Abstract:
:Recently, cancer has been characterized as a heterogeneous disease composed of many different subtypes. Early diagnosis of cancer subtypes is an important study of cancer research, which can be of tremendous help to patients after treatment. In this paper, we first extract a novel dataset, which contains gene expression, miRNA expression, and isoform expression of five cancers from The Cancer Genome Atlas (TCGA). Next, to avoid the effect of noise existing in 60, 483 genes, we select a small number of genes by using LASSO that employs gene expression and survival time of patients. Then, we construct one similarity kernel for each expression data by using Chebyshev distance. And also, We used SKF to fused the three similarity matrix composed of gene, Iso, and miRNA, and finally clustered the fused similarity matrix with spectral clustering. In the experimental results, our method has better P-value in the Cox model than other methods on 10 cancer data from Jiang Dataset and Novel Dataset. We have drawn different survival curves for different cancers and found that some genes play a key role in cancer. For breast cancer, we find out that HSPA2A, RNASE1, CLIC6, and IFITM1 are highly expressed in some specific groups. For lung cancer, we ensure that C4BPA, SESN3, and IRS1 are highly expressed in some specific groups. The code and all supporting data files are available from https://github.com/guofei-tju/Uncovering-Cancer-Subtypes-via-LASSO.
journal_name
Front Genetjournal_title
Frontiers in geneticsauthors
Li S,Jiang L,Tang J,Gao N,Guo Fdoi
10.3389/fgene.2020.00979subject
Has Abstractpub_date
2020-09-10 00:00:00pages
979issn
1664-8021journal_volume
11pub_type
杂志文章abstract::Circadian rhythms produce a biological measure of the time of day. In plants, circadian regulation forms an essential adaptation to the fluctuating environment. Most of our knowledge of the molecular aspects of circadian regulation in plants is derived from laboratory experiments that are performed under controlled co...
journal_title:Frontiers in genetics
pub_type: 杂志文章,评审
doi:10.3389/fgene.2019.01239
更新日期:2019-11-29 00:00:00
abstract::Cytotoxicity assays of immortalized lymphoblastoid cell lines (LCLs) represent a promising new in vitro approach in pharmacogenomics research. However, previous studies employing LCLs in gene mapping have used simple association methods, which may not adequately capture the true differences in non-linear response prof...
journal_title:Frontiers in genetics
pub_type: 杂志文章
doi:10.3389/fgene.2011.00086
更新日期:2011-12-14 00:00:00
abstract::One of the challenges in the analysis of large data sets, particularly in a population-based setting, is the ability to perform comparisons across projects. This has to be done in such a way that the integrity of each individual project is maintained, while ensuring that the data are comparable across projects. These ...
journal_title:Frontiers in genetics
pub_type: 杂志文章
doi:10.3389/fgene.2014.00325
更新日期:2014-09-18 00:00:00
abstract::The aging of the population represents one of the largest healthcare challenges facing the world today. The available scientific evidence shows that interventions are available now that can target fundamental "aging" processes or pathways. Sufficient economic evidence is available to argue convincingly that this appro...
journal_title:Frontiers in genetics
pub_type: 杂志文章
doi:10.3389/fgene.2015.00171
更新日期:2015-07-14 00:00:00
abstract::Human exposure to mercury is a serious problem of public health in Amazon. As in other vulnerable populations throughout the world, Amazonian riverine populations are chronically exposed to this metal and some symptoms of mercury intoxication were already detected in these populations. However, studies on the genetic ...
journal_title:Frontiers in genetics
pub_type: 杂志文章
doi:10.3389/fgene.2018.00285
更新日期:2018-07-27 00:00:00
abstract::Through linkage and candidate gene screening, many breast cancer (BC) predisposition genes have been identified in the past 20 years. However, the majority of genetic risks that contribute to familial BC remains undetermined. In this study, we revisited whole exome sequencing datasets from non-BRCA1/2 familial BC pati...
journal_title:Frontiers in genetics
pub_type: 杂志文章
doi:10.3389/fgene.2019.00527
更新日期:2019-06-04 00:00:00
abstract::Known as the "fifth RNA nucleotide", pseudouridine (Ψ or psi) is the first-discovered and most abundant RNA modification occurring at the Uridine site, and it plays a prominent role in a number of biological processes. Thousands of Ψ sites have been identified within different biological contexts thanks to the advance...
journal_title:Frontiers in genetics
pub_type: 杂志文章
doi:10.3389/fgene.2020.00088
更新日期:2020-03-12 00:00:00
abstract::Integration of scientific knowledge into negotiations of the Multilateral Environment Agreements (MEAs) is crucial to effective implementation of those MEAs by ensuring uniformity in their terminology. Recent innovations in the field of biotechnology provoked a discussion over "Digital Sequence Information" (DSI) in f...
journal_title:Frontiers in genetics
pub_type: 杂志文章
doi:10.3389/fgene.2020.01028
更新日期:2020-09-16 00:00:00
abstract::Mitogen-activated protein kinases (MAPKs) play a regulatory role and influence various biological activities, such as cell proliferation, differentiation, and survival. Our group has demonstrated through functional studies that Schistosoma mansoni c-Jun N-terminal kinase (SmJNK) MAPK is involved in the parasite's deve...
journal_title:Frontiers in genetics
pub_type: 杂志文章
doi:10.3389/fgene.2019.01036
更新日期:2019-10-18 00:00:00
abstract::Rheumatoid arthritis (RA) is a complex disease triggered by the interaction between genetics and the environment, especially through the shared epitope (SE) and cell surface calreticulin (CSC) theory. However, the available evidence shows that genetic diversity and environmental exposure cannot explain all the clinica...
journal_title:Frontiers in genetics
pub_type: 杂志文章,评审
doi:10.3389/fgene.2020.00811
更新日期:2020-08-04 00:00:00
abstract::It is time to review all the available data and find the distinctive characteristics of actin that make it such an important cell molecule. The presented double-stranded organization of filamentous actin cannot explain the strong polymorphism of actin fibrils. In this work, we performed bioinformatics analysis of a se...
journal_title:Frontiers in genetics
pub_type: 杂志文章
doi:10.3389/fgene.2020.617763
更新日期:2020-12-10 00:00:00
abstract::Tumorigenesis is a multi-step process, involving the acquisition of multiple oncogenic mutations that transform cells, resulting in systemic dysregulation that enables proliferation, invasion, and other cancer hallmarks. The goal of precision medicine is to identify therapeutically-actionable mutations from large-scal...
journal_title:Frontiers in genetics
pub_type: 杂志文章
doi:10.3389/fgene.2015.00341
更新日期:2015-12-23 00:00:00
abstract::An increasing number of studies have shown that long intergenic non-coding RNAs (lincRNAs) are a very important class of non-coding RNAs that plays a vital role in many biological processes. Adipose tissue is an important place for storing energy, but few studies on lincRNAs were related to pig subcutaneous fat develo...
journal_title:Frontiers in genetics
pub_type: 杂志文章
doi:10.3389/fgene.2019.00160
更新日期:2019-03-04 00:00:00
abstract::In spite of the significant advancements in the treatment modalities, 30% of advanced stage ovarian cancer (OC) patients do not respond to the standard chemotherapeutic regimen and most of the responders finally relapse over time due to the escalation of multidrug resistance (MDR) Phenomenon. Our present study evaluat...
journal_title:Frontiers in genetics
pub_type: 杂志文章
doi:10.3389/fgene.2020.00516
更新日期:2020-05-26 00:00:00
abstract::Our ability to overcome the challenges behind metabolic disorders will require a detailed understanding of the regulation of responses to nutrition. The Creb3 transcription factor family appears to have a unique regulatory role that links cellular secretory capacity with development, nutritional state, infection, and ...
journal_title:Frontiers in genetics
pub_type: 杂志文章,评审
doi:10.3389/fgene.2019.00591
更新日期:2019-06-21 00:00:00
abstract::In this article, we make a theoretical and in silico study for uncovering and evaluating biomarkers in colon and rectal cancer (CRC) by the dynamic network biomarker (DNB) theory. We propose a strategy to employ the theoretical concept of UICC TNM classification in CRC. To reveal the critical transition of CRC, the DN...
journal_title:Frontiers in genetics
pub_type: 杂志文章
doi:10.3389/fgene.2020.555540
更新日期:2020-10-20 00:00:00
abstract::Liver is the main organ of lipid metabolism in chicken, especially for laying hens. To explore the molecular mechanism of lipid metabolism in chicken, five novel genes discovered in chicken liver tissue were systematically studied. Bioinformatic analysis was used to analyze the gene characteristics. The expression pat...
journal_title:Frontiers in genetics
pub_type: 杂志文章
doi:10.3389/fgene.2020.00271
更新日期:2020-03-31 00:00:00
abstract::Ubiquitination is a reversible protein modification broadly implicated in cellular functions. Signaling processes mediated by ubiquitin (ub) are crucial for the cellular response to DNA double-strand breaks (DSBs), one of the most dangerous types of DNA lesions. In particular, the DSB response critically relies on act...
journal_title:Frontiers in genetics
pub_type: 杂志文章,评审
doi:10.3389/fgene.2015.00282
更新日期:2015-09-08 00:00:00
abstract::The genetic resources available for the commercially important fish species Yellowtail kingfish (YTK) (Seriola lalandi) are relative sparse. To overcome this, we aimed (1) to develop a linkage map for this species, and (2) to identify markers/variants associated with economically important traits in kingfish (with an ...
journal_title:Frontiers in genetics
pub_type: 杂志文章
doi:10.3389/fgene.2018.00127
更新日期:2018-04-17 00:00:00
abstract::Complex traits are manifestations of intricate gene interaction networks. Evolution of complex traits revolves around the genetic variation in such networks. Genomics has increased our ability to investigate the complex gene interaction networks, and characterize the extent of genetic variation in these networks. Immu...
journal_title:Frontiers in genetics
pub_type: 杂志文章
doi:10.3389/fgene.2015.00222
更新日期:2015-06-19 00:00:00
abstract::Genotype imputation is a powerful tool for increasing statistical power in an association analysis. Meta-analysis of multiple study datasets also requires a substantial overlap of SNPs for a successful association analysis, which can be achieved by imputation. Quality of imputed datasets is largely dependent on the so...
journal_title:Frontiers in genetics
pub_type: 杂志文章
doi:10.3389/fgene.2019.00034
更新日期:2019-02-05 00:00:00
abstract::Cell secretion is an important physiological process that ensures smooth metabolic activities and tissue repair as well as growth and immunological functions in the body. Apocrine secretion occurs when the secretory process is accomplished with a partial loss of cell cytoplasm. The secretory materials are contained wi...
journal_title:Frontiers in genetics
pub_type: 杂志文章
doi:10.3389/fgene.2012.00306
更新日期:2013-01-02 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::Simple sequence repeats (SSRs) of short nucleotide motifs occur very frequently in the 5' untranslated coding region (5'-UTR) of genes and have been implicated in the regulation of gene expression. In this study, we identified an SSR with a variable number of CT repeats in the 5'-UTR of the Litopenaeus vannamei IRF (L...
journal_title:Frontiers in genetics
pub_type: 杂志文章
doi:10.3389/fgene.2019.01257
更新日期:2019-12-06 00:00:00
abstract::Seed dormancy and germination are important agronomic traits in wheat (Triticum aestivum L.) because they determine pre-harvest sprouting (PHS) resistance and thus affect grain production. These processes are regulated by Gibberellic Acid-Stimulated Regulator (GASR) genes. In this study, we identified 37 GASR genes in...
journal_title:Frontiers in genetics
pub_type: 杂志文章
doi:10.3389/fgene.2019.00980
更新日期:2019-10-18 00:00:00
abstract::Several cyanobacterial species are dominant primary producers in hot spring microbial mats. To date, hot spring cyanobacterial taxonomy, as well as the evolution of their genomic adaptations to high temperatures, are poorly understood, with genomic information currently available for only a few dominant genera, includ...
journal_title:Frontiers in genetics
pub_type: 杂志文章
doi:10.3389/fgene.2020.568223
更新日期:2020-11-05 00:00:00
abstract::Mutations in CHD7 have been shown to be a major cause of CHARGE syndrome, which presents many symptoms and features common to other syndromes making its diagnosis difficult. Next generation sequencing (NGS) of a panel of intellectual disability related genes was performed in an adult patient without molecular diagnosi...
journal_title:Frontiers in genetics
pub_type: 杂志文章
doi:10.3389/fgene.2018.00007
更新日期:2018-01-26 00:00:00
abstract::At least six different proteins of the spliceosome, including PRPF3, PRPF4, PRPF6, PRPF8, PRPF31, and SNRNP200, are mutated in autosomal dominant retinitis pigmentosa (adRP). These proteins have recently been shown to localize to the base of the connecting cilium of the retinal photoreceptor cells, elucidating this fo...
journal_title:Frontiers in genetics
pub_type: 杂志文章
doi:10.3389/fgene.2019.00248
更新日期:2019-03-22 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::The termites evolved eusociality and complex societies before the ants, but have been studied much less. The recent publication of the first two termite genomes provides a unique comparative opportunity, particularly because the sequenced termites represent opposite ends of the social complexity spectrum. Zootermopsis...
journal_title:Frontiers in genetics
pub_type: 杂志文章
doi:10.3389/fgene.2015.00009
更新日期:2015-03-04 00:00:00