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 variation in expression have not been explored sufficiently to define the true extent of usability and limitations of such amplification techniques. RESULTS:We show that expression ratios are occasionally distorted by amplification using the Affymetrix small sample protocol version 2 due to a disproportional shift in intensity across biological samples. This occurs when a shift in one sample cannot be reflected in the other sample because the intensity would lie outside the dynamic range of the scanner. Interestingly, such distortions most commonly result in smaller ratios with the consequence of reducing the statistical significance of the ratios. This becomes more critical for less pronounced ratios where the evidence for differential expression is not strong. Indeed, statistical analysis by limma suggests that up to 87% of the genes with the largest and therefore most significant ratios (p < 10e(-20)) in the unamplified group have a p-value below 10e(-20) in the amplified group. On the other hand, only 69% of the more moderate ratios (10e(-20) < p < 10e(-10)) in the unamplified group have a p-value below 10e(-10) in the amplified group. Our analysis also suggests that, overall, limma shows better overlap of genes found to be significant in the amplified and unamplified groups than the Z-scores statistics. CONCLUSION:We conclude that microarray analysis of amplified samples performs best at detecting differences in gene expression, when these are large and when limma statistics are used.

journal_name

BMC Genomics

journal_title

BMC genomics

authors

Diboun I,Wernisch L,Orengo CA,Koltzenburg M

doi

10.1186/1471-2164-7-252

subject

Has Abstract

pub_date

2006-10-09 00:00:00

pages

252

issn

1471-2164

pii

1471-2164-7-252

journal_volume

7

pub_type

杂志文章
  • Differentially expressed genes from RNA-Seq and functional enrichment results are affected by the choice of single-end versus paired-end reads and stranded versus non-stranded protocols.

    abstract:BACKGROUND:RNA-Seq is now widely used as a research tool. Choices must be made whether to use paired-end (PE) or single-end (SE) sequencing, and whether to use strand-specific or non-specific (NS) library preparation kits. To date there has been no analysis of the effect of these choices on identifying differentially e...

    journal_title:BMC genomics

    pub_type: 杂志文章

    doi:10.1186/s12864-017-3797-0

    authors: Corley SM,MacKenzie KL,Beverdam A,Roddam LF,Wilkins MR

    更新日期:2017-05-23 00:00:00

  • Comprehensive whole genome sequence analyses yields novel genetic and structural insights for Intellectual Disability.

    abstract:BACKGROUND:Intellectual Disability (ID) is among the most common global disorders, yet etiology is unknown in ~30% of patients despite clinical assessment. Whole genome sequencing (WGS) is able to interrogate the entire genome, providing potential to diagnose idiopathic patients. METHODS:We conducted WGS on eight chil...

    journal_title:BMC genomics

    pub_type: 杂志文章

    doi:10.1186/s12864-017-3671-0

    authors: Zahir FR,Mwenifumbo JC,Chun HE,Lim EL,Van Karnebeek CDM,Couse M,Mungall KL,Lee L,Makela N,Armstrong L,Boerkoel CF,Langlois SL,McGillivray BM,Jones SJM,Friedman JM,Marra MA

    更新日期:2017-05-24 00:00:00

  • Muscle regeneration in dystrophin-deficient mdx mice studied by gene expression profiling.

    abstract:BACKGROUND:Duchenne muscular dystrophy (DMD), caused by mutations in the dystrophin gene, is lethal. In contrast, dystrophin-deficient mdx mice recover due to effective regeneration of affected muscle tissue. To characterize the molecular processes associated with regeneration, we compared gene expression levels in hin...

    journal_title:BMC genomics

    pub_type: 杂志文章

    doi:10.1186/1471-2164-6-98

    authors: Turk R,Sterrenburg E,de Meijer EJ,van Ommen GJ,den Dunnen JT,'t Hoen PA

    更新日期:2005-07-13 00:00:00

  • Recurrent miscalling of missense variation from short-read genome sequence data.

    abstract:BACKGROUND:Short-read resequencing of genomes produces abundant information of the genetic variation of individuals. Due to their numerous nature, these variants are rarely exhaustively validated. Furthermore, low levels of undetected variant miscalling will have a systematic and disproportionate impact on the interpre...

    journal_title:BMC genomics

    pub_type: 杂志文章

    doi:10.1186/s12864-019-5863-2

    authors: Field MA,Burgio G,Chuah A,Al Shekaili J,Hassan B,Al Sukaiti N,Foote SJ,Cook MC,Andrews TD

    更新日期:2019-07-16 00:00:00

  • RNA sequencing for global gene expression associated with muscle growth in a single male modern broiler line compared to a foundational Barred Plymouth Rock chicken line.

    abstract:BACKGROUND:Modern broiler chickens exhibit very rapid growth and high feed efficiency compared to unselected chicken breeds. The improved production efficiency in modern broiler chickens was achieved by the intensive genetic selection for meat production. This study was designed to investigate the genetic alterations a...

    journal_title:BMC genomics

    pub_type: 杂志文章

    doi:10.1186/s12864-016-3471-y

    authors: Kong BW,Hudson N,Seo D,Lee S,Khatri B,Lassiter K,Cook D,Piekarski A,Dridi S,Anthony N,Bottje W

    更新日期:2017-01-13 00:00:00

  • InvBFM: finding genomic inversions from high-throughput sequence data based on feature mining.

    abstract:BACKGROUND:Genomic inversion is one type of structural variations (SVs) and is known to play an important biological role. An established problem in sequence data analysis is calling inversions from high-throughput sequence data. It is more difficult to detect inversions because they are surrounded by duplication or ot...

    journal_title:BMC genomics

    pub_type: 杂志文章

    doi:10.1186/s12864-020-6585-1

    authors: Wu Z,Wu Y,Gao J

    更新日期:2020-03-05 00:00:00

  • Profile and functional analysis of small RNAs derived from Aspergillus fumigatus infected with double-stranded RNA mycoviruses.

    abstract:BACKGROUND:Mycoviruses are viruses that naturally infect and replicate in fungi. Aspergillus fumigatus, an opportunistic pathogen causing fungal lung diseases in humans and animals, was recently shown to harbour several different types of mycoviruses. A well-characterised defence against virus infection is RNA silencin...

    journal_title:BMC genomics

    pub_type: 杂志文章

    doi:10.1186/s12864-017-3773-8

    authors: Özkan S,Mohorianu I,Xu P,Dalmay T,Coutts RHA

    更新日期:2017-05-30 00:00:00

  • Genomic insights into virulence mechanisms of Leishmania donovani: evidence from an atypical strain.

    abstract:BACKGROUND:Leishmaniasis is a neglected tropical disease with diverse clinical phenotypes, determined by parasite, host and vector interactions. Despite the advances in molecular biology and the availability of more Leishmania genome references in recent years, the association between parasite species and distinct clin...

    journal_title:BMC genomics

    pub_type: 杂志文章

    doi:10.1186/s12864-018-5271-z

    authors: Samarasinghe SR,Samaranayake N,Kariyawasam UL,Siriwardana YD,Imamura H,Karunaweera ND

    更新日期:2018-11-28 00:00:00

  • Functional Annotation of All Salmonid Genomes (FAASG): an international initiative supporting future salmonid research, conservation and aquaculture.

    abstract::We describe an emerging initiative - the 'Functional Annotation of All Salmonid Genomes' (FAASG), which will leverage the extensive trait diversity that has evolved since a whole genome duplication event in the salmonid ancestor, to develop an integrative understanding of the functional genomic basis of phenotypic var...

    journal_title:BMC genomics

    pub_type: 社论

    doi:10.1186/s12864-017-3862-8

    authors: Macqueen DJ,Primmer CR,Houston RD,Nowak BF,Bernatchez L,Bergseth S,Davidson WS,Gallardo-Escárate C,Goldammer T,Guiguen Y,Iturra P,Kijas JW,Koop BF,Lien S,Maass A,Martin SAM,McGinnity P,Montecino M,Naish KA,Nichols K

    更新日期:2017-06-27 00:00:00

  • Comparative mitogenomic analysis of the superfamily Pentatomoidea (Insecta: Hemiptera: Heteroptera) and phylogenetic implications.

    abstract:BACKGROUND:Insect mitochondrial genomes (mitogenomes) are the most extensively used genetic marker for evolutionary and population genetics studies of insects. The Pentatomoidea superfamily is economically important and the largest superfamily within Pentatomomorpha with over 7,000 species. To better understand the div...

    journal_title:BMC genomics

    pub_type: 杂志文章

    doi:10.1186/s12864-015-1679-x

    authors: Yuan ML,Zhang QL,Guo ZL,Wang J,Shen YY

    更新日期:2015-06-16 00:00:00

  • Comprehensive SNP array study of frequently used neuroblastoma cell lines; copy neutral loss of heterozygosity is common in the cell lines but uncommon in primary tumors.

    abstract:BACKGROUND:Copy neutral loss of heterozygosity (CN-LOH) refers to a special case of LOH occurring without any resulting loss in copy number. These alterations is sometimes seen in tumors as a way to inactivate a tumor suppressor gene and have been found to be important in several types of cancer. RESULTS:We have used ...

    journal_title:BMC genomics

    pub_type: 杂志文章

    doi:10.1186/1471-2164-12-443

    authors: Kryh H,Carén H,Erichsen J,Sjöberg RM,Abrahamsson J,Kogner P,Martinsson T

    更新日期:2011-09-07 00:00:00

  • Patterned sequence in the transcriptome of vascular plants.

    abstract:BACKGROUND:Microsatellites (repeated subsequences based on motifs of one to six nucleotides) are widely used as codominant genetic markers because of their frequent polymorphism and relative selective neutrality. Minisatellites are repeats of motifs having seven or more nucleotides. The large number of EST sequences no...

    journal_title:BMC genomics

    pub_type: 杂志文章

    doi:10.1186/1471-2164-8-173

    authors: Crane CF

    更新日期:2007-06-15 00:00:00

  • Exploiting combinatorial cultivation conditions to infer transcriptional regulation.

    abstract:BACKGROUND:Regulatory networks often employ the model that attributes changes in gene expression levels, as observed across different cellular conditions, to changes in the activity of transcription factors (TFs). Although the actual conditions that trigger a change in TF activity should form an integral part of the ge...

    journal_title:BMC genomics

    pub_type: 杂志文章

    doi:10.1186/1471-2164-8-25

    authors: Knijnenburg TA,de Winde JH,Daran JM,Daran-Lapujade P,Pronk JT,Reinders MJ,Wessels LF

    更新日期:2007-01-22 00:00:00

  • Genome-wide analysis of consistently RNA edited sites in human blood reveals interactions with mRNA processing genes and suggests correlations with cell types and biological variables.

    abstract:BACKGROUND:A-to-I RNA editing is a co-/post-transcriptional modification catalyzed by ADAR enzymes, that deaminates Adenosines (A) into Inosines (I). Most of known editing events are located within inverted ALU repeats, but they also occur in coding sequences and may alter the function of encoded proteins. RNA editing ...

    journal_title:BMC genomics

    pub_type: 杂志文章

    doi:10.1186/s12864-018-5364-8

    authors: Giacopuzzi E,Gennarelli M,Sacco C,Filippini A,Mingardi J,Magri C,Barbon A

    更新日期:2018-12-27 00:00:00

  • Transcriptome profiling of aging Drosophila photoreceptors reveals gene expression trends that correlate with visual senescence.

    abstract:BACKGROUND:Aging is associated with functional decline of neurons and increased incidence of both neurodegenerative and ocular disease. Photoreceptor neurons in Drosophila melanogaster provide a powerful model for studying the molecular changes involved in functional senescence of neurons since decreased visual behavio...

    journal_title:BMC genomics

    pub_type: 杂志文章

    doi:10.1186/s12864-017-4304-3

    authors: Hall H,Medina P,Cooper DA,Escobedo SE,Rounds J,Brennan KJ,Vincent C,Miura P,Doerge R,Weake VM

    更新日期:2017-11-21 00:00:00

  • Efficient depletion of ribosomal RNA for RNA sequencing in planarians.

    abstract:BACKGROUND:The astounding regenerative abilities of planarian flatworms prompt steadily growing interest in examining their molecular foundation. Planarian regeneration was found to require hundreds of genes and is hence a complex process. Thus, RNA interference followed by transcriptome-wide gene expression analysis b...

    journal_title:BMC genomics

    pub_type: 杂志文章

    doi:10.1186/s12864-019-6292-y

    authors: Kim IV,Ross EJ,Dietrich S,Döring K,Sánchez Alvarado A,Kuhn CD

    更新日期:2019-11-29 00:00:00

  • Ion channel profiling of the Lymnaea stagnalis ganglia via transcriptome analysis.

    abstract:BACKGROUND:The pond snail Lymnaea stagnalis (L. stagnalis) has been widely used as a model organism in neurobiology, ecotoxicology, and parasitology due to the relative simplicity of its central nervous system (CNS). However, its usefulness is restricted by a limited availability of transcriptome data. While sequence i...

    journal_title:BMC genomics

    pub_type: 杂志文章

    doi:10.1186/s12864-020-07287-2

    authors: Dong N,Bandura J,Zhang Z,Wang Y,Labadie K,Noel B,Davison A,Koene JM,Sun HS,Coutellec MA,Feng ZP

    更新日期:2021-01-06 00:00:00

  • A SNP in intron 8 of CD46 causes a novel transcript associated with mastitis in Holsteins.

    abstract:BACKGROUND:The membrane protein CD46, a ubiquitous cell surface pathogen receptor, can bind Streptococcus to trigger cell autophagy, which is a critical step in the control of infection. RESULTS:In this study, we found a new splice variant designated CD46 transcript variant (CD46-TV). The splice variant is characteriz...

    journal_title:BMC genomics

    pub_type: 杂志文章

    doi:10.1186/1471-2164-15-630

    authors: Wang X,Zhong J,Gao Y,Ju Z,Huang J

    更新日期:2014-07-28 00:00:00

  • Differences in DNA curvature-related sequence periodicity between prokaryotic chromosomes and phages, and relationship to chromosomal prophage content.

    abstract:BACKGROUND:Periodic spacing of A-tracts (short runs of A or T) with the DNA helical period of ~10-11 bp is characteristic of intrinsically bent DNA. In eukaryotes, the DNA bending is related to chromatin structure and nucleosome positioning. However, the physiological role of strong sequence periodicity detected in man...

    journal_title:BMC genomics

    pub_type: 杂志文章

    doi:10.1186/1471-2164-13-188

    authors: Abel J,Mrázek J

    更新日期:2012-05-15 00:00:00

  • Genetic diversity of male and female Chinese bayberry (Myrica rubra) populations and identification of sex-associated markers.

    abstract:BACKGROUND:Chinese bayberry (Myrica rubra Sieb. & Zucc.) is an important subtropical evergreen fruit tree in southern China. Generally dioecious, the female plants are cultivated for fruit and have been studied extensively, but male plants have received very little attention. Knowledge of males may have a major impact ...

    journal_title:BMC genomics

    pub_type: 杂志文章

    doi:10.1186/s12864-015-1602-5

    authors: Jia HM,Jiao Y,Wang GY,Li YH,Jia HJ,Wu HX,Chai CY,Dong X,Guo Y,Zhang L,Gao QK,Chen W,Song LJ,van de Weg E,Gao ZS

    更新日期:2015-05-19 00:00:00

  • A comparison of gene transcription profiles of domesticated and wild Atlantic salmon (Salmo salar L.) at early life stages, reared under controlled conditions.

    abstract:BACKGROUND:Atlantic salmon have been subject to domestication for approximately ten generations, beginning in the early 1970s. This process of artificial selection will have created various genetic differences between wild and farmed stocks. Each year, hundreds of thousands of farmed fish escape into the wild. These es...

    journal_title:BMC genomics

    pub_type: 杂志文章

    doi:10.1186/1471-2164-15-884

    authors: Bicskei B,Bron JE,Glover KA,Taggart JB

    更新日期:2014-10-09 00:00:00

  • Characterization of the lipoxygenase (LOX) gene family in the Chinese white pear (Pyrus bretschneideri) and comparison with other members of the Rosaceae.

    abstract:BACKGROUND:Lipoxygenases (LOXs), a type of non-haem iron-containing dioxygenase, are ubiquitous enzymes in plants and participate in the formation of fruit aroma which is a very important aspect of fruit quality. Amongst the various aroma volatiles, saturated and unsaturated alcohols and aldehydes provide the character...

    journal_title:BMC genomics

    pub_type: 杂志文章

    doi:10.1186/1471-2164-15-444

    authors: Li M,Li L,Dunwell JM,Qiao X,Liu X,Zhang S

    更新日期:2014-06-07 00:00:00

  • Inference of gene interaction networks using conserved subsequential patterns from multiple time course gene expression datasets.

    abstract:MOTIVATION:Deciphering gene interaction networks (GINs) from time-course gene expression (TCGx) data is highly valuable to understand gene behaviors (e.g., activation, inhibition, time-lagged causality) at the system level. Existing methods usually use a global or local proximity measure to infer GINs from a single dat...

    journal_title:BMC genomics

    pub_type: 杂志文章

    doi:10.1186/1471-2164-16-S12-S4

    authors: Liu Q,Song R,Li J

    更新日期:2015-01-01 00:00:00

  • Genome-wide identification of novel intergenic enhancer-like elements: implications in the regulation of transcription in Plasmodium falciparum.

    abstract:BACKGROUND:The molecular mechanisms of transcriptional regulation are poorly understood in Plasmodium falciparum. In addition, most of the genes in Plasmodium falciparum are transcriptionally poised and only a handful of cis-regulatory elements are known to operate in transcriptional regulation. Here, we employed an ep...

    journal_title:BMC genomics

    pub_type: 杂志文章

    doi:10.1186/s12864-017-4052-4

    authors: Ubhe S,Rawat M,Verma S,Anamika K,Karmodiya K

    更新日期:2017-08-23 00:00:00

  • Characterization of the transcriptome of an ecologically important avian species, the Vinous-throated Parrotbill Paradoxornis webbianus bulomachus (Paradoxornithidae; Aves).

    abstract:BACKGROUND:Adaptive divergence driven by environmental heterogeneity has long been a fascinating topic in ecology and evolutionary biology. The study of the genetic basis of adaptive divergence has, however, been greatly hampered by a lack of genomic information. The recent development of transcriptome sequencing provi...

    journal_title:BMC genomics

    pub_type: 杂志文章

    doi:10.1186/1471-2164-13-149

    authors: Chu JH,Lin RC,Yeh CF,Hsu YC,Li SH

    更新日期:2012-04-24 00:00:00

  • Protein acetylation in mitochondria plays critical functions in the pathogenesis of fatty liver disease.

    abstract:BACKGROUND:Fatty liver is a high incidence of perinatal disease in dairy cows caused by negative energy balance, which seriously threatens the postpartum health and milk production. It has been reported that lysine acetylation plays an important role in substance and energy metabolism. Predictably, most metabolic proce...

    journal_title:BMC genomics

    pub_type: 杂志文章

    doi:10.1186/s12864-020-06837-y

    authors: Le-Tian Z,Cheng-Zhang H,Xuan Z,Zhang Q,Zhen-Gui Y,Qing-Qing W,Sheng-Xuan W,Zhong-Jin X,Ran-Ran L,Ting-Jun L,Zhong-Qu S,Zhong-Hua W,Ke-Rong S

    更新日期:2020-06-26 00:00:00

  • ProSeeK: a web server for MLPA probe design.

    abstract:BACKGROUND:The technological evolution of platforms for detecting genome-wide copy number imbalances has allowed the discovery of an unexpected amount of human sequence that is variable in copy number among individuals. This type of human variation can make an important contribution to human diversity and disease susce...

    journal_title:BMC genomics

    pub_type: 杂志文章

    doi:10.1186/1471-2164-9-573

    authors: Pantano L,Armengol L,Villatoro S,Estivill X

    更新日期:2008-11-28 00:00:00

  • UDiTaS™, a genome editing detection method for indels and genome rearrangements.

    abstract:BACKGROUND:Understanding the diversity of repair outcomes after introducing a genomic cut is essential for realizing the therapeutic potential of genomic editing technologies. Targeted PCR amplification combined with Next Generation Sequencing (NGS) or enzymatic digestion, while broadly used in the genome editing field...

    journal_title:BMC genomics

    pub_type: 杂志文章

    doi:10.1186/s12864-018-4561-9

    authors: Giannoukos G,Ciulla DM,Marco E,Abdulkerim HS,Barrera LA,Bothmer A,Dhanapal V,Gloskowski SW,Jayaram H,Maeder ML,Skor MN,Wang T,Myer VE,Wilson CJ

    更新日期:2018-03-21 00:00:00

  • Endogenous siRNAs and piRNAs derived from transposable elements and genes in the malaria vector mosquito Anopheles gambiae.

    abstract:BACKGROUND:The siRNA and piRNA pathways have been shown in insects to be essential for regulation of gene expression and defence against exogenous and endogenous genetic elements (viruses and transposable elements). The vast majority of endogenous small RNAs produced by the siRNA and piRNA pathways originate from repet...

    journal_title:BMC genomics

    pub_type: 杂志文章

    doi:10.1186/s12864-015-1436-1

    authors: Biryukova I,Ye T

    更新日期:2015-04-10 00:00:00

  • DAIRYdb: a manually curated reference database for improved taxonomy annotation of 16S rRNA gene sequences from dairy products.

    abstract:BACKGROUND:Reads assignment to taxonomic units is a key step in microbiome analysis pipelines. To date, accurate taxonomy annotation of 16S reads, particularly at species rank, is still challenging due to the short size of read sequences and differently curated classification databases. The close phylogenetic relations...

    journal_title:BMC genomics

    pub_type: 杂志文章

    doi:10.1186/s12864-019-5914-8

    authors: Meola M,Rifa E,Shani N,Delbès C,Berthoud H,Chassard C

    更新日期:2019-07-08 00:00:00