Autocorrelation analysis reveals widespread spatial biases in microarray experiments.


BACKGROUND:DNA microarrays provide the ability to interrogate multiple genes in a single experiment and have revolutionized genomic research. However, the microarray technology suffers from various forms of biases and relatively low reproducibility. A particular source of false data has been described, in which non-random placement of gene probes on the microarray surface is associated with spurious correlations between genes. RESULTS:In order to assess the prevalence of this effect and better understand its origins, we applied an autocorrelation analysis of the relationship between chromosomal position and expression level to a database of over 2000 individual yeast microarray experiments. We show that at least 60% of these experiments exhibit spurious chromosomal position-dependent gene correlations, which nonetheless appear in a stochastic manner within each experimental dataset. Using computer simulations, we show that large spatial biases caused in the microarray hybridization step and independently of printing procedures can exclusively account for the observed spurious correlations, in contrast to previous suggestions. Our data suggest that such biases may generate more than 15% false data per experiment. Importantly, spatial biases are expected to occur regardless of microarray design and over a wide range of microarray platforms, organisms and experimental procedures. CONCLUSIONS:Spatial biases comprise a major source of noise in microarray studies; revision of routine experimental practices and normalizations to account for these biases may significantly and comprehensively improve the quality of new as well as existing DNA microarray data.


BMC Genomics


BMC genomics


Koren A,Tirosh I,Barkai N




Has Abstract


2007-06-12 00:00:00










  • Bidirectional promoters exhibit characteristic chromatin modification signature associated with transcription elongation in both sense and antisense directions.

    abstract:BACKGROUND:In contrast to unidirectional promoters wherein antisense transcription results in short transcripts which are rapidly degraded, bidirectional promoters produce mature transcripts in both sense and antisense orientation. To understand the molecular mechanism of how productive bidirectional transcription is r...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Jangid RK,Kelkar A,Muley VY,Galande S

    更新日期:2018-05-02 00:00:00

  • Visualizing tumor evolution with the fishplot package for R.

    abstract:BACKGROUND:Massively-parallel sequencing at depth is now enabling tumor heterogeneity and evolution to be characterized in unprecedented detail. Tracking these changes in clonal architecture often provides insight into therapeutic response and resistance. In complex cases involving multiple timepoints, standard visuali...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Miller CA,McMichael J,Dang HX,Maher CA,Ding L,Ley TJ,Mardis ER,Wilson RK

    更新日期:2016-11-07 00:00:00

  • Fast multiclonal clusterization of V(D)J recombinations from high-throughput sequencing.

    abstract:BACKGROUND:V(D)J recombinations in lymphocytes are essential for immunological diversity. They are also useful markers of pathologies. In leukemia, they are used to quantify the minimal residual disease during patient follow-up. However, the full breadth of lymphocyte diversity is not fully understood. RESULTS:We prop...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Giraud M,Salson M,Duez M,Villenet C,Quief S,Caillault A,Grardel N,Roumier C,Preudhomme C,Figeac M

    更新日期:2014-05-28 00:00:00

  • Delineation of condition specific Cis- and Trans-acting elements in plant promoters under various Endo- and exogenous stimuli.

    abstract:BACKGROUND:Transcription factors (TFs) play essential roles during plant development and response to environmental stresses. However, the relationships among transcription factors, cis-acting elements and target gene expression under endo- and exogenous stimuli have not been systematically characterized. RESULTS:Here,...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Chow CN,Chiang-Hsieh YF,Chien CH,Zheng HQ,Lee TY,Wu NY,Tseng KC,Hou PF,Chang WC

    更新日期:2018-05-09 00:00:00

  • Comparative genomic analysis revealed great plasticity and environmental adaptation of the genomes of Enterococcus faecium.

    abstract:BACKGROUND:As an important nosocomial pathogen, Enterococcus faecium has received increasing attention in recent years. However, a large number of studies have focused on the hospital-associated isolates and ignored isolates originated from the natural environments. RESULTS:In this study, comparative genomic analysis ...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Zhong Z,Kwok LY,Hou Q,Sun Y,Li W,Zhang H,Sun Z

    更新日期:2019-07-22 00:00:00

  • A deconvolution method and its application in analyzing the cellular fractions in acute myeloid leukemia samples.

    abstract:BACKGROUND:The identification of cell type-specific genes (markers) is an essential step for the deconvolution of the cellular fractions, primarily, from the gene expression data of a bulk sample. However, the genes with significant changes identified by pair-wise comparisons cannot indeed represent the specificity of ...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Li H,Sharma A,Ming W,Sun X,Liu H

    更新日期:2020-09-23 00:00:00

  • Topology and expressed repertoire of the Felis catus T cell receptor loci.

    abstract:BACKGROUND:The domestic cat (Felis catus) is an important companion animal and is used as a large animal model for human disease. However, the comprehensive study of adaptive immunity in this species is hampered by the lack of data on lymphocyte antigen receptor genes and usage. The objectives of this study were to ann...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Radtanakatikanon A,Keller SM,Darzentas N,Moore PF,Folch G,Nguefack Ngoune V,Lefranc MP,Vernau W

    更新日期:2020-01-06 00:00:00

  • Unraveling Mycobacterium tuberculosis genomic diversity and evolution in Lisbon, Portugal, a highly drug resistant setting.

    abstract:BACKGROUND:Multidrug- (MDR) and extensively drug resistant (XDR) tuberculosis (TB) presents a challenge to disease control and elimination goals. In Lisbon, Portugal, specific and successful XDR-TB strains have been found in circulation for almost two decades. RESULTS:In the present study we have genotyped and sequenc...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Perdigão J,Silva H,Machado D,Macedo R,Maltez F,Silva C,Jordao L,Couto I,Mallard K,Coll F,Hill-Cawthorne GA,McNerney R,Pain A,Clark TG,Viveiros M,Portugal I

    更新日期:2014-11-18 00:00:00

  • Generation of a de novo transcriptome from equine lamellar tissue.

    abstract:BACKGROUND:Laminitis, the structural failure of interdigitated tissue that suspends the distal skeleton within the hoof capsule, is a devastating disease that is the second leading cause of both lameness and euthanasia in the horse. Current transcriptomic research focuses on the expression of known genes. However, as t...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Holl HM,Gao S,Fei Z,Andrews C,Brooks SA

    更新日期:2015-10-03 00:00:00

  • Microarray analysis after RNA amplification can detect pronounced differences in gene expression using limma.

    abstract:BACKGROUND:RNA amplification is necessary for profiling gene expression from small tissue samples. Previous studies have shown that the T7 based amplification techniques are reproducible but may distort the true abundance of targets. However, the consequences of such distortions on the ability to detect biological vari...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Diboun I,Wernisch L,Orengo CA,Koltzenburg M

    更新日期:2006-10-09 00:00:00

  • Comparative genomics of 84 Pectobacterium genomes reveals the variations related to a pathogenic lifestyle.

    abstract:BACKGROUND:Pectobacterium spp. are necrotrophic bacterial plant pathogens of the family Pectobacteriaceae, responsible for a wide spectrum of diseases of important crops and ornamental plants including soft rot, blackleg, and stem wilt. P. carotovorum is a genetically heterogeneous species consisting of three valid sub...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Li X,Ma Y,Liang S,Tian Y,Yin S,Xie S,Xie H

    更新日期:2018-12-07 00:00:00

  • How to evaluate performance of prediction methods? Measures and their interpretation in variation effect analysis.

    abstract:BACKGROUND:Prediction methods are increasingly used in biosciences to forecast diverse features and characteristics. Binary two-state classifiers are the most common applications. They are usually based on machine learning approaches. For the end user it is often problematic to evaluate the true performance and applica...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Vihinen M

    更新日期:2012-06-18 00:00:00

  • Comparative genomics of Eucalyptus and Corymbia reveals low rates of genome structural rearrangement.

    abstract:BACKGROUND:Previous studies suggest genome structure is largely conserved between Eucalyptus species. However, it is unknown if this conservation extends to more divergent eucalypt taxa. We performed comparative genomics between the eucalypt genera Eucalyptus and Corymbia. Our results will facilitate transfer of genomi...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Butler JB,Vaillancourt RE,Potts BM,Lee DJ,King GJ,Baten A,Shepherd M,Freeman JS

    更新日期:2017-05-22 00:00:00

  • BMP signaling components in embryonic transcriptomes of the hover fly Episyrphus balteatus (Syrphidae).

    abstract:BACKGROUND:In animals, signaling of Bone Morphogenetic Proteins (BMPs) is essential for dorsoventral (DV) patterning of the embryo, but how BMP signaling evolved with changes in embryonic DV differentiation is largely unclear. Based on the extensive knowledge of BMP signaling in Drosophila melanogaster, the morphologic...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Lemke S,Antonopoulos DA,Meyer F,Domanus MH,Schmidt-Ott U

    更新日期:2011-05-31 00:00:00

  • angaGEDUCI: Anopheles gambiae gene expression database with integrated comparative algorithms for identifying conserved DNA motifs in promoter sequences.

    abstract:BACKGROUND:The completed sequence of the Anopheles gambiae genome has enabled genome-wide analyses of gene expression and regulation in this principal vector of human malaria. These investigations have created a demand for efficient methods of cataloguing and analyzing the large quantities of data that have been produc...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Dissanayake SN,Marinotti O,Ribeiro JM,James AA

    更新日期:2006-05-17 00:00:00

  • SNP identification and marker assay development for high-throughput selection of soybean cyst nematode resistance.

    abstract:BACKGROUND:Soybean cyst nematode (SCN) is the most economically devastating pathogen of soybean. Two resistance loci, Rhg1 and Rhg4 primarily contribute resistance to SCN race 3 in soybean. Peking and PI 88788 are the two major sources of SCN resistance with Peking requiring both Rhg1 and Rhg4 alleles and PI 88788 only...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Shi Z,Liu S,Noe J,Arelli P,Meksem K,Li Z

    更新日期:2015-04-18 00:00:00

  • CpGAVAS, an integrated web server for the annotation, visualization, analysis, and GenBank submission of completely sequenced chloroplast genome sequences.

    abstract:BACKGROUND:The complete sequences of chloroplast genomes provide wealthy information regarding the evolutionary history of species. With the advance of next-generation sequencing technology, the number of completely sequenced chloroplast genomes is expected to increase exponentially, powerful computational tools annota...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Liu C,Shi L,Zhu Y,Chen H,Zhang J,Lin X,Guan X

    更新日期:2012-12-20 00:00:00

  • Transcriptome analysis reveals the complexity of alternative splicing regulation in the fungus Verticillium dahliae.

    abstract:BACKGROUND:Alternative splicing (AS) regulation is extensive and shapes the functional complexity of higher organisms. However, the contribution of alternative splicing to fungal biology is not well studied. RESULTS:This study provides sequences of the transcriptomes of the plant wilt pathogen Verticillium dahliae, us...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Jin L,Li G,Yu D,Huang W,Cheng C,Liao S,Wu Q,Zhang Y

    更新日期:2017-02-06 00:00:00

  • Transcriptome deep-sequencing and clustering of expressed isoforms from Favia corals.

    abstract:BACKGROUND:Genomic and transcriptomic sequence data are essential tools for tackling ecological problems. Using an approach that combines next-generation sequencing, de novo transcriptome assembly, gene annotation and synthetic gene construction, we identify and cluster the protein families from Favia corals from the n...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Pooyaei Mehr SF,DeSalle R,Kao HT,Narechania A,Han Z,Tchernov D,Pieribone V,Gruber DF

    更新日期:2013-08-12 00:00:00

  • Altered microRNA expression in frontotemporal lobar degeneration with TDP-43 pathology caused by progranulin mutations.

    abstract:BACKGROUND:Frontotemporal lobar degeneration (FTLD) is a progressive neurodegenerative disorder that can be triggered through genetic or sporadic mechanisms. MicroRNAs (miRNAs) have become a major therapeutic focus as their pervasive expression and powerful regulatory roles in disease pathogenesis become increasingly a...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Kocerha J,Kouri N,Baker M,Finch N,DeJesus-Hernandez M,Gonzalez J,Chidamparam K,Josephs KA,Boeve BF,Graff-Radford NR,Crook J,Dickson DW,Rademakers R

    更新日期:2011-10-27 00:00:00

  • RNA-seq analysis of galaninergic neurons from ventrolateral preoptic nucleus identifies expression changes between sleep and wake.

    abstract:BACKGROUND:Previous studies show that galanin neurons in ventrolateral preoptic nucleus (VLPO-Gal) are essential for sleep regulation. Here, we explored the transcriptional regulation of the VLPO-Gal neurons in sleep by comparing their transcriptional responses between sleeping mice and those kept awake, sacrificed at ...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Guo X,Gao X,Keenan BT,Zhu J,Sarantopoulou D,Lian J,Galante RJ,Grant GR,Pack AI

    更新日期:2020-09-14 00:00:00

  • Genome-wide identification of the histone acetyltransferase gene family in Triticum aestivum.

    abstract:BACKGROUND:Histone acetylation is a ubiquitous and reversible post-translational modification in eukaryotes and prokaryotes that is co-regulated by histone acetyltransferase (HAT) and histone deacetylase (HDAC). HAT activity is important for the modification of chromatin structure in eukaryotic cells, affecting gene tr...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Gao S,Li L,Han X,Liu T,Jin P,Cai L,Xu M,Zhang T,Zhang F,Chen J,Yang J,Zhong K

    更新日期:2021-01-11 00:00:00

  • De novo transcriptome analysis of Perna viridis highlights tissue-specific patterns for environmental studies.

    abstract:BACKGROUND:The tropical green-lipped mussel Perna viridis is a common biomonitor throughout the Indo-Pacific region that is used for environmental monitoring and ecotoxicological investigations. However, there is limited molecular data available regarding this species. We sought to establish a global transcriptome data...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Leung PT,Ip JC,Mak SS,Qiu JW,Lam PK,Wong CK,Chan LL,Leung KM

    更新日期:2014-09-19 00:00:00

  • Comparison of leaf transcriptome in response to Rhizoctonia solani infection between resistant and susceptible rice cultivars.

    abstract:BACKGROUND:Sheath blight (SB), caused by Rhizoctonia solani, is a common rice disease worldwide. Currently, rice cultivars with robust resistance to R. solani are still lacking. To provide theoretic basis for molecular breeding of R. solani-resistant rice cultivars, the changes of transcriptome profiles in response to ...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Shi W,Zhao SL,Liu K,Sun YB,Ni ZB,Zhang GY,Tang HS,Zhu JW,Wan BJ,Sun HQ,Dai JY,Sun MF,Yan GH,Wang AM,Zhu GY

    更新日期:2020-03-19 00:00:00

  • Genome-wide association study using family-based cohorts identifies the WLS and CCDC170/ESR1 loci as associated with bone mineral density.

    abstract:BACKGROUND:Osteoporosis is a common and debilitating bone disease that is characterised by a low bone mineral density (BMD), a highly heritable trait. Genome-wide association studies (GWAS) have proven to be very successful in identifying common genetic variants associated with BMD adjusted for age, gender and weight, ...

    journal_title:BMC genomics

    pub_type: 杂志文章,meta分析


    authors: Mullin BH,Walsh JP,Zheng HF,Brown SJ,Surdulescu GL,Curtis C,Breen G,Dudbridge F,Richards JB,Spector TD,Wilson SG

    更新日期:2016-02-25 00:00:00

  • The development and characterization of a 60K SNP chip for chicken.

    abstract:BACKGROUND:In livestock species like the chicken, high throughput single nucleotide polymorphism (SNP) genotyping assays are increasingly being used for whole genome association studies and as a tool in breeding (referred to as genomic selection). To be of value in a wide variety of breeds and populations, the success ...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Groenen MA,Megens HJ,Zare Y,Warren WC,Hillier LW,Crooijmans RP,Vereijken A,Okimoto R,Muir WM,Cheng HH

    更新日期:2011-05-31 00:00:00

  • Genetic variation and population structure of maize inbred lines adapted to the mid-altitude sub-humid maize agro-ecology of Ethiopia using single nucleotide polymorphic (SNP) markers.

    abstract:BACKGROUND:Molecular characterization is important for efficient utilization of germplasm and development of improved varieties. In the present study, we investigated the genetic purity, relatedness and population structure of 265 maize inbred lines from the Ethiopian Institute of Agricultural Research (EIAR), the Inte...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Ertiro BT,Semagn K,Das B,Olsen M,Labuschagne M,Worku M,Wegary D,Azmach G,Ogugo V,Keno T,Abebe B,Chibsa T,Menkir A

    更新日期:2017-10-12 00:00:00

  • Disease gene identification by random walk on multigraphs merging heterogeneous genomic and phenotype data.

    abstract:BACKGROUND:High throughput experiments resulted in many genomic datasets and hundreds of candidate disease genes. To discover the real disease genes from a set of candidate genes, computational methods have been proposed and worked on various types of genomic data sources. As a single source of genomic data is prone of...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Li Y,Li J

    更新日期:2012-01-01 00:00:00

  • Evaluation of variant identification methods for whole genome sequencing data in dairy cattle.

    abstract:BACKGROUND:Advances in human genomics have allowed unprecedented productivity in terms of algorithms, software, and literature available for translating raw next-generation sequence data into high-quality information. The challenges of variant identification in organisms with lower quality reference genomes are less we...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Baes CF,Dolezal MA,Koltes JE,Bapst B,Fritz-Waters E,Jansen S,Flury C,Signer-Hasler H,Stricker C,Fernando R,Fries R,Moll J,Garrick DJ,Reecy JM,Gredler B

    更新日期:2014-11-01 00:00:00

  • Next generation genome sequencing reveals phylogenetic clades with different level of virulence among Salmonella Typhimurium clinical human isolates in Hong Kong.

    abstract:BACKGROUND:Salmonella Typhimurium is frequently isolated from foodborne infection cases in Hong Kong, but the lack of genome sequences has hindered in-depth epidemiological and phylogenetic studies. In this study, we sought to reconstruct the phylogenetic relationship and investigate the distribution and mutation patte...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Cheng CK,Cheung MK,Nong W,Law PT,Qin J,Ling JM,Kam KM,Cheung WM,Kwan HS

    更新日期:2015-09-14 00:00:00