Normalization of cDNA microarray data using wavelet regressions.

Abstract:

:Normalization is an essential step in microarray data mining and analysis. For cDNA microarray data, the primary purpose of normalization is removing the intensity-dependent bias across different slides within an experimental group or between multiple groups. The locally weighted regression (lowess) procedure has been widely used for this purpose but can be comparatively time consuming when the dataset becomes relatively large. In this study, we applied wavelet regressions, a new smoothing method for recovering a regression function from data that is supposed to outperform other methods in many cases, such as spline or local polynomial fitting, to normalize two cDNA microarray datasets. Relative to the lowess procedure, we found that wavelet regressions not only produced reliable normalization results but also ran much faster. The computing speed represents one of the most important advantages over other algorithms, especially when one is interested in analyzing a large microarray experiment involving hundreds of slides.

authors

Wang J,Ma JZ,Li MD

doi

10.2174/1386207043328274

subject

Has Abstract

pub_date

2004-12-01 00:00:00

pages

783-91

issue

8

eissn

1386-2073

issn

1875-5402

journal_volume

7

pub_type

杂志文章
  • Screening for xenobiotic electrophilic metabolites using pulsed ultrafiltration-mass spectrometry.

    abstract::A pulsed ultrafiltration-mass spectrometric screening assay has been developed to generate and identify electrophilic metabolites of xenobiotic compounds formed by hepatic cytochrome P450 enzymes. This assay would be suitable for the early identification of potentially toxic compounds during the initial phase of drug ...

    journal_title:Combinatorial chemistry & high throughput screening

    pub_type: 杂志文章

    doi:

    authors: Nikolic D,Fan PW,Bolton JL,van Breemen RB

    更新日期:1999-06-01 00:00:00

  • The design and synthesis of a herbicide targeted library of N-[1-(1,3-benzoxazol-2-yl)alkyl]-6-alkyl-1,3,5-triazine-2,4-diamines.

    abstract::Amino acids were immobilised by attaching them via a carbamate linker to Wang resin. These intermediates were converted to 1-(1,3-benzoxazol-2-yl)alkanamines over three steps, followed by coupling with 4-alkyl-6-chloro-1,3,5-triazine-2-amines to furnish the desired N-[1-(1,3-benzoxazol-2-yl)alkyl]-6-alkyl-1,3,5-triazi...

    journal_title:Combinatorial chemistry & high throughput screening

    pub_type: 杂志文章

    doi:10.2174/138620705774575409

    authors: Dietrich H,Giencke W,Klein R

    更新日期:2005-11-01 00:00:00

  • Parallel synthesis of tri- and tetrasubstituted ureas from carbamoyl imidazolium salts.

    abstract::A method for producing tri- and tetrasubstituted ureas from carbamoyl imidazolium salts is presented. Carbamoyl imidazolium salts are prepared from the reaction of N,N carbonyldiimidazole (CDI) with secondary amines, followed by alkylation with iodomethane. These stable salts can be stored for extended periods and ar...

    journal_title:Combinatorial chemistry & high throughput screening

    pub_type: 杂志文章

    doi:10.2174/1386207024607211

    authors: Batey RA,Shen M,Santhakumar V,Yoshina-Ishii C

    更新日期:2002-05-01 00:00:00

  • Mass spectrometry in high-throughput screening: a case study on acetyl-coenzyme a carboxylase using RapidFire--mass spectrometry (RF-MS).

    abstract::In this review various technologies and approaches for the utilization of mass spectrometry in high-throughput analyses are discussed. The use of quadrupole-based mass spectrometry in the screening of chemical libraries against enzymatic targets for the identification of inhibitors and/or activators is highlighted. Th...

    journal_title:Combinatorial chemistry & high throughput screening

    pub_type: 杂志文章,评审

    doi:10.2174/138620709789104924

    authors: Jonas M,LaMarr WA,Ozbal C

    更新日期:2009-09-01 00:00:00

  • High content screening for compounds that induce early stages of human embryonic stem cell differentiation.

    abstract::Embryonic stem cells, due to their self-renewal and pluripotency properties, can be used to repair damaged tissues and as an unlimited source of differentiated cells. Although stem cells represent an important opportunity for cell based therapy and small molecules screening (in the context of drug or target discovery)...

    journal_title:Combinatorial chemistry & high throughput screening

    pub_type: 杂志文章

    doi:10.2174/138620712802650540

    authors: Jee J,Jeon H,Hwang D,Sommer P,Park Z,Cechetto J,Dorval T

    更新日期:2012-09-01 00:00:00

  • Determination of Antiproliferative Activities of Volatile Contents and HPLC Profiles of Dicranum scoparium (Dicranaceae, Bryophyta).

    abstract::The aim of this study was to examine the anticancer activities and phytochemical profiles of Dicranum scoparium against HeLa cell lines. The bio-guided fractionation studies of dichloromethane extract have high antiproliferative activities. Fractions 7, 9, 19, 20 are rich source of unsaturated fatty acids, and- in the...

    journal_title:Combinatorial chemistry & high throughput screening

    pub_type: 杂志文章

    doi:10.2174/1386207318666150305112504

    authors: Abay G,Altun M,Koldaş S,Tüfekçi AR,Demirtas I

    更新日期:2015-01-01 00:00:00

  • Design of phenotypic screens for bioactive chemicals and identification of their targets by genetic and proteomic approaches.

    abstract::Cell-based screening using phenotypic assays is a useful means of identifying bioactive chemicals for use as tools to elucidate complex cellular processes. However, the chemicals must display sufficient selectivity and their targets have to be identified. We describe how cell-based screening assays can be designed to ...

    journal_title:Combinatorial chemistry & high throughput screening

    pub_type: 杂志文章,评审

    doi:10.2174/138620708785739934

    authors: Schriemer DC,Kemmer D,Roberge M

    更新日期:2008-09-01 00:00:00

  • Network Pharmacology and Reverse Molecular Docking-Based Prediction of the Molecular Targets and Pathways for Avicularin Against Cancer.

    abstract:AIM AND OBJECTIVE:Avicularin has been found to inhibit the proliferation of HepG-2 cells in vitro in the screening of our laboratory. We intended to explain the molecular mechanism of this effect. Therefore, the combined methods of reverse molecular docking and network pharmacology were used in order to illuminate the ...

    journal_title:Combinatorial chemistry & high throughput screening

    pub_type: 杂志文章

    doi:10.2174/1386207322666190206163409

    authors: Duan C,Li Y,Dong X,Xu W,Ma Y

    更新日期:2019-01-01 00:00:00

  • Review on lazy learning regressors and their applications in QSAR.

    abstract::Building accurate quantitative structure-activity relationships (QSAR) is important in drug design, environmental modeling, toxicology, and chemical property prediction. QSAR methods can be utilized to solve mainly two types of problems viz., pattern recognition, (or classification) where output is discrete (i.e. clas...

    journal_title:Combinatorial chemistry & high throughput screening

    pub_type: 杂志文章,评审

    doi:10.2174/138620709788167908

    authors: Kulkarni AJ,Jayaraman VK,Kulkarni BD

    更新日期:2009-05-01 00:00:00

  • Validation of an UPLC-DAD method for the quantification of phenolic acids, verbascoside and 6-epi-aububin in Crescentia cujete fruit.

    abstract:BACKGROUND:The fruit pulp decoction of Crescentia cujete, commonly known as calabash, is traditionally used for the treatment of several respiratory diseases and is available as syrup formulations. Unfortunately, there is no detailed investigation on analytical methods for warranting the quality of these products. AIM...

    journal_title:Combinatorial chemistry & high throughput screening

    pub_type: 杂志文章

    doi:10.2174/1386207323666201207114302

    authors: Rivera-Mondragón A,Caballero-George C,Pieters L,Foubert K

    更新日期:2020-12-06 00:00:00

  • Extraction, Identification and Biological Activities of Saponins in Sea Cucumber Pearsonothuria graeffei.

    abstract:AIMS AND OBJECTIVES:Secondary metabolism in marine organisms produces a diversity of biologically important natural compounds that are not present in terrestrial species. Sea cucumbers belong to the invertebrate Echinodermata and are famous for their nutraceutical, medical and food values. They are known for possession...

    journal_title:Combinatorial chemistry & high throughput screening

    pub_type: 杂志文章

    doi:10.2174/1386207321666180212165448

    authors: Khattab RA,Elbandy M,Lawrence A,Paget T,Rae-Rho J,Binnaser YS,Ali I

    更新日期:2018-01-01 00:00:00

  • A collaborative hit-to-lead investigation leveraging medicinal chemistry expertise with high throughput library design, synthesis and purification capabilities.

    abstract::High throughput screening (HTS) campaigns, where laboratory automation is used to expose biological targets to large numbers of materials from corporate compound collections, have become commonplace within the lead generation phase of pharmaceutical discovery. Advances in genomics and related fields have afforded a we...

    journal_title:Combinatorial chemistry & high throughput screening

    pub_type: 杂志文章

    doi:10.2174/138620706775541891

    authors: Yang X,Parker D,Whitehead L,Ryder NS,Weidmann B,Stabile-Harris M,Kizer D,McKinnon M,Smellie A,Powers D

    更新日期:2006-02-01 00:00:00

  • Oligonucleotide fingerprinting of arrayed genomic DNA sequences using LNA-modified hybridization probes.

    abstract::Recently, we established a robust method for the detection of hybridization events using a DNA microarray deposited on a nanoporous membrane. Here, in a follow-up study, we demonstrate the performance of this approach on a larger set of LNA-modified oligoprobes and genomic DNA sequences. Twenty-six different LNA-modif...

    journal_title:Combinatorial chemistry & high throughput screening

    pub_type: 杂志文章

    doi:10.2174/138620707780636637

    authors: Liu JP,Drungowski M,Nyársik L,Schwartz R,Lehrach H,Herwig R,Janitz M

    更新日期:2007-05-01 00:00:00

  • Phenotypic screening of small molecule libraries by high throughput cell imaging.

    abstract::We have developed high throughput fluorescence cell imaging methods to screen chemical libraries for compounds with effects on diverse aspects of cell physiology. We describe screens for compounds that arrest cells in mitosis, that block cell migration, and that block the secretory pathway. Each of these screens yield...

    journal_title:Combinatorial chemistry & high throughput screening

    pub_type: 杂志文章

    doi:10.2174/138620703106298527

    authors: Yarrow JC,Feng Y,Perlman ZE,Kirchhausen T,Mitchison TJ

    更新日期:2003-06-01 00:00:00

  • Systematic Comparison of the Performance of Different 2D and 3D Ligand-Based Virtual Screening Methodologies to Discover Anticonvulsant Drugs.

    abstract::Virtual screening encompasses a wide range of computational approaches aimed at the high-throughput, cost-efficient exploration of chemical libraries or databases to discover new bioactive compounds or novel medical indications of known drugs. Here, we have performed a systematic comparison of the performance of a lar...

    journal_title:Combinatorial chemistry & high throughput screening

    pub_type: 杂志文章

    doi:10.2174/1386207318666150305151420

    authors: Di Ianni ME,Gantner ME,Ruiz ME,Castro EA,Bruno-Blanch LE,Talevi A

    更新日期:2015-01-01 00:00:00

  • Streamlined in vivo selection and screening of human prostate carcinoma avid phage particles for development of peptide based in vivo tumor imaging agents.

    abstract::Bacteriophage (phage) display has been exploited for the purpose of discovering new cancer specific targeting peptides. However, this approach has resulted in only a small number of tumor targeting peptides useful as in vivo imaging agents. We hypothesize that in vivo screening for tumor uptake of fluorescently tagged...

    journal_title:Combinatorial chemistry & high throughput screening

    pub_type: 杂志文章

    doi:10.2174/1386207311107010009

    authors: Newton-Northup JR,Figueroa SD,Deutscher SL

    更新日期:2011-01-01 00:00:00

  • Three-component green reaction of arylaldehydes, 6-amino-1,3- dimethyluracil and active methylene compounds catalyzed by Zr(HSO4)4 under solvent-free conditions.

    abstract::A convenient one-pot, three-component reaction of aromatic aldehydes, 6-amino-1,3-dimethyluracil and active methylene compounds in the presence of Zr(HSO4)4 as a heterogeneous catalyst, under solvent-free conditions brings a very simple and highly efficient method for the preparation of pyrimido[4,5-b]quinolines, pyri...

    journal_title:Combinatorial chemistry & high throughput screening

    pub_type: 杂志文章

    doi:

    authors: Abdolmohammadi S,Balalaie S,Barari M,Rominger F

    更新日期:2013-02-01 00:00:00

  • A novel machine learning method for cytokine-receptor interaction prediction.

    abstract::Most essential functions are associated with various protein-protein interactions, particularly the cytokine-receptor interaction. Knowledge of the heterogeneous network of cytokine- receptor interactions provides insights into various human physiological functions. However, only a few studies are focused on the compu...

    journal_title:Combinatorial chemistry & high throughput screening

    pub_type: 杂志文章

    doi:10.2174/1386207319666151110122621

    authors: Wei L,Zou Q,Liao M,Lu H,Zhao Y

    更新日期:2016-01-01 00:00:00

  • Identification of Genes Associated with Lung Adenocarcinoma Prognosis.

    abstract:OBJECTIVE:Lung cancer is the most prevalent cancer in the world, and lung adenocarcinoma is the most common lung cancer subtype. Identification and determination of relevant prognostic markers are the key steps to personalized cancer management. METHODS:We collected the gene expression profiles from 265 tumor tissues ...

    journal_title:Combinatorial chemistry & high throughput screening

    pub_type: 杂志文章

    doi:10.2174/1386207322666190404152140

    authors: He ZH,Lv W,Wang LM,Wang YQ,Hu J

    更新日期:2019-01-01 00:00:00

  • Expression Levels of A Disintegrin-like Metalloproteinase with Thrombospondin Motifs-4 and -5 (ADAMTS-4 and ADAMTS-5) in Inflamed and Healthy Gingival Tissues.

    abstract:BACKGROUND:ADAMTS (A disintegrin-like metalloproteinase with thrombospondin motifs) is a group of 19 zinc-dependent metalloproteases known to function in many pathological and physiological processes, such as adhesion, cell fusion, signaling, proteolysis and ECM degradation. OBJECTIVES:The aim of this study was to dem...

    journal_title:Combinatorial chemistry & high throughput screening

    pub_type: 杂志文章

    doi:10.2174/1386207323666200218113000

    authors: Tayman MA,Koyuncu İ,Köklü NÖ

    更新日期:2020-01-01 00:00:00

  • A high throughput scintillation proximity imaging assay for protein methyltransferases.

    abstract::Protein methyltransferases (PMTs) orchestrate epigenetic modifications through post-translational methylation of various protein substrates including histones. Since dysregulation of this process is widely implicated in many cancers, it is of pertinent interest to screen inhibitors of PMTs, as they offer novel target-...

    journal_title:Combinatorial chemistry & high throughput screening

    pub_type: 杂志文章

    doi:10.2174/138620712800194468

    authors: Ibanez G,Shum D,Blum G,Bhinder B,Radu C,Antczak C,Luo M,Djaballah H

    更新日期:2012-06-01 00:00:00

  • Dendrobium officinalis Flower Improves Learning and Reduces Memory Impairment by Mediating Antioxidant Effect and Balancing the Release of Neurotransmitters in Senescent Rats.

    abstract:AIM AND OBJECTIVE:The Dendrobium officinalis flower (DOF) is popular in China due to common belief in its anti-aging properties and positive effects on "nourish yin". However, there have been relatively few confirmatory pharmacological experiments conducted to date. The aim of this work was to evaluate whether DOF has ...

    journal_title:Combinatorial chemistry & high throughput screening

    pub_type: 杂志文章

    doi:10.2174/1386207323666200407080352

    authors: Li LZ,Lei SS,Li B,Zhou FC,Chen YH,Su J,Lv GY,Chen SH

    更新日期:2020-01-01 00:00:00

  • Investigation of electrochemical behavior of lipid lowering agent atorvastatin calcium in aqueous media and its determination from pharmaceutical dosage forms and biological fluids using boron-doped diamond and glassy carbon electrodes.

    abstract::The electrochemical behavior of atorvastatin calcium at glassy carbon and boron-doped diamond electrodes has been studied using voltammetric techniques. The possible mechanism of oxidation was discussed with model compounds. The dependence of the peak current and potentials on pH, concentration, scan rate and nature o...

    journal_title:Combinatorial chemistry & high throughput screening

    pub_type: 杂志文章

    doi:10.2174/138620707782152407

    authors: Dogan-Topal B,Uslu B,Ozkan SA

    更新日期:2007-08-01 00:00:00

  • Development and application of a highly selective biomimetic sensor for detection of captopril, an important ally in hypertension control.

    abstract::A biomimetic sensor is proposed as a promising new analytical method for determination of captopril in different classes of samples. The sensor was prepared by modifying a carbon paste electrode with iron (II) phthalocyanine bis(pyridine) [FePc(dipy)] complex. Amperometric measurements in a batch analytical mode were ...

    journal_title:Combinatorial chemistry & high throughput screening

    pub_type: 杂志文章

    doi:10.2174/138620710791920392

    authors: Wong A,Lanza MR,Sotomayor MD

    更新日期:2010-09-01 00:00:00

  • High throughput genetic screening for the detection of hereditary non-polyposis colon cancer (HNPCC) using capillary electrophoresis.

    abstract::Approximately 5-10% of all colorectal carcinomas arise from cancer predisposition syndromes caused by heterozygote germline mutations in post-replicative DNA mismatch repair (MMR) genes. In contrast to gastrointestinal polyposis syndromes, carcinomas in these patients do not occur on the background of increased number...

    journal_title:Combinatorial chemistry & high throughput screening

    pub_type: 杂志文章

    doi:10.2174/1386207003331409

    authors: Merkelbach-Bruse S,Köse S,Losen I,Bosserhoff AK,Buettner R

    更新日期:2000-12-01 00:00:00

  • Influence of polarity on the scalability and reproducibility of solvent-free microwave-assisted reactions.

    abstract::Organic reactions performed in the absence of solvent in domestic ovens without appropriate temperature control are generally considered as not reproducible, particularly when different instruments are used. For this reason, reproducibility has historically been one of the major issues associated with Microwave-Assist...

    journal_title:Combinatorial chemistry & high throughput screening

    pub_type: 杂志文章

    doi:10.2174/138620711794474088

    authors: Díaz-Ortiz A,de la Hoz A,Alcázar J,Carrillo JR,Herrero MA,Fontana A,Muñoz Jde M,Prieto P,de Cózar A

    更新日期:2011-02-01 00:00:00

  • Combinatorial libraries: studies in molecular recognition.

    abstract::In recent years, combinatorial libraries have become a major tool for drug discovery and drug development. Along the way, one potential use of combinatorial chemistry libraries almost been neglected: the basic study of intermolecular interactions. Especially "one-bead-one-structure" libraries can be a powerful means f...

    journal_title:Combinatorial chemistry & high throughput screening

    pub_type: 杂志文章,评审

    doi:

    authors: Nestler HP,Liu R

    更新日期:1998-10-01 00:00:00

  • Microwave-assisted multicomponent reactions: rapid and regioselective formation of new extended angular fused aza-heterocycles.

    abstract::A new multicomponent domino reaction for rapid and regioselective synthesis of highly functionalized benzo[h]naphtho[2,3-a]acridine-15,16(5H,14H)-diones has been established. The reaction can be conducted by using readily available and inexpensive substrates under microwave irradiation. The procedures are facile, avoi...

    journal_title:Combinatorial chemistry & high throughput screening

    pub_type: 杂志文章

    doi:10.2174/138620712800194459

    authors: Wang SL,Zhang G,Jie D,Jiang B,Wang XH,Tu SJ

    更新日期:2012-06-01 00:00:00

  • The influence of diabetes mellitus on rotator cuff repair: A systematic review and meta-analysis.

    abstract:BACKGROUND:Clinical outcomes after rotator cuff repair associated with diabetes mellitus(DM) are generally favorable, but no study has attempted to establish the influence of DM on outcomes after rotator cuff repair. PURPOSE:To conduct a meta-analysis of clinical studies evaluating patient outcomes between people with...

    journal_title:Combinatorial chemistry & high throughput screening

    pub_type: meta分析

    doi:10.2174/1386207323666201020114034

    authors: Lu X,Sun H,Xu Y,Cao X

    更新日期:2020-10-20 00:00:00

  • Fluorescence polarization for single nucleotide polymorphism genotyping.

    abstract::Single nucleotide polymorphisms (SNPs) are the most abundant variations in the human genome and have become the primary markers for genetic studies for mapping and identifying susceptible genes for complex diseases. Methods that genotype SNPs quickly and economically are of high values for these studies because they r...

    journal_title:Combinatorial chemistry & high throughput screening

    pub_type: 杂志文章,评审

    doi:10.2174/138620703106298392

    authors: Chen X

    更新日期:2003-05-01 00:00:00