similar injury characteristics, do not. Interpatient genomic differences, in the form of single nucleotide polymorphisms (SNPs), have been associated p...
journal_title：Frontiers in genetics
pub_type： 杂志文章
doi：10.3389/fgene.2019.01115
更新日期：2019-11-08 00:00:00
abstract：:Genetically inherited defects in lipoprotein metabolism affect more than 10 million individuals around the globe with preponderance in some parts where consanguinity played a major role in establishing founder mutations. Mutations in four genes have been so far linked to the dominant and recessive form of the disease....
journal_title：Frontiers in genetics
pub_type： 杂志文章,评审
doi：10.3389/fgene.2020.572045
更新日期：2021-01-15 00:00:00
abstract：:There is a paradigm shift from the traditional focus on the "average" individual towards the definition and analysis of trait variation within individual life-history and among individuals in populations. This is a result of increasing availability of individual phenotypic data. The shift allows the use of genetic and...
journal_title：Frontiers in genetics
pub_type： 杂志文章
doi：10.3389/fgene.2019.00727
更新日期：2019-09-20 00:00:00
abstract：:The TempO-SeqTM platform allows for targeted transcriptomic analysis and is currently used by many groups to perform high-throughput gene expression analysis. Herein we performed a comparison of gene expression characteristics measured using 45 purified RNA samples from the livers of rats exposed to chemicals that fal...
journal_title：Frontiers in genetics
pub_type： 杂志文章
doi：10.3389/fgene.2018.00485
更新日期：2018-10-30 00:00:00
abstract：:The prophase of meiosis I ensures the correct segregation of chromosomes to each daughter cell. This includes the pairing, synapsis, and recombination of homologous chromosomes. A subset of chromosomal abnormalities, including translocation and inversion, disturbs these processes, resulting in the failure to complete ...
journal_title：Frontiers in genetics
pub_type： 杂志文章
doi：10.3389/fgene.2012.00112
更新日期：2012-06-18 00:00:00
abstract：:Determining the target genes that interact with drugs-drug-target interactions-plays an important role in drug discovery. Identification of drug-target interactions through biological experiments is time consuming, laborious, and costly. Therefore, using computational approaches to predict candidate targets is a good ...
journal_title：Frontiers in genetics
pub_type： 杂志文章
doi：10.3389/fgene.2019.00459
更新日期：2019-05-31 00:00:00
abstract：:Communication disorders have complex genetic origins, with constellations of relevant gene markers that vary across individuals. Some genetic variants are present in healthy individuals as well as those affected by developmental disorders. Growing evidence suggests that some variants may increase susceptibility to the...
journal_title：Frontiers in genetics
pub_type： 杂志文章
doi：10.3389/fgene.2015.00272
更新日期：2015-08-24 00:00:00
abstract：:The codon redundancy ("degeneracy") found in protein-coding regions of mRNA also prescribes Translational Pausing (TP). When coupled with the appropriate interpreters, multiple meanings and functions are programmed into the same sequence of configurable switch-settings. This additional layer of Ontological Prescriptiv...
journal_title：Frontiers in genetics
pub_type： 杂志文章,评审
doi：10.3389/fgene.2014.00140
更新日期：2014-05-20 00:00:00
abstract：:Leukocyte telomere length is believed to measure cellular aging in humans, and short leukocyte telomere length is associated with increased risks of late onset diseases, including cardiovascular disease, dementia, etc. Many studies have shown that leukocyte telomere length is a heritable trait, and several candidate g...
journal_title：Frontiers in genetics
pub_type： 杂志文章
doi：10.3389/fgene.2013.00310
更新日期：2014-01-17 00:00:00
abstract：:[This corrects the article on p. 23 in vol. 9, PMID: 29456554.]. ...
journal_title：Frontiers in genetics
pub_type： 杂志文章,已发布勘误
doi：10.3389/fgene.2018.00109
更新日期：2018-04-04 00:00:00
abstract：:Background: Limb-girdle muscular dystrophy (LGMD) is an increasingly heterogeneous category of inherited muscle diseases, mainly affecting the muscles of shoulder areas and the hip, segregating in both autosomal recessive and dominant manner. To-date, thirty-one loci have been identified for LGMD including seven autos...
journal_title：Frontiers in genetics
pub_type： 杂志文章
doi：10.3389/fgene.2018.00727
更新日期：2019-01-23 00:00:00
abstract：:In the last few years, the role of non-coding regulatory elements and their involvement in human disease have received great attention. Among the non-coding regulatory sequences, enhancers are particularly important for the proper establishment of cell type-specific gene-expression programs. Furthermore, the disruptio...
journal_title：Frontiers in genetics
pub_type： 杂志文章,评审
doi：10.3389/fgene.2020.00688
更新日期：2020-07-20 00:00:00
abstract：:Predicting how species interactions evolve requires that we understand the mechanistic basis of coevolution, and thus the functional genotype-by-genotype interactions (G × G) that drive reciprocal natural selection. Theory on host-parasite coevolution provides testable hypotheses for empiricists, but depends upon mode...
journal_title：Frontiers in genetics
pub_type： 杂志文章
doi：10.3389/fgene.2014.00077
更新日期：2014-04-11 00:00:00
abstract：:ncRNAs are key genes in many human diseases including cancer and viral infection, as well as providing critical functions in pathogenic organisms such as fungi, bacteria, viruses, and protists. Until now the identification and characterization of ncRNAs associated with disease has been slow or inaccurate requiring man...
journal_title：Frontiers in genetics
pub_type： 杂志文章
doi：10.3389/fgene.2011.00096
更新日期：2011-12-27 00:00:00
abstract：:Bovine viral diarrhea virus (BVDV) is an RNA virus that is often associated with respiratory disease in cattle. MicroRNAs have been proposed as indicators of exposure to respiratory pathogens. The objective of this study was to identify microRNAs in cattle that had been challenged with a non-cytopathic field strain of...
journal_title：Frontiers in genetics
pub_type： 杂志文章
doi：10.3389/fgene.2017.00091
更新日期：2017-06-28 00:00:00
abstract：:At the end of introns, the polypyrimidine tract (Py) is often close to the 3' AG in a consensus (Y)20NCAGgt in humans. Interestingly, we have found that they could also be separated by purine-rich elements including G tracts in thousands of human genes. These regulatory elements between the Py and 3' AG (REPA) mainly ...
journal_title：Frontiers in genetics
pub_type： 杂志文章
doi：10.3389/fgene.2018.00741
更新日期：2019-01-14 00:00:00
abstract：:Glioblastoma (GBM) is characterized by rapid and lethal infiltration of brain tissue, which is the primary cause of treatment failure and deaths for GBM. Therefore, understanding the molecular mechanisms of tumor cell invasion is crucial for the treatment of GBM. In this study, we dissected the single-cell RNA-seq dat...
journal_title：Frontiers in genetics
pub_type： 杂志文章
doi：10.3389/fgene.2020.633455
更新日期：2021-01-11 00:00:00
abstract：:Anther extrusion (AE) is the most important male floral trait for hybrid wheat seed production. AE is a complex quantitative trait that is difficult to phenotype reliably in field experiments not only due to high genotype-by-environment effects but also due to the short expression window in the field condition. In thi...
journal_title：Frontiers in genetics
pub_type： 杂志文章
doi：10.3389/fgene.2020.586687
更新日期：2020-12-08 00:00:00
abstract：:Clear cell renal cell carcinoma (ccRCC) is one of the most common histological subtypes of renal cancer, with a poor prognosis. Our study aimed to identify a biomarker that is significantly associated with ccRCC prognosis and novel immunotherapeutic targets, as well as some novel molecular drugs for ccRCC. Based on th...
journal_title：Frontiers in genetics
pub_type： 杂志文章
doi：10.3389/fgene.2020.00810
更新日期：2020-08-18 00:00:00
abstract：:Plants are subjected to strong fluctuations in light intensity in their natural growth environment, caused both by unpredictable changes due to weather conditions and movement of clouds and upper canopy leaves and predictable changes during day-night cycle. The mechanisms of long-term acclimation to fluctuating light ...
journal_title：Frontiers in genetics
pub_type： 杂志文章
doi：10.3389/fgene.2020.00154
更新日期：2020-03-05 00:00:00
abstract：:Pharmacogenomics is the study of how genes affect a person's response to drugs. Thus, understanding the effect of drug at the molecular level can be helpful in both drug discovery and personalized medicine. Over the years, transcriptome data upon drug treatment has been collected and several databases compiled before ...
journal_title：Frontiers in genetics
pub_type： 杂志文章
doi：10.3389/fgene.2020.564792
更新日期：2020-11-12 00:00:00
abstract：:In this study, the genetic diversity of 115 common bean germplasm resources collected from 27 counties in Chongqing over 3 years (2015-2017) was assessed. The results showed that the genetic diversity of the common bean germplasm resources was high, with an average diversity index of 1.447. The diversity of the qualit...
journal_title：Frontiers in genetics
pub_type： 杂志文章
doi：10.3389/fgene.2020.00697
更新日期：2020-07-08 00:00:00
abstract：:Cardiac myocytes (CMs) proliferate robustly during fetal life but withdraw permanently from the cell cycle soon after birth and undergo terminal differentiation. This cell cycle exit is associated with the upregulation of a host of adult cardiac-specific genes. The vast majority of adult CMs (ACMs) do not reenter cell...
journal_title：Frontiers in genetics
pub_type： 杂志文章,评审
doi：10.3389/fgene.2014.00375
更新日期：2014-11-04 00:00:00
abstract：:This study examined reasons for participation in a genetic study of risk for multiple sclerosis (MS). Our sample consisted of 101 patients diagnosed with MS who were approached about enrolling in the Multiple Sclerosis Genetic Susceptibility Study. Participants were predominantly Hispanic (80%), female (80%), and well...
journal_title：Frontiers in genetics
pub_type： 杂志文章
doi：10.3389/fgene.2020.00120
更新日期：2020-03-13 00:00:00
abstract：:Metastasis is a complex process that involved in various genetic and epigenetic alterations during the progression of breast cancer. Recent evidences have indicated that the mutation in the genome sequence may not be the key factor for increasing metastatic potential. Epigenetic changes were revealed to be important f...
journal_title：Frontiers in genetics
pub_type： 杂志文章,评审
doi：10.3389/fgene.2020.603552
更新日期：2020-10-29 00:00:00
abstract：:Our understanding of the biological role of N6-methyladenosine (m6A), a ubiquitous non-editing RNA modification, has increased greatly since 2011. More recently, work from several labs revealed that m6A methylation regulates several aspects of mRNA metabolism. The "writer" protein METTL3, known as MT-A70 in humans, Dm...
journal_title：Frontiers in genetics
pub_type： 杂志文章,评审
doi：10.3389/fgene.2019.00987
更新日期：2019-11-12 00:00:00
abstract：:Identifying driver genes that contribute to cancer progression from numerous passenger genes, although a central goal, is a major challenge. The protein-protein interaction network provides convenient and reasonable assistance for driver gene discovery. Random walk-based methods have been widely used to prioritize nod...
journal_title：Frontiers in genetics
pub_type： 杂志文章
doi：10.3389/fgene.2020.00377
更新日期：2020-04-28 00:00:00
abstract：:Long non-coding RNAs (lncRNAs) are an emerging class of RNA species that may play a critical regulatory role in gene expression. However, the association between lncRNAs and atrial fibrillation (AF) is still not fully understood. In this study, we used RNA sequencing data to identify and quantify the both protein codi...
journal_title：Frontiers in genetics
pub_type： 杂志文章
doi：10.3389/fgene.2019.00908
更新日期：2019-10-02 00:00:00
