当前位置： SCI文献检索 > GENOME BIOLOGY期刊下所有文献 > Permutation-validated principal components analysis of microarray data.

Permutation-validated principal components analysis of microarray data.

Abstract：

BACKGROUND:In microarray data analysis, the comparison of gene-expression profiles with respect to different conditions and the selection of biologically interesting genes are crucial tasks. Multivariate statistical methods have been applied to analyze these large datasets. Less work has been published concerning the assessment of the reliability of gene-selection procedures. Here we describe a method to assess reliability in multivariate microarray data analysis using permutation-validated principal components analysis (PCA). The approach is designed for microarray data with a group structure. RESULTS:We used PCA to detect the major sources of variance underlying the hybridization conditions followed by gene selection based on PCA-derived and permutation-based test statistics. We validated our method by applying it to well characterized yeast cell-cycle data and to two datasets from our laboratory. We could describe the major sources of variance, select informative genes and visualize the relationship of genes and arrays. We observed differences in the level of the explained variance and the interpretability of the selected genes. CONCLUSIONS:Combining data visualization and permutation-based gene selection, permutation-validated PCA enables one to illustrate gene-expression variance between several conditions and to select genes by taking into account the relationship of between-group to within-group variance of genes. The method can be used to extract the leading sources of variance from microarray data, to visualize relationships between genes and hybridizations and to select informative genes in a statistically reliable manner. This selection accounts for the level of reproducibility of replicates or group structure as well as gene-specific scatter. Visualization of the data can support a straightforward biological interpretation.

journal_name

Genome Biol

journal_title

Genome biology

authors

Landgrebe J,Wurst W,Welzl G

doi

10.1186/gb-2002-3-4-research0019

keywords:

subject

Has Abstract

pub_date

2002-01-01 00:00:00

pages

RESEARCH0019

issue

4

eissn

1474-7596

issn

1474-760X

journal_volume

3

pub_type

杂志文章

相关文献

GENOME BIOLOGY文献大全
  • The small RNA diversity from Medicago truncatula roots under biotic interactions evidences the environmental plasticity of the miRNAome.

    abstract：BACKGROUND:Legume roots show a remarkable plasticity to adapt their architecture to biotic and abiotic constraints, including symbiotic interactions. However, global analysis of miRNA regulation in roots is limited, and a global view of the evolution of miRNA-mediated diversification in different ecotypes is lacking. ...

    journal_title：Genome biology

    pub_type： 杂志文章

    doi：10.1186/s13059-014-0457-4

    authors： Formey D,Sallet E,Lelandais-Brière C,Ben C,Bustos-Sanmamed P,Niebel A,Frugier F,Combier JP,Debellé F,Hartmann C,Poulain J,Gavory F,Wincker P,Roux C,Gentzbittel L,Gouzy J,Crespi M

    更新日期：2014-09-24 00:00:00

  • Comparative genome sequence analysis underscores mycoparasitism as the ancestral life style of Trichoderma.

    abstract：BACKGROUND:Mycoparasitism, a lifestyle where one fungus is parasitic on another fungus, has special relevance when the prey is a plant pathogen, providing a strategy for biological control of pests for plant protection. Probably, the most studied biocontrol agents are species of the genus Hypocrea/Trichoderma. RESULTS...

    journal_title：Genome biology

    pub_type： 杂志文章

    doi：10.1186/gb-2011-12-4-r40

    authors： Kubicek CP,Herrera-Estrella A,Seidl-Seiboth V,Martinez DA,Druzhinina IS,Thon M,Zeilinger S,Casas-Flores S,Horwitz BA,Mukherjee PK,Mukherjee M,Kredics L,Alcaraz LD,Aerts A,Antal Z,Atanasova L,Cervantes-Badillo MG,Challac

    更新日期：2011-01-01 00:00:00

  • Genome-wide analysis of plant nat-siRNAs reveals insights into their distribution, biogenesis and function.

    abstract：BACKGROUND:Many eukaryotic genomes encode cis-natural antisense transcripts (cis-NATs). Sense and antisense transcripts may form double-stranded RNAs that are processed by the RNA interference machinery into small interfering RNAs (siRNAs). A few so-called nat-siRNAs have been reported in plants, mammals, Drosophila, a...

    journal_title：Genome biology

    pub_type： 杂志文章

    doi：10.1186/gb-2012-13-3-r20

    authors： Zhang X,Xia J,Lii YE,Barrera-Figueroa BE,Zhou X,Gao S,Lu L,Niu D,Chen Z,Leung C,Wong T,Zhang H,Guo J,Li Y,Liu R,Liang W,Zhu JK,Zhang W,Jin H

    更新日期：2012-01-01 00:00:00

  • External signals shape the epigenome.

    abstract：:A new study shows how a single cytokine, interleukin-4, regulates hematopoietic lineage choice by activating the JAK3-STAT6 pathway, which causes dendritic-cell-specific DNA demethylation. ...

    journal_title：Genome biology

    pub_type： 杂志文章

    doi：10.1186/s13059-016-0884-5

    authors： Lennartsson A

    更新日期：2016-02-01 00:00:00

  • Functional constraint and small insertions and deletions in the ENCODE regions of the human genome.

    abstract：BACKGROUND:We describe the distribution of indels in the 44 Encyclopedia of DNA Elements (ENCODE) regions (about 1% of the human genome) and evaluate the potential contributions of small insertion and deletion polymorphisms (indels) to human genetic variation. We relate indels to known genomic annotation features and m...

    journal_title：Genome biology

    pub_type： 杂志文章

    doi：10.1186/gb-2007-8-9-r180

    authors： Clark TG,Andrew T,Cooper GM,Margulies EH,Mullikin JC,Balding DJ

    更新日期：2007-01-01 00:00:00

  • Differential DNA methylation in discrete developmental stages of the parasitic nematode Trichinella spiralis.

    abstract：BACKGROUND:DNA methylation plays an essential role in regulating gene expression under a variety of conditions and it has therefore been hypothesized to underlie the transitions between life cycle stages in parasitic nematodes. So far, however, 5'-cytosine methylation has not been detected during any developmental stag...

    journal_title：Genome biology

    pub_type： 杂志文章

    doi：10.1186/gb-2012-13-10-r100

    authors： Gao F,Liu X,Wu XP,Wang XL,Gong D,Lu H,Xia Y,Song Y,Wang J,Du J,Liu S,Han X,Tang Y,Yang H,Jin Q,Zhang X,Liu M

    更新日期：2012-10-17 00:00:00

  • The relationship between proteome size, structural disorder and organism complexity.

    abstract：BACKGROUND:Sequencing the genomes of the first few eukaryotes created the impression that gene number shows no correlation with organism complexity, often referred to as the G-value paradox. Several attempts have previously been made to resolve this paradox, citing multifunctionality of proteins, alternative splicing, ...

    journal_title：Genome biology

    pub_type： 杂志文章

    doi：10.1186/gb-2011-12-12-r120

    authors： Schad E,Tompa P,Hegyi H

    更新日期：2011-12-19 00:00:00

  • Comparative sequence analysis reveals an intricate network among REST, CREB and miRNA in mediating neuronal gene expression.

    abstract：BACKGROUND:Two distinct classes of regulators have been implicated in regulating neuronal gene expression and mediating neuronal identity: transcription factors such as REST/NRSF (RE1 silencing transcription factor) and CREB (cAMP response element-binding protein), and microRNAs (miRNAs). How these two classes of regul...

    journal_title：Genome biology

    pub_type： 杂志文章

    doi：10.1186/gb-2006-7-9-r85

    authors： Wu J,Xie X

    更新日期：2006-01-01 00:00:00

  • Bovine breed-specific augmented reference graphs facilitate accurate sequence read mapping and unbiased variant discovery.

    abstract：BACKGROUND:The current bovine genomic reference sequence was assembled from a Hereford cow. The resulting linear assembly lacks diversity because it does not contain allelic variation, a drawback of linear references that causes reference allele bias. High nucleotide diversity and the separation of individuals by hundr...

    journal_title：Genome biology

    pub_type： 杂志文章

    doi：10.1186/s13059-020-02105-0

    authors： Crysnanto D,Pausch H

    更新日期：2020-07-27 00:00:00

  • Pigs taking wing with transposons and recombinases.

    abstract：:Swine production has been an important part of our lives since the late Mesolithic or early Neolithic periods, and ranks number one in world meat production. Pig production also contributes to high-value-added medical markets in the form of pharmaceuticals, heart valves, and surgical materials. Genetic engineering, in...

    journal_title：Genome biology

    pub_type： 杂志文章,评审

    doi：10.1186/gb-2007-8-s1-s13

    authors： Clark KJ,Carlson DF,Fahrenkrug SC

    更新日期：2007-01-01 00:00:00

  • Transcriptional profiling of long non-coding RNAs and novel transcribed regions across a diverse panel of archived human cancers.

    abstract：BACKGROUND:Molecular characterization of tumors has been critical for identifying important genes in cancer biology and for improving tumor classification and diagnosis. Long non-coding RNAs, as a new, relatively unstudied class of transcripts, provide a rich opportunity to identify both functional drivers and cancer-t...

    journal_title：Genome biology

    pub_type： 杂志文章

    doi：10.1186/gb-2012-13-8-r75

    authors： Brunner AL,Beck AH,Edris B,Sweeney RT,Zhu SX,Li R,Montgomery K,Varma S,Gilks T,Guo X,Foley JW,Witten DM,Giacomini CP,Flynn RA,Pollack JR,Tibshirani R,Chang HY,van de Rijn M,West RB

    更新日期：2012-08-28 00:00:00

  • Fate by RNA methylation: m6A steers stem cell pluripotency.

    abstract：:The N 6-methyladenosine (m6A) modification of mRNA has a crucial function in regulating pluripotency in murine stem cells: it facilitates resolution of naïve pluripotency towards differentiation. ...

    journal_title：Genome biology

    pub_type： 杂志文章,评审

    doi：10.1186/s13059-015-0609-1

    authors： Zhao BS,He C

    更新日期：2015-02-22 00:00:00

  • Accuracy and quality of massively parallel DNA pyrosequencing.

    abstract：BACKGROUND:Massively parallel pyrosequencing systems have increased the efficiency of DNA sequencing, although the published per-base accuracy of a Roche GS20 is only 96%. In genome projects, highly redundant consensus assemblies can compensate for sequencing errors. In contrast, studies of microbial diversity that cat...

    journal_title：Genome biology

    pub_type： 杂志文章

    doi：10.1186/gb-2007-8-7-r143

    authors： Huse SM,Huber JA,Morrison HG,Sogin ML,Welch DM

    更新日期：2007-01-01 00:00:00

  • GWASs and the age of human as the model organism for autoimmune genetic research.

    abstract：:Genetic studies have identified more than 150 autoimmune loci, and next-generation sequencing will identify more. Is it time to make human the model organism for autoimmune research? ...

    journal_title：Genome biology

    pub_type： 杂志文章

    doi：10.1186/gb-2010-11-5-212

    authors： Plenge R

    更新日期：2010-01-01 00:00:00

  • Detection of circular RNA expression and related quantitative trait loci in the human dorsolateral prefrontal cortex.

    abstract：BACKGROUND:Circular RNAs (circRNAs) are implicated in various biological processes. As a layer of the gene regulatory network, circRNA expression is also an intermediate phenotype bridging genetic variation and phenotypic changes. Thus, analyzing circRNA expression variation will shed light on molecular fundamentals of...

    journal_title：Genome biology

    pub_type： 杂志文章

    doi：10.1186/s13059-019-1701-8

    authors： Liu Z,Ran Y,Tao C,Li S,Chen J,Yang E

    更新日期：2019-05-20 00:00:00

  • Exploiting microarrays to reveal differential gene expression in the nervous system.

    abstract：:Microarrays have been used in a wide variety of experimental systems, but realizing their full potential is contingent on sophisticated and rigorous experimental design and data analysis. This article highlights what is needed to get the most out of microarrays in terms of accurately and effectively revealing differen...

    journal_title：Genome biology

    pub_type： 杂志文章

    doi：10.1186/gb-2003-4-2-105

    authors： Griffin RS,Mills CD,Costigan M,Woolf CJ

    更新日期：2003-01-01 00:00:00

  • Systematic identification of genetic influences on methylation across the human life course.

    abstract：BACKGROUND:The influence of genetic variation on complex diseases is potentially mediated through a range of highly dynamic epigenetic processes exhibiting temporal variation during development and later life. Here we present a catalogue of the genetic influences on DNA methylation (methylation quantitative trait loci ...

    journal_title：Genome biology

    pub_type： 杂志文章

    doi：10.1186/s13059-016-0926-z

    authors： Gaunt TR,Shihab HA,Hemani G,Min JL,Woodward G,Lyttleton O,Zheng J,Duggirala A,McArdle WL,Ho K,Ring SM,Evans DM,Davey Smith G,Relton CL

    更新日期：2016-03-31 00:00:00

  • Surfing waves of data in San Diego: sophisticated analyses provide a broad view of human genetic diversity.

    abstract：:A report on the 64th annual American Society of Human Genetics meeting held in San Diego, USA, 18-22 October, 2014. ...

    journal_title：Genome biology

    pub_type：

    doi：10.1186/s13059-014-0562-4

    authors： Reppell M,Koch E,Peter BM,Novembre J

    更新日期：2014-12-17 00:00:00

  • The rate of the molecular clock and the cost of gratuitous protein synthesis.

    abstract：BACKGROUND:The nature of the protein molecular clock, the protein-specific rate of amino acid substitutions, is among the central questions of molecular evolution. Protein expression level is the dominant determinant of the clock rate in a number of organisms. It has been suggested that highly expressed proteins evolve...

    journal_title：Genome biology

    pub_type： 杂志文章

    doi：10.1186/gb-2010-11-9-r98

    authors： Plata G,Gottesman ME,Vitkup D

    更新日期：2010-01-01 00:00:00

  • The functional spectrum of low-frequency coding variation.

    abstract：BACKGROUND:Rare coding variants constitute an important class of human genetic variation, but are underrepresented in current databases that are based on small population samples. Recent studies show that variants altering amino acid sequence and protein function are enriched at low variant allele frequency, 2 to 5%, b...

    journal_title：Genome biology

    pub_type： 杂志文章

    doi：10.1186/gb-2011-12-9-r84

    authors： Marth GT,Yu F,Indap AR,Garimella K,Gravel S,Leong WF,Tyler-Smith C,Bainbridge M,Blackwell T,Zheng-Bradley X,Chen Y,Challis D,Clarke L,Ball EV,Cibulskis K,Cooper DN,Fulton B,Hartl C,Koboldt D,Muzny D,Smith R,Soug

    更新日期：2011-09-14 00:00:00

  • The phytochrome red/far-red photoreceptor superfamily.

    abstract：:Proteins of the phytochrome superfamily of red/far-red light receptors have a variety of biological roles in plants, algae, bacteria and fungi and demonstrate a diversity of spectral sensitivities and output signaling mechanisms. Over the past few years the first three-dimensional structures of phytochrome light-sensi...

    journal_title：Genome biology

    pub_type： 杂志文章,评审

    doi：10.1186/gb-2008-9-8-230

    authors： Sharrock RA

    更新日期：2008-01-01 00:00:00

  • Benchmarking of computational error-correction methods for next-generation sequencing data.

    abstract：BACKGROUND:Recent advancements in next-generation sequencing have rapidly improved our ability to study genomic material at an unprecedented scale. Despite substantial improvements in sequencing technologies, errors present in the data still risk confounding downstream analysis and limiting the applicability of sequenc...

    journal_title：Genome biology

    pub_type： 杂志文章

    doi：10.1186/s13059-020-01988-3

    authors： Mitchell K,Brito JJ,Mandric I,Wu Q,Knyazev S,Chang S,Martin LS,Karlsberg A,Gerasimov E,Littman R,Hill BL,Wu NC,Yang HT,Hsieh K,Chen L,Littman E,Shabani T,Enik G,Yao D,Sun R,Schroeder J,Eskin E,Zelikovsky A,S

    更新日期：2020-03-17 00:00:00

  • Improved reference genome of the arboviral vector Aedes albopictus.

    abstract：BACKGROUND:The Asian tiger mosquito Aedes albopictus is globally expanding and has become the main vector for human arboviruses in Europe. With limited antiviral drugs and vaccines available, vector control is the primary approach to prevent mosquito-borne diseases. A reliable and accurate DNA sequence of the Ae. albop...

    journal_title：Genome biology

    pub_type： 杂志文章

    doi：10.1186/s13059-020-02141-w

    authors： Palatini U,Masri RA,Cosme LV,Koren S,Thibaud-Nissen F,Biedler JK,Krsticevic F,Johnston JS,Halbach R,Crawford JE,Antoshechkin I,Failloux AB,Pischedda E,Marconcini M,Ghurye J,Rhie A,Sharma A,Karagodin DA,Jenrette J,Ga

    更新日期：2020-08-26 00:00:00

  • The uses of genome-wide yeast mutant collections.

    abstract：:We assess five years of usage of the major genome-wide collections of mutants from Saccharomyces cerevisiae: single deletion mutants, double mutants conferring 'synthetic' lethality and the 'TRIPLES' collection of mutants obtained by random transposon insertion. Over 100 experimental conditions have been tested and mo...

    journal_title：Genome biology

    pub_type： 杂志文章,评审

    doi：10.1186/gb-2004-5-7-229

    authors： Scherens B,Goffeau A

    更新日期：2004-01-01 00:00:00

  • Changes in the organization of the genome during the mammalian cell cycle.

    abstract：:By using chromosome conformation capture technology, a recent study has revealed two alternative three-dimensional folding states of the human genome during the cell cycle. ...

    journal_title：Genome biology

    pub_type： 杂志文章

    doi：10.1186/gb4147

    authors： Giorgetti L,Servant N,Heard E

    更新日期：2013-12-24 00:00:00

  • Concept recognition for extracting protein interaction relations from biomedical text.

    abstract：BACKGROUND:Reliable information extraction applications have been a long sought goal of the biomedical text mining community, a goal that if reached would provide valuable tools to benchside biologists in their increasingly difficult task of assimilating the knowledge contained in the biomedical literature. We present ...

    journal_title：Genome biology

    pub_type： 杂志文章

    doi：10.1186/gb-2008-9-s2-s9

    authors： Baumgartner WA Jr,Lu Z,Johnson HL,Caporaso JG,Paquette J,Lindemann A,White EK,Medvedeva O,Cohen KB,Hunter L

    更新日期：2008-01-01 00:00:00

  • Evolution enters the genomic era.

    abstract：:A report on the 18th Congress of the European Society for Evolutionary Biology (ESEB), Aarhus, Denmark, 20-25 August, 2001. ...

    journal_title：Genome biology

    pub_type：

    doi：10.1186/gb-2001-2-11-reports4026

    authors： Liberles DA

    更新日期：2001-01-01 00:00:00

  • Phytophthora capsici-tomato interaction features dramatic shifts in gene expression associated with a hemi-biotrophic lifestyle.

    abstract：BACKGROUND:Plant-microbe interactions feature complex signal interplay between pathogens and their hosts. Phytophthora species comprise a destructive group of fungus-like plant pathogens, collectively affecting a wide range of plants important to agriculture and natural ecosystems. Despite the availability of genome se...

    journal_title：Genome biology

    pub_type： 杂志文章

    doi：10.1186/gb-2013-14-6-r63

    authors： Jupe J,Stam R,Howden AJ,Morris JA,Zhang R,Hedley PE,Huitema E

    更新日期：2013-06-25 00:00:00

  • Personalized and graph genomes reveal missing signal in epigenomic data.

    abstract：BACKGROUND:Epigenomic studies that use next generation sequencing experiments typically rely on the alignment of reads to a reference sequence. However, because of genetic diversity and the diploid nature of the human genome, we hypothesize that using a generic reference could lead to incorrectly mapped reads and bias ...

    journal_title：Genome biology

    pub_type： 杂志文章

    doi：10.1186/s13059-020-02038-8

    authors： Groza C,Kwan T,Soranzo N,Pastinen T,Bourque G

    更新日期：2020-05-25 00:00:00

  • Opening sequence: computational genomics in the era of high-throughput sequencing.

    abstract：:A report on the 11th Cold Spring Harbor Laboratory/Wellcome Trust conference on Genome Informatics, Cold Spring Harbor Laboratories, New York, USA, November 2-5, 2011. ...

    journal_title：Genome biology

    pub_type：

    doi：10.1186/gb-2011-12-12-310

    authors： Chambers EV,Kindt AS,Semple CA

    更新日期：2011-12-28 00:00:00