Identifying Discriminative Biological Function Features and Rules for Cancer-Related Long Non-coding RNAs.

Abstract:

:Cancer has been a major public health problem worldwide for many centuries. Cancer is a complex disease associated with accumulative genetic mutations, epigenetic aberrations, chromosomal instability, and expression alteration. Increasing lines of evidence suggest that many non-coding transcripts, which are termed as non-coding RNAs, have important regulatory roles in cancer. In particular, long non-coding RNAs (lncRNAs) play crucial roles in tumorigenesis. Cancer-related lncRNAs serve as oncogenic factors or tumor suppressors. Although many lncRNAs are identified as potential regulators in tumorigenesis by using traditional experimental methods, they are time consuming and expensive considering the tremendous amount of lncRNAs needed. Thus, effective and fast approaches to recognize tumor-related lncRNAs should be developed. The proposed approach should help us understand not only the mechanisms of lncRNAs that participate in tumorigenesis but also their satisfactory performance in distinguishing cancer-related lncRNAs. In this study, we utilized a decision tree (DT), a type of rule learning algorithm, to investigate cancer-related lncRNAs with functional annotation contents [gene ontology (GO) terms and KEGG pathways] of their co-expressed genes. Cancer-related and other lncRNAs encoded by the key enrichment features of GO and KEGG filtered by feature selection methods were used to build an informative DT, which further induced several decision rules. The rules provided not only a new tool for identifying cancer-related lncRNAs but also connected the lncRNAs and cancers with the combinations of GO terms. Results provided new directions for understanding cancer-related lncRNAs.

journal_name

Front Genet

journal_title

Frontiers in genetics

authors

Zhu L,Yang X,Zhu R,Yu L

doi

10.3389/fgene.2020.598773

subject

Has Abstract

pub_date

2020-12-16 00:00:00

pages

598773

issn

1664-8021

journal_volume

11

pub_type

杂志文章
  • Cigarette smoke exposure-associated alterations to non-coding RNA.

    abstract::Environmental exposures vary by timing, severity, and frequency and may have a number of deleterious effects throughout the life course. The period of in utero development, for example, is one of the most crucial stages of development during which adverse environmental exposures can both alter the growth and developme...

    journal_title:Frontiers in genetics

    pub_type: 杂志文章

    doi:10.3389/fgene.2012.00053

    authors: Maccani MA,Knopik VS

    更新日期:2012-04-09 00:00:00

  • Transcriptome Profiling of Pacu (Piaractus mesopotamicus) Challenged With Pathogenic Aeromonas hydrophila: Inference on Immune Gene Response.

    abstract::Pacu (Piaractus mesopotamicus) is a Neotropical fish of major importance for South American aquaculture. Septicemia caused by Aeromonas hydrophila bacteria is currently considered a substantial threat for pacu aquaculture that have provoked infectious disease outbreaks with high economic losses. The understanding of m...

    journal_title:Frontiers in genetics

    pub_type: 杂志文章

    doi:10.3389/fgene.2020.00604

    authors: Mastrochirico-Filho VA,Hata ME,Kuradomi RY,de Freitas MV,Ariede RB,Pinheiro DG,Robledo D,Houston R,Hashimoto DT

    更新日期:2020-06-09 00:00:00

  • Correlations between Risk Factors for Breast Cancer and Genetic Instability in Cancer Patients-A Clinical Perspective Study.

    abstract::Molecular epidemiological studies have identified several risk factors linking to the genes and external factors in the pathogenesis of breast cancer. In this sense, genetic instability caused by DNA damage and DNA repair inefficiencies are important molecular events for the diagnosis and prognosis of therapies. There...

    journal_title:Frontiers in genetics

    pub_type: 杂志文章

    doi:10.3389/fgene.2017.00236

    authors: Paz MFCJ,de Alencar MVOB,Gomes Junior AL,da Conceição Machado K,Islam MT,Ali ES,Shill MC,Ahmed MI,Uddin SJ,da Mata AMOF,de Carvalho RM,da Conceição Machado K,Sobral ALP,da Silva FCC,de Castro E Souza JM,Arcanjo DDR,Ferrei

    更新日期:2018-02-16 00:00:00

  • Identification of 13 Key Genes Correlated With Progression and Prognosis in Hepatocellular Carcinoma by Weighted Gene Co-expression Network Analysis.

    abstract::Hepatocellular carcinoma (HCC) remains hard to diagnose early and cure due to a lack of accurate biomarkers and effective treatments. Hence, it is necessary to explore the tumorigenesis and tumor progression of HCC to discover new biomarkers for clinical treatment. We performed weighted gene co-expression network anal...

    journal_title:Frontiers in genetics

    pub_type: 杂志文章

    doi:10.3389/fgene.2020.00153

    authors: Gu Y,Li J,Guo D,Chen B,Liu P,Xiao Y,Yang K,Liu Z,Liu Q

    更新日期:2020-02-28 00:00:00

  • Integrated Analysis of Large-Scale Omics Data Revealed Relationship Between Tissue Specificity and Evolutionary Dynamics of Small RNAs in Maize (Zea mays).

    abstract::The evolutionary dynamics and tissue specificity of protein-coding genes are well documented in plants. However, the evolutionary consequences of small RNAs (sRNAs) on tissue-specific functions remain poorly understood. Here, we performed integrated analysis of 195 deeply sequenced sRNA libraries of maize B73, represe...

    journal_title:Frontiers in genetics

    pub_type: 杂志文章

    doi:10.3389/fgene.2020.00051

    authors: Xu Y,Zhang T,Li Y,Miao Z

    更新日期:2020-02-11 00:00:00

  • Phenome-wide association study (PheWAS) in EMR-linked pediatric cohorts, genetically links PLCL1 to speech language development and IL5-IL13 to Eosinophilic Esophagitis.

    abstract:OBJECTIVE:We report the first pediatric specific Phenome-Wide Association Study (PheWAS) using electronic medical records (EMRs). Given the early success of PheWAS in adult populations, we investigated the feasibility of this approach in pediatric cohorts in which associations between a previously known genetic variant...

    journal_title:Frontiers in genetics

    pub_type: 杂志文章

    doi:10.3389/fgene.2014.00401

    authors: Namjou B,Marsolo K,Caroll RJ,Denny JC,Ritchie MD,Verma SS,Lingren T,Porollo A,Cobb BL,Perry C,Kottyan LC,Rothenberg ME,Thompson SD,Holm IA,Kohane IS,Harley JB

    更新日期:2014-11-18 00:00:00

  • The m6A Dynamics of Profilin in Neurogenesis.

    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

    authors: Rockwell AL,Hongay CF

    更新日期:2019-11-12 00:00:00

  • Now and next-generation sequencing techniques: future of sequence analysis using cloud computing.

    abstract::Advances in the field of sequencing techniques have resulted in the greatly accelerated production of huge sequence datasets. This presents immediate challenges in database maintenance at datacenters. It provides additional computational challenges in data mining and sequence analysis. Together these represent a signi...

    journal_title:Frontiers in genetics

    pub_type: 杂志文章

    doi:10.3389/fgene.2012.00280

    authors: Thakur RS,Bandopadhyay R,Chaudhary B,Chatterjee S

    更新日期:2012-12-11 00:00:00

  • A Quasi-Domesticate Relic Hybrid Population of Saccharomyces cerevisiae × S. paradoxus Adapted to Olive Brine.

    abstract::The adaptation of the yeast Saccharomyces cerevisiae to man-made environments for the fermentation of foodstuffs and beverages illustrates the scientific, social, and economic relevance of microbe domestication. Here we address a yet unexplored aspect of S. cerevisiae domestication, that of the emergence of lineages h...

    journal_title:Frontiers in genetics

    pub_type: 杂志文章

    doi:10.3389/fgene.2019.00449

    authors: Pontes A,Čadež N,Gonçalves P,Sampaio JP

    更新日期:2019-05-29 00:00:00

  • Combined QTL-Seq and Traditional Linkage Analysis to Identify Candidate Genes for Purple Skin of Radish Fleshy Taproots.

    abstract::Taproot skin color is a crucial visual and nutritional quality trait of radish, and purple skin is most attractive to consumers. However, the genetic mechanism underlying this character is unknown. Herein, F2 segregating populations were constructed to investigate radish genomic regions with purple skin genes. Segrega...

    journal_title:Frontiers in genetics

    pub_type: 杂志文章

    doi:10.3389/fgene.2019.00808

    authors: Liu T,Wang J,Wu C,Zhang Y,Zhang X,Li X,Wang H,Song J,Li X

    更新日期:2019-09-20 00:00:00

  • Distinguishing Glioblastoma Subtypes by Methylation Signatures.

    abstract::Glioblastoma, also called glioblastoma multiform (GBM), is the most aggressive cancer that initiates within the brain. GBM is produced in the central nervous system. Cancer cells in GBM are similar to stem cells. Several different schemes for GBM stratification exist. These schemes are based on intertumoral molecular ...

    journal_title:Frontiers in genetics

    pub_type: 杂志文章

    doi:10.3389/fgene.2020.604336

    authors: Zhang YH,Li Z,Zeng T,Pan X,Chen L,Liu D,Li H,Huang T,Cai YD

    更新日期:2020-11-24 00:00:00

  • A systematic experimental evaluation of microRNA markers of human bladder cancer.

    abstract:BACKGROUND:MicroRNAs (miRNAs) are a class of small RNAs that regulate gene expression. They are aberrantly expressed in many human cancers and are potential therapeutic targets and molecular biomarkers. METHODS:In this study, we for the first time validated the reported data on the entire set of published differential...

    journal_title:Frontiers in genetics

    pub_type: 杂志文章

    doi:10.3389/fgene.2013.00247

    authors: Zabolotneva AA,Zhavoronkov AA,Shegay PV,Gaifullin NM,Alekseev BY,Roumiantsev SA,Garazha AV,Kovalchuk O,Aravin A,Buzdin AA

    更新日期:2013-11-15 00:00:00

  • Experimental assessment of static and dynamic algorithms for gene regulation inference from time series expression data.

    abstract::Accurate inference of causal gene regulatory networks from gene expression data is an open bioinformatics challenge. Gene interactions are dynamical processes and consequently we can expect that the effect of any regulation action occurs after a certain temporal lag. However such lag is unknown a priori and temporal a...

    journal_title:Frontiers in genetics

    pub_type: 杂志文章

    doi:10.3389/fgene.2013.00303

    authors: Lopes M,Bontempi G

    更新日期:2013-12-24 00:00:00

  • Comprehensive Cis-Regulation Analysis of Genetic Variants in Human Lymphoblastoid Cell Lines.

    abstract::Genetic variants can influence the expression of mRNA and protein. Genetic regulatory loci such as expression quantitative trait loci (eQTLs) and protein quantitative trait loci (pQTLs) exist in several species. However, it remains unclear how human genetic variants regulate mRNA and protein expression. Here, we chara...

    journal_title:Frontiers in genetics

    pub_type: 杂志文章

    doi:10.3389/fgene.2019.00806

    authors: Wang Y,He B,Zhao Y,Reiter JL,Chen SX,Simpson E,Feng W,Liu Y

    更新日期:2019-09-10 00:00:00

  • Functional Analyses of a Novel Splice Variant in the CHD7 Gene, Found by Next Generation Sequencing, Confirm Its Pathogenicity in a Spanish Patient and Diagnose Him with CHARGE Syndrome.

    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

    authors: Villate O,Ibarluzea N,Fraile-Bethencourt E,Valenzuela A,Velasco EA,Grozeva D,Raymond FL,Botella MP,Tejada MI

    更新日期:2018-01-26 00:00:00

  • Connecting functional and statistical definitions of genotype by genotype interactions in coevolutionary studies.

    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

    authors: Heath KD,Nuismer SL

    更新日期:2014-04-11 00:00:00

  • Using The Cancer Genome Atlas as an Inquiry Tool in the Undergraduate Classroom.

    abstract::Undergraduate students in the biomedical sciences are often interested in future health-focused careers. This presents opportunities for instructors in genetics, molecular biology, and cancer biology to capture their attention using lab experiences built around clinically relevant data. As biomedical science in genera...

    journal_title:Frontiers in genetics

    pub_type: 杂志文章

    doi:10.3389/fgene.2020.573992

    authors: Hankey W,Zanghi N,Crow MM,Dow WH,Kratz A,Robinson AM,Robinson MR,Segarra VA

    更新日期:2020-12-16 00:00:00

  • Photoprotective Acclimation of the Arabidopsis thaliana Leaf Proteome to Fluctuating Light.

    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

    authors: Niedermaier S,Schneider T,Bahl MO,Matsubara S,Huesgen PF

    更新日期:2020-03-05 00:00:00

  • Modeling the Metabolism of Arabidopsis thaliana: Application of Network Decomposition and Network Reduction in the Context of Petri Nets.

    abstract::Motivation:Arabidopsis thaliana is a well-established model system for the analysis of the basic physiological and metabolic pathways of plants. Nevertheless, the system is not yet fully understood, although many mechanisms are described, and information for many processes exists. However, the combination and interpre...

    journal_title:Frontiers in genetics

    pub_type: 杂志文章

    doi:10.3389/fgene.2017.00085

    authors: Koch I,Nöthen J,Schleiff E

    更新日期:2017-06-30 00:00:00

  • Evolinc: A Tool for the Identification and Evolutionary Comparison of Long Intergenic Non-coding RNAs.

    abstract::Long intergenic non-coding RNAs (lincRNAs) are an abundant and functionally diverse class of eukaryotic transcripts. Reported lincRNA repertoires in mammals vary, but are commonly in the thousands to tens of thousands of transcripts, covering ~90% of the genome. In addition to elucidating function, there is particular...

    journal_title:Frontiers in genetics

    pub_type: 杂志文章

    doi:10.3389/fgene.2017.00052

    authors: Nelson ADL,Devisetty UK,Palos K,Haug-Baltzell AK,Lyons E,Beilstein MA

    更新日期:2017-05-09 00:00:00

  • Worming forward: amyotrophic lateral sclerosis toxicity mechanisms and genetic interactions in Caenorhabditis elegans.

    abstract::Neurodegenerative diseases share pathogenic mechanisms at the cellular level including protein misfolding, excitotoxicity and altered RNA homeostasis among others. Recent advances have shown that the genetic causes underlying these pathologies overlap, hinting at the existence of a genetic network for neurodegeneratio...

    journal_title:Frontiers in genetics

    pub_type: 杂志文章,评审

    doi:10.3389/fgene.2014.00085

    authors: Therrien M,Parker JA

    更新日期:2014-04-17 00:00:00

  • Microrefugia and species persistence in the Galápagos highlands: a 26,000-year paleoecological perspective.

    abstract::The Galápagos Islands are known to have experienced significant drought during the Quaternary. The loss of mesophytic upland habitats has been suggested to underlie the relatively lower endemism of upland compared with lowland plant assemblages. A fossil pollen record spanning the last 26,000 years from an upland bog ...

    journal_title:Frontiers in genetics

    pub_type: 杂志文章

    doi:10.3389/fgene.2013.00269

    authors: Collins AF,Bush MB,Sachs JP

    更新日期:2013-12-03 00:00:00

  • The functional consequences of relative substrate specificity in complex biochemical systems.

    abstract::A biochemical activity, that is, enzymatic reaction or molecular interaction, frequently involves a molecule, for example, an enzyme, capable of interacting with numerous substrates or partners. Specificity is a fundamental property of biochemical activities, and relative specificity refers to the situation whereby a ...

    journal_title:Frontiers in genetics

    pub_type: 杂志文章

    doi:10.3389/fgene.2011.00065

    authors: Zeng Y

    更新日期:2011-09-20 00:00:00

  • Concordance Study Between IBM Watson for Oncology and Real Clinical Practice for Cervical Cancer Patients in China: A Retrospective Analysis.

    abstract::Watson for Oncology (WFO) is a artificial intelligence clinical decision-support system with evidence-based treatment options for oncologists. WFO has been gradually used in China, but limited reports on whether WFO is suitable for Chinese patients. This study aims to investigate the concordance of treatment options b...

    journal_title:Frontiers in genetics

    pub_type: 杂志文章

    doi:10.3389/fgene.2020.00200

    authors: Zou FW,Tang YF,Liu CY,Ma JA,Hu CH

    更新日期:2020-03-24 00:00:00

  • Genome-Wide Association Study Uncovers Novel Genomic Regions Associated With Coleoptile Length in Hard Winter Wheat.

    abstract::Successful seedling establishment depends on the optimum depth of seed placement especially in drought-prone conditions, providing an opportunity to exploit subsoil water and increase winter survival in winter wheat. Coleoptile length is a key determinant for the appropriate depth at which seed can be sown. Thus, unde...

    journal_title:Frontiers in genetics

    pub_type: 杂志文章

    doi:10.3389/fgene.2019.01345

    authors: Sidhu JS,Singh D,Gill HS,Brar NK,Qiu Y,Halder J,Al Tameemi R,Turnipseed B,Sehgal SK

    更新日期:2020-02-05 00:00:00

  • Network Diffusion-Based Prioritization of Autism Risk Genes Identifies Significantly Connected Gene Modules.

    abstract::Autism spectrum disorder (ASD) is marked by a strong genetic heterogeneity, which is underlined by the low overlap between ASD risk gene lists proposed in different studies. In this context, molecular networks can be used to analyze the results of several genome-wide studies in order to underline those network regions...

    journal_title:Frontiers in genetics

    pub_type: 杂志文章

    doi:10.3389/fgene.2017.00129

    authors: Mosca E,Bersanelli M,Gnocchi M,Moscatelli M,Castellani G,Milanesi L,Mezzelani A

    更新日期:2017-09-25 00:00:00

  • Genome-Wide Association Mapping and Gene Expression Analyses Reveal Genetic Mechanisms of Disease Resistance Variations in Cynoglossus semilaevis.

    abstract::The sustainable development of aquaculture has been impeded by infectious diseases worldwide. However, the genomic architecture and the genetic basis underlying the disease resistance remain poorly understood, which severely hampers both the understanding of the evolution of fish disease resistance traits and the prev...

    journal_title:Frontiers in genetics

    pub_type: 杂志文章

    doi:10.3389/fgene.2019.01167

    authors: Zhou Q,Su Z,Li Y,Liu Y,Wang L,Lu S,Wang S,Gan T,Liu F,Zhou X,Wei M,Liu G,Chen S

    更新日期:2019-11-20 00:00:00

  • Cardiovascular extracellular microRNAs: emerging diagnostic markers and mechanisms of cell-to-cell RNA communication.

    abstract::Cardiovascular diseases are a leading cause of morbidity and mortality in Western societies. It is now well established that microRNAs (miRNAs) are determinant regulators in various medical conditions including cardiovascular diseases. The recent discovery that miRNAs, while associated with different carriers, can be ...

    journal_title:Frontiers in genetics

    pub_type: 杂志文章,评审

    doi:10.3389/fgene.2013.00214

    authors: Kinet V,Halkein J,Dirkx E,Windt LJ

    更新日期:2013-11-12 00:00:00

  • Leveraging ethnic group incidence variation to investigate genetic susceptibility to glioma: a novel candidate SNP approach.

    abstract:OBJECTIVES:Using a novel candidate SNP approach, we aimed to identify a possible genetic basis for the higher glioma incidence in Whites relative to East Asians and African-Americans. METHODS:  We hypothesized that genetic regions containing SNPs with extreme differences in allele frequencies across ethnicities are mo...

    journal_title:Frontiers in genetics

    pub_type: 杂志文章

    doi:10.3389/fgene.2012.00203

    authors: Jacobs DI,Walsh KM,Wrensch M,Wiencke J,Jenkins R,Houlston RS,Bondy M,Simon M,Sanson M,Gousias K,Schramm J,Labussière M,Di Stefano AL,Wichmann HE,Müller-Nurasyid M,Schreiber S,Franke A,Moebus S,Eisele L,Dewan AT,Du

    更新日期:2012-10-12 00:00:00

  • Estimation of Genomic Breed Composition for Purebred and Crossbred Animals Using Sparsely Regularized Admixture Models.

    abstract::A variety of statistical methods, such as admixture models, have been used to estimate genomic breed composition (GBC). These methods, however, tend to produce non-zero components to reference breeds that shared some genomic similarity with a test animal. These non-essential GBC components, in turn, offset the estimat...

    journal_title:Frontiers in genetics

    pub_type: 杂志文章

    doi:10.3389/fgene.2020.00576

    authors: Wang Y,Wu XL,Li Z,Bao Z,Tait RG Jr,Bauck S,Rosa GJM

    更新日期:2020-06-11 00:00:00