A comparative analysis of biomarker selection techniques.

Abstract:

:Feature selection has become the essential step in biomarker discovery from high-dimensional genomics data. It is recognized that different feature selection techniques may result in different set of biomarkers, that is, different groups of genes highly correlated to a given pathological condition, but few direct comparisons exist which quantify these differences in a systematic way. In this paper, we propose a general methodology for comparing the outcomes of different selection techniques in the context of biomarker discovery. The comparison is carried out along two dimensions: (i) measuring the similarity/dissimilarity of selected gene sets; (ii) evaluating the implications of these differences in terms of both predictive performance and stability of selected gene sets. As a case study, we considered three benchmarks deriving from DNA microarray experiments and conducted a comparative analysis among eight selection methods, representatives of different classes of feature selection techniques. Our results show that the proposed approach can provide useful insight about the pattern of agreement of biomarker discovery techniques.

journal_name

Biomed Res Int

authors

Dessì N,Pascariello E,Pes B

doi

10.1155/2013/387673

subject

Has Abstract

pub_date

2013-01-01 00:00:00

pages

387673

eissn

2314-6133

issn

2314-6141

journal_volume

2013

pub_type

杂志文章
  • Comparison of Arthroscopic Partial Meniscectomy to Physical Therapy following Degenerative Meniscus Tears: A Systematic Review and Meta-analysis.

    abstract:Objective:To compare the effectiveness of arthroscopic partial meniscectomy (APM) and physical therapy (PT) for degenerative meniscus tears. Method:We conducted a literature search through PubMed, Embase, the Cochrane Central Register of Controlled Trials, and ClinicalTrials.gov. Randomized controlled trials in adults...

    journal_title:BioMed research international

    pub_type: 杂志文章,meta分析

    doi:10.1155/2020/1709415

    authors: Li J,Zhu W,Gao X,Li X

    更新日期:2020-03-03 00:00:00

  • How Inflammation Impinges on NAFLD: A Role for Kupffer Cells.

    abstract::Nonalcoholic fatty liver disease (NAFLD) is rapidly becoming the most prevalent cause of liver disease worldwide and afflicts adults and children as currently associated with obesity and insulin resistance. Even though lately some advances have been made to elucidate the mechanism and causes of the disease much remain...

    journal_title:BioMed research international

    pub_type: 杂志文章,评审

    doi:10.1155/2015/984578

    authors: Duarte N,Coelho IC,Patarrão RS,Almeida JI,Penha-Gonçalves C,Macedo MP

    更新日期:2015-01-01 00:00:00

  • Application of stochastic automata networks for creation of continuous time Markov chain models of voltage gating of gap junction channels.

    abstract::The primary goal of this work was to study advantages of numerical methods used for the creation of continuous time Markov chain models (CTMC) of voltage gating of gap junction (GJ) channels composed of connexin protein. This task was accomplished by describing gating of GJs using the formalism of the stochastic autom...

    journal_title:BioMed research international

    pub_type: 杂志文章

    doi:10.1155/2015/936295

    authors: Snipas M,Pranevicius H,Pranevicius M,Pranevicius O,Paulauskas N,Bukauskas FF

    更新日期:2015-01-01 00:00:00

  • Odontogenic Abscess-Related Emergency Hospital Admissions: A Retrospective Data Analysis of 120 Children and Young People Requiring Surgical Drainage.

    abstract:Introduction:Even today, despite medical progress and intensive health education, odontogenic infections leading to surgical intervention and hospitalization are common in children and young people. The aim of this study was to give a detailed overview of clinical and economic data on children and young people treated ...

    journal_title:BioMed research international

    pub_type: 杂志文章

    doi:10.1155/2018/3504727

    authors: Doll C,Carl F,Neumann K,Voss JO,Hartwig S,Waluga R,Heiland M,Raguse JD

    更新日期:2018-08-26 00:00:00

  • The SDF-1α3'A genetic variation is correlated with susceptibility of asthma in Iranian patients.

    abstract:BACKGROUND AND AIM:Chemokine/receptor axis is a predominant actor of clinical disorders. They are key factors of pathogenesis of almost all clinical situations including asthma. Correspondingly, CXCL12 is involved in the immune responses. Therefore, this study was designed to explore the association between gene polymo...

    journal_title:BioMed research international

    pub_type: 杂志文章

    doi:10.1155/2013/759361

    authors: Rafatpanah H,Amin M,Ghasemshirazi M,Kazemiarababadi M,Khorramdelazad H,Abousaidi H,Shabani Z,Sayadi A,Hassanshahi G,Samadi J

    更新日期:2013-01-01 00:00:00

  • Preparation and Characterization of a Novel Polysaccharide-Iron(III) Complex in Auricularia auricula Potentially Used as an Iron Supplement.

    abstract::Iron deficiency anemia has been a widespread disease. As an effective and stable iron supplement, the physiochemical properties of the polysaccharide iron complex have been widely studied. In this study, we characterized a novel polysaccharide-iron(III) complex extracted in an edible fungal species Auricularia auricul...

    journal_title:BioMed research international

    pub_type: 杂志文章

    doi:10.1155/2019/6416941

    authors: Liu T,Liu T,Liu H,Fan H,Chen B,Wang D,Zhang Y,Sun F

    更新日期:2019-06-11 00:00:00

  • Diffusion tensor histogram analysis of pediatric diffuse intrinsic pontine glioma.

    abstract:PURPOSE:To evaluate tumor structure in children with diffuse intrinsic pontine glioma (DIPG) using histogram analyses of mean diffusivity (MD), determine potential treatment and corticosteroid-related effects on MD, and monitor changes in MD distributions over time. MATERIALS AND METHODS:DTI was performed on a 1.5T GE...

    journal_title:BioMed research international

    pub_type: 杂志文章

    doi:10.1155/2014/647356

    authors: Steffen-Smith EA,Sarlls JE,Pierpaoli C,Shih JH,Bent RS,Walker L,Warren KE

    更新日期:2014-01-01 00:00:00

  • Global Methylation and Hydroxymethylation in DNA from Blood and Saliva in Healthy Volunteers.

    abstract::Aims. We describe a liquid chromatography-tandem mass spectrometry (LC-MS/MS) method to quantify and compare simultaneously global methylation and hydroxymethylation in human DNA of different tissues. Materials and Methods. Blood and saliva DNA from fourteen volunteers was processed for epigenetic endpoints using LC-M...

    journal_title:BioMed research international

    pub_type: 杂志文章

    doi:10.1155/2015/845041

    authors: Godderis L,Schouteden C,Tabish A,Poels K,Hoet P,Baccarelli AA,Van Landuyt K

    更新日期:2015-01-01 00:00:00

  • Histological, histochemical, and protein changes after induced malocclusion by occlusion alteration of Wistar rats.

    abstract::Although disorders of the stomatognathic system are common, the mechanisms involved are unknown. Our objective was to study the changes in the masseter muscles after unilateral exodontia. Molar extraction was performed on Wistar rats (left side), and the animals were sacrificed after either 14 or 26 days. The masseter...

    journal_title:BioMed research international

    pub_type: 杂志文章

    doi:10.1155/2014/563463

    authors: Guerra Cde S,Carla Lara Pereira Y,Issa JP,Luiz KG,Guimarães EA,Gerlach RF,Iyomasa MM

    更新日期:2014-01-01 00:00:00

  • In Silico Integration Approach Reveals Key MicroRNAs and Their Target Genes in Follicular Thyroid Carcinoma.

    abstract::To better understand the molecular mechanism for the pathogenesis of follicular thyroid carcinoma (FTC), this study aimed at identifying key miRNAs and their target genes associated with FTC, as well as analyzing their interactions. Based on the gene microarray data GSE82208 and microRNA dataset GSE62054, the differen...

    journal_title:BioMed research international

    pub_type: 杂志文章

    doi:10.1155/2019/2725192

    authors: Hu S,Liao Y,Zheng J,Gou L,Regmi A,Zafar MI,Chen L

    更新日期:2019-03-28 00:00:00

  • Dissociation of Calcium Transients and Force Development following a Change in Stimulation Frequency in Isolated Rabbit Myocardium.

    abstract::As the heart transitions from one exercise intensity to another, changes in cardiac output occur, which are modulated by alterations in force development and calcium handling. Although the steady-state force-calcium relationship at various heart rates is well investigated, regulation of these processes during transiti...

    journal_title:BioMed research international

    pub_type: 杂志文章

    doi:10.1155/2015/468548

    authors: Haizlip KM,Milani-Nejad N,Brunello L,Varian KD,Slabaugh JL,Walton SD,Gyorke S,Davis JP,Biesiadecki BJ,Janssen PM

    更新日期:2015-01-01 00:00:00

  • Predicting the types of J-proteins using clustered amino acids.

    abstract::J-proteins are molecular chaperones and present in a wide variety of organisms from prokaryote to eukaryote. Based on their domain organizations, J-proteins can be classified into 4 types, that is, Type I, Type II, Type III, and Type IV. Different types of J-proteins play distinct roles in influencing cancer propertie...

    journal_title:BioMed research international

    pub_type: 杂志文章

    doi:10.1155/2014/935719

    authors: Feng P,Lin H,Chen W,Zuo Y

    更新日期:2014-01-01 00:00:00

  • Advanced Age as a Predictor of Survival and Weaning in Venoarterial Extracorporeal Oxygenation: A Retrospective Observational Study.

    abstract::Background. In most reports on ECMO treatment, advanced age is classified as a contraindication to VA ECMO. We attempted to investigate whether advanced age would be a main risk factor deciding VA ECMO application and performing VA ECMO support. We determined whether advanced age should be regarded as an absolute or r...

    journal_title:BioMed research international

    pub_type: 临床试验,杂志文章

    doi:10.1155/2017/3505784

    authors: Lee W,Kim Y,Choi H,Kim H,Lee S,Lee H,Chee H,Kim J,Hwang J,Lee S,Kim Y,Cho S,Ryu S,Park S

    更新日期:2017-01-01 00:00:00

  • Effects of Cobalt Chloride, a Hypoxia-Mimetic Agent, on Autophagy and Atrophy in Skeletal C2C12 Myotubes.

    abstract:BACKGROUND:Hypoxia-induced autophagy and muscle wasting occur in several environmental and pathological conditions. However, the molecular mechanisms underlying the effects of the hypoxia-mimetic agent CoCl2 on autophagy and muscle atrophy are still unclear. METHODS:C2C12 myotubes were exposed to increasing concentrat...

    journal_title:BioMed research international

    pub_type: 杂志文章

    doi:10.1155/2017/7097580

    authors: Chen R,Jiang T,She Y,Xu J,Li C,Zhou S,Shen H,Shi H,Liu S

    更新日期:2017-01-01 00:00:00

  • Body Mass Index and Primary Headache: A Hospital-Based Study in China.

    abstract:Objective:Primary headache and obesity are highly prevalent disorders in the general population. Although many studies have reported an association between the two, there is still no overall comprehension about this relationship. To gain a more accurate understanding in this regard, we analyzed data from a 2011 cross-s...

    journal_title:BioMed research international

    pub_type: 杂志文章

    doi:10.1155/2019/4630490

    authors: Huang Q,Yu H,Zhang N,Guo B,Feng C,Wang S,Liang X

    更新日期:2019-04-15 00:00:00

  • HMGB1-Induced Cross Talk between PTEN and miRs 221/222 in Thyroid Cancer.

    abstract::High mobility group box 1 (HMGB1) is an ubiquitous protein that plays different roles in the nucleus, cytoplasm, and extracellular space. It is an important DAMP molecule that allows communication between damaged or tumor cells and the immune system. Tumor cells exploit HMGB1's ability to activate intracellular pathwa...

    journal_title:BioMed research international

    pub_type: 杂志文章

    doi:10.1155/2015/512027

    authors: Mardente S,Mari E,Massimi I,Fico F,Faggioni A,Pulcinelli F,Antonaci A,Zicari A

    更新日期:2015-01-01 00:00:00

  • Validation of an Endoscopic Fibre-Optic Pressure Sensor for Noninvasive Measurement of Variceal Pressure.

    abstract::In this study, the authors have developed endoscopic fibre-optic pressure sensor to detect variceal pressure and presented the validation of in vivo and in vitro studies, because the HVPG requires catheterization of hepatic veins, which is invasive and inconvenient. Compared with HVPG, it is better to measure directly...

    journal_title:BioMed research international

    pub_type: 杂志文章

    doi:10.1155/2016/1893474

    authors: Sun B,Kong DR,Li SW,Yu DF,Wang GJ,Yu FF,Wu Q,Xu JM

    更新日期:2016-01-01 00:00:00

  • Anti-Candida properties of urauchimycins from actinobacteria associated with trachymyrmex ants.

    abstract::After decades of intensive searching for antimicrobial compounds derived from actinobacteria, the frequency of isolation of new molecules has decreased. To cope with this concern, studies have focused on the exploitation of actinobacteria from unexplored environments and actinobacteria symbionts of plants and animals....

    journal_title:BioMed research international

    pub_type: 杂志文章

    doi:10.1155/2013/835081

    authors: Mendes TD,Borges WS,Rodrigues A,Solomon SE,Vieira PC,Duarte MC,Pagnocca FC

    更新日期:2013-01-01 00:00:00

  • Sequence Analysis of the K13-Propeller Gene in Artemisinin Challenging Plasmodium falciparum Isolates from Malaria Endemic Areas of Odisha, India: A Molecular Surveillance Study.

    abstract::Estimation of the spread and advancement of Plasmodium falciparum artemisinin-resistant parasites can be done by probing polymorphisms in the kelch (Pfk13) domain (a validated molecular marker). This study aimed to provide baseline information for future artemisinin surveillance by analyzing the k13-propeller domain i...

    journal_title:BioMed research international

    pub_type: 杂志文章

    doi:10.1155/2020/8475246

    authors: Rana R,Ranjit M,Bal M,Khuntia HK,Pati S,Krishna S,Das A

    更新日期:2020-03-15 00:00:00

  • Tanshinone IIA induces apoptosis in human oral cancer KB cells through a mitochondria-dependent pathway.

    abstract::Tanshinone IIA (Tan IIA), an active phytochemical in the dried root of Salvia miltiorrhiza Bunge, has shown an antiproliferative activity on various human cancer cell lines including nasopharyngeal carcinoma cells. However, the effects of Tan IIA on human oral cancer cells are still unknown. This study aimed to invest...

    journal_title:BioMed research international

    pub_type: 杂志文章,收录出版

    doi:10.1155/2014/540516

    authors: Tseng PY,Lu WC,Hsieh MJ,Chien SY,Chen MK

    更新日期:2014-01-01 00:00:00

  • The increase of intra-abdominal pressure can affect intraocular pressure.

    abstract:OBJECTIVE:This study aims to explore the usage of intraocular pressure measurements as the early indicator of the increase in intra-abdominal pressure. METHODS:In this prospective study, 40 patients undergoing elective surgery were included. Patients were divided into four groups of 10 patients. The control group (Gro...

    journal_title:BioMed research international

    pub_type: 临床试验,杂志文章

    doi:10.1155/2015/986895

    authors: Ece I,Vatansev C,Kucukkartallar T,Tekin A,Kartal A,Okka M

    更新日期:2015-01-01 00:00:00

  • Salivary Antioxidant Status in Patients with Oral Lichen Planus: Correlation with Clinical Signs and Evolution during Treatment with Chamaemelum nobile.

    abstract::Oral lichen planus (OLP) is a chronic inflammatory mucocutaneous disease, which manifests as a succession of outbreaks. OLP was associated with salivary oxidative stress. Randomized, double blind, parallel-group study was performed. The sample consisted of 55 clinically and histopathologically diagnosed OLP patients. ...

    journal_title:BioMed research international

    pub_type: 杂志文章,随机对照试验

    doi:10.1155/2018/5187549

    authors: Tvarijonaviciute A,Aznar-Cayuela C,Rubio CP,Tecles F,Ceron JJ,López-Jornet P

    更新日期:2018-05-27 00:00:00

  • A Novel Phosphorylation Site-Kinase Network-Based Method for the Accurate Prediction of Kinase-Substrate Relationships.

    abstract::Protein phosphorylation is catalyzed by kinases which regulate many aspects that control death, movement, and cell growth. Identification of the phosphorylation site-specific kinase-substrate relationships (ssKSRs) is important for understanding cellular dynamics and provides a fundamental basis for further disease-re...

    journal_title:BioMed research international

    pub_type: 杂志文章

    doi:10.1155/2017/1826496

    authors: Wang M,Wang T,Wang B,Liu Y,Li A

    更新日期:2017-01-01 00:00:00

  • The longitudinal assessment of osteomyelitis development by molecular imaging in a rabbit model.

    abstract:INTRODUCTION:Osteomyelitis is a severe orthopaedic complication which is difficult to diagnose and treat. Previous experimental studies mainly focussed on evaluating osteomyelitis in the presence of an implant or used a sclerosing agent to promote infection onset. In contrast, we focused on the longitudinal assessment ...

    journal_title:BioMed research international

    pub_type: 杂志文章

    doi:10.1155/2014/424652

    authors: Odekerken JC,Walenkamp GH,Brans BT,Welting TJ,Arts JJ

    更新日期:2014-01-01 00:00:00

  • Network Based Approach in the Establishment of the Relationship between Type 2 Diabetes Mellitus and Its Complications at the Molecular Level Coupled with Molecular Docking Mechanism.

    abstract::Diabetes mellitus (DM) is one of the major metabolic disorders that is currently threatening the world. DM is seen associated with obesity and diabetic retinopathy (DR). In the present paper we tried to evaluate the relationship between the three aliments at the gene level and further performed the molecular docking t...

    journal_title:BioMed research international

    pub_type: 杂志文章

    doi:10.1155/2016/6068437

    authors: Rampogu S,Rampogu Lemuel M

    更新日期:2016-01-01 00:00:00

  • Study of the polycarbonate-urethane/metal contact in different positions during gait cycle.

    abstract::Nowadays, a growing number of young and more active patients receive hip replacement. More strenuous activities in such patients involve higher friction and wear rates, with friction on the bearing surface being crucial to ensure arthroplasty survival in the long term. Over the last years, the polycarbonate-urethane h...

    journal_title:BioMed research international

    pub_type: 杂志文章

    doi:10.1155/2014/548968

    authors: Gabarre S,Herrera A,Mateo J,Ibarz E,Lobo-Escolar A,Gracia L

    更新日期:2014-01-01 00:00:00

  • Interferon-α enhances 5'-deoxy-5-fluorouridine-induced apoptosis by ERK-dependant upregulation of thymidine phosphorylase.

    abstract::5-Florouracil (5-FU) is the basic agent used in the treatment of gastric cancer. Capecitabine, a prodrug of 5-FU, displays increased antitumor efficacy compared with 5-FU in the clinic. 5'-Deoxy-5-fluorouracil (5'-DFUR), the metabolite of capecitabine, is converted to 5-FU by the enzyme thymidine phosphorylase (TP), w...

    journal_title:BioMed research international

    pub_type: 杂志文章

    doi:10.1155/2013/132793

    authors: Zhu Y,Xu L,Fan Y,Li C,Zhang Y,Zheng H,Hou K,Qu X,Liu Y

    更新日期:2013-01-01 00:00:00

  • Stem cell therapy for lower extremity diabetic ulcers: where do we stand?

    abstract::The impairment of wound healing in diabetic patients is an important clinical problem affecting millions of patients worldwide. Various clinical and basic science studies show that stem cell therapy, as a regenerative medical therapy, can be a good solution. In this paper, we begin with an introduction of the cellular...

    journal_title:BioMed research international

    pub_type: 杂志文章,评审

    doi:10.1155/2013/462179

    authors: Yang M,Sheng L,Zhang TR,Li Q

    更新日期:2013-01-01 00:00:00

  • Statistical optimization of fibrinolytic enzyme production using agroresidues by Bacillus cereus IND1 and its thrombolytic activity in vitro.

    abstract::A potent fibrinolytic enzyme-producing Bacillus cereus IND1 was isolated from the Indian food, rice. Solid-state fermentation was carried out using agroresidues for the production of fibrinolytic enzyme. Among the substrates, wheat bran supported more enzyme production and has been used for the optimized enzyme produc...

    journal_title:BioMed research international

    pub_type: 杂志文章

    doi:10.1155/2014/725064

    authors: Vijayaraghavan P,Vincent SG

    更新日期:2014-01-01 00:00:00

  • The best choice of treatment for acute colonic diverticulitis with purulent peritonitis is uncertain.

    abstract::Severe stages of acute, colonic diverticulitis can progress into intestinal perforations with peritonitis. In such cases, urgent treatment is needed, and Hartmann's procedure is the standard treatment for cases with fecal peritonitis. Peritoneal lavage may be an alternative to resection for acute diverticulitis with p...

    journal_title:BioMed research international

    pub_type: 杂志文章,评审

    doi:10.1155/2014/380607

    authors: Hupfeld L,Burcharth J,Pommergaard HC,Rosenberg J

    更新日期:2014-01-01 00:00:00