Articles

Whole-genome microarrays of fission yeast: characteristics, accuracy, reproducibility, and processing of array data

The genome of the fission yeast Schizosaccharomyces pombe has recently been sequenced, setting the stage for the post-genomic era of this increasingly popular model organism. We have built fission yeast microarra...

Authors: Rachel Lyne, Gavin Burns, Juan Mata, Chris J Penkett, Gabriella Rustici, Dongrong Chen, Cordelia Langford, David Vetrie and Jürg Bähler

Identification of nutrient partitioning genes participating in rice grain filling by singular value decomposition (SVD) of genome expression data

In order to identify rice genes involved in nutrient partitioning, microarray experiments have been done to quantify genomic scale gene expression. Genes involved in nutrient partitioning, specifically grain f...

Authors: Abraham Anderson, Matthew Hudson, Wenqiong Chen and Tong Zhu

A transcription map of the 6p22.3 reading disability locus identifying candidate genes

Reading disability (RD) is a common syndrome with a large genetic component. Chromosome 6 has been identified in several linkage studies as playing a significant role. A more recent study identified a peak of ...

Authors: Eric R Londin, Haiying Meng and Jeffrey R Gruen

TMC and EVER genes belong to a larger novel family, the TMC gene family encoding transmembrane proteins

Mutations in the transmembrane cochlear expressed gene 1 (TMC1) cause deafness in human and mouse. Mutations in two homologous genes, EVER1 and EVER2 increase the susceptibility to infection with certain human pa...

Authors: Gabor Keresztes, Hideki Mutai and Stefan Heller

The construction and use of bacterial DNA microarrays based on an optimized two-stage PCR strategy

DNA microarrays are a powerful tool with important applications such as global gene expression profiling. Construction of bacterial DNA microarrays from genomic sequence data using a two-stage PCR amplificatio...

Authors: Bradley L Postier, Hong-Liang Wang, Abhay Singh, Lori Impson, Heather L Andrews, Jessica Klahn, Hong Li, George Risinger, David Pesta, Michael Deyholos, David W Galbraith, Louis A Sherman and Robert L Burnap

Gene discovery in the hamster: a comparative genomics approach for gene annotation by sequencing of hamster testis cDNAs

Complete genome annotation will likely be achieved through a combination of computer-based analysis of available genome sequences combined with direct experimental characterization of expressed regions of indi...

Authors: Sreedhar Oduru, Janee L Campbell, SriTulasi Karri, William J Hendry, Shafiq A Khan and Simon C Williams

High accuracy genotyping directly from genomic DNA using a rolling circle amplification based assay

Rolling circle amplification of ligated probes is a simple and sensitive means for genotyping directly from genomic DNA. SNPs and mutations are interrogated with open circle probes (OCP) that can be circulariz...

Authors: Osama A Alsmadi, Carole J Bornarth, Wanmin Song, Michele Wisniewski, Jing Du, Joel P Brockman, A Fawad Faruqi, Seiyu Hosono, Zhenyu Sun, Yuefen Du, Xiaohong Wu, Michael Egholm, Patricio Abarzúa, Roger S Lasken and Mark D Driscoll

A high resolution physical and RH map of pig chromosome 6q1.2 and comparative analysis with human chromosome 19q13.1

The generation of BAC/PAC contigs in targeted genome regions is a powerful method to establish high-resolution physical maps. In domestic animal species the generation of such contigs is typically initiated wi...

Authors: Flávia Martins-Wess, Denis Milan, Cord Drögemüller, Rodja Voβ-Nemitz, Bertram Brenig, Annie Robic, Martine Yerle and Tosso Leeb

Development and validation of a T7 based linear amplification for genomic DNA

Genomic maps of transcription factor binding sites and histone modification patterns provide unique insight into the nature of gene regulatory networks and chromatin structure. These systematic studies use mic...

Authors: Chih Long Liu, Stuart L Schreiber and Bradley E Bernstein

The gene structure and expression of human ABHD1: overlapping polyadenylation signal sequence with Sec12

Overlapping sense/antisense genes orientated in a tail-to-tail manner, often involving only the 3'UTRs, form the majority of gene pairs in mammalian genomes and can lead to the formation of double-stranded RNA...

Authors: Alasdair J Edgar

Wavelet to predict bacterial ori and ter: a tendency towards a physical balance

Chromosomal DNA replication in bacteria starts at the origin (ori) and the two replicores propagate in opposite directions up to the terminus (ter) region. We hypothesize that the two replicores need to reach ter

Authors: Jiuzhou Song, Antony Ware and Shu-Lin Liu

A general cloning system to selectively isolate any eukaryotic or prokaryotic genomic region in yeast

Transformation-associated recombination (TAR) cloning in yeast is a unique method for selective isolation of large chromosomal fragments or entire genes from complex genomes. The technique involves homologous ...

Authors: Vladimir N Noskov, Natalay Kouprina, Sun-Hee Leem, Ilia Ouspenski, J Carl Barrett and Vladimir Larionov

Partial duplication of the APBA2 gene in chromosome 15q13 corresponds to duplicon structures

Chromosomal abnormalities affecting human chromosome 15q11-q13 underlie multiple genomic disorders caused by deletion, duplication and triplication of intervals in this region. These events are mediated by hig...

Authors: James S Sutcliffe, Michael K Han, Taneem Amin, Robert A Kesterson and Erika L Nurmi

Unusual misregulation of RNA splicing caused by insertion of a transposable element into the T (Brachyury) locus

The T ^Wis mutant allele of the Brachyury, or T, gene was created by insertion of an endogenous retrovirus-like early transposon (ETn) element into the exon 7 splice donor con...

Authors: Sarah N Goldin and Virginia E Papaioannou

TOX defines a conserved subfamily of HMG-box proteins

HMG-box proteins are a large and diverse superfamily of architectural factors that share one or more copies of a sequence- and structurally-related DNA binding domain. These proteins can modify chromatin struc...

Authors: Emmett O'Flaherty and Jonathan Kaye

Analysis of two large functionally uncharacterized regions in the Methanopyrus kandleri AV19 genome

For most sequenced prokaryotic genomes, about a third of the protein coding genes annotated are "orphan proteins", that is, they lack homology to known proteins. These hypothetical genes are typically short an...

Authors: Lars Juhl Jensen, Marie Skovgaard, Thomas Sicheritz-Pontén, Merete Kjær Jørgensen, Christiane Lundegaard, Corinna Cavan Pedersen, Nanna Petersen and David Ussery

Effects of mRNA amplification on gene expression ratios in cDNA experiments estimated by analysis of variance

A limiting factor of cDNA microarray technology is the need for a substantial amount of RNA per labeling reaction. Thus, 20–200 micro-grams total RNA or 0.5–2 micro-grams poly (A) RNA is typically required for...

Authors: Vigdis Nygaard, Anders Løland, Marit Holden, Mette Langaas, Håvard Rue, Fang Liu, Ola Myklebost, Øystein Fodstad, Eivind Hovig and Birgitte Smith-Sørensen

Simple sequence repeats and compositional bias in the bipartite Ralstonia solanacearum GMI1000 genome

Ralstonia solanacearum is an important plant pathogen. The genome of R. solananearum GMI1000 is organised into two replicons (a 3.7-Mb chromosome and a 2.1-Mb megaplasmid) and this bipartite genome structure is c...

Authors: Tom Coenye and Peter Vandamme

Refined physical map of the human PAX2/HOX11/NFKB2 cancer gene region at 10q24 and relocalization of the HPV6AI1 viral integration site to 14q13.3-q21.1

Chromosome band 10q24 is a gene-rich domain and host to a number of cancer, developmental, and neurological genes. Recurring translocations, deletions and mutations involving this chromosome band have been obs...

Authors: Sheryl M Gough, Margaret McDonald, Xiao-Ning Chen, Julie R Korenberg, Antonino Neri, Tomas Kahn, Michael R Eccles and Christine M Morris

Development of a porcine skeletal muscle cDNA microarray: analysis of differential transcript expression in phenotypically distinct muscles

Microarray profiling has the potential to illuminate the molecular processes that govern the phenotypic characteristics of porcine skeletal muscles, such as hypertrophy or atrophy, and the expression of specif...

Authors: Qianfan Bai, Christine McGillivray, Nuno da Costa, Saffron Dornan, Gary Evans, Michael James Stear and Kin-Chow Chang

Sequence determinants in human polyadenylation site selection

Differential polyadenylation is a widespread mechanism in higher eukaryotes producing mRNAs with different 3' ends in different contexts. This involves several alternative polyadenylation sites in the 3' UTR, ...

Authors: Matthieu Legendre and Daniel Gautheret

STRP Screening Sets for the human genome at 5 cM density

Short tandem repeat polymorphisms (STRPs) are powerful tools for gene mapping and other applications. A STRP genome scan of 10 cM is usually adequate for mapping single gene disorders. However mapping studies ...

Authors: Nader Ghebranious, David Vaske, Adong Yu, Chengfeng Zhao, Gabor Marth and James L Weber

Ancient conserved domains shared by animal soluble guanylyl cyclases and bacterial signaling proteins

Soluble guanylyl cyclases (SGCs) are dimeric enzymes that transduce signals downstream of nitric oxide (NO) in animals. They sense NO by means of a heme moiety that is bound to their N-terminal extensions.

Authors: Lakshminarayan M Iyer, Vivek Anantharaman and L Aravind

Reproducibility of oligonucleotide arrays using small samples

Low RNA yields from small tissue samples can limit the use of oligonucleotide microarrays (Affymetrix GeneChips^®). Methods using less cRNA for hybridization or amplifying the cRNA have been reported to reduce the...

Authors: Jeanette N McClintick, Ronald E Jerome, Charles R Nicholson, David W Crabb and Howard J Edenberg

In silico characterisation and chromosomal localisation of human RRH (peropsin) – implications for opsin evolution

The vertebrate opsins are proteins which utilise a retinaldehyde chromophore in their photosensory or photoisomerase roles in the visual/irradiance detection cycle. The majority of the opsins, such as rod and ...

Authors: James Bellingham, Dominic J Wells and Russell G Foster

Gene trap mutagenesis of hnRNP A2/B1: a cryptic 3' splice site in the neomycin resistance gene allows continued expression of the disrupted cellular gene

Tagged sequence mutagenesis is a process for constructing libraries of sequenced insertion mutations in embryonic stem cells that can be transmitted into the mouse germline. To better predict the functional co...

Authors: Michael Roshon, James V DeGregori and H Earl Ruley

Comparative study of methyl-CpG-binding domain proteins

Methylation at CpG dinucleotides in genomic DNA is a fundamental epigenetic mechanism of gene expression control in vertebrates. Proteins with a methyl-CpG-binding domain (MBD) can bind to single methylated Cp...

Authors: Tim C Roloff, H Hilger Ropers and Ulrike A Nuber

Cynomolgus monkey testicular cDNAs for discovery of novel human genes in the human genome sequence

In order to contribute to the establishment of a complete map of transcribed regions of the human genome, we constructed a testicular cDNA library for the cynomolgus monkey, and attempted to find novel transcr...

Authors: Naoki Osada, Munetomo Hida, Jun Kusuda, Reiko Tanuma, Makoto Hirata, Yumiko Suto, Momoki Hirai, Keiji Terao, Sumio Sugano and Katsuyuki Hashimoto

Outliers involving the Poly(A) effect among highly-expressed genes in microarrays

The Poly(A) effect is a cross-hybridization artifact in which poly(T)-containing molecules, which are produced by the reverse transcription of a poly(A)⁺ RNA mixture, bind promiscuously to the poly(A) stretches o...

Authors: Shujia J Pan, David R Rigney and John L Ivy

DNA sequence conservation between the Bacillus anthracis pXO2 plasmid and genomic sequence from closely related bacteria

Complete sequencing and annotation of the 96.2 kb Bacillus anthracis plasmid, pXO2, predicted 85 open reading frames (ORFs). Bacillus cereus and Bacillus thuringiensis isolates that ranged in genomic similarity t...

Authors: James Pannucci, Richard T Okinaka, Erin Williams, Robert Sabin, Lawrence O Ticknor and Cheryl R Kuske

The catalytic domains of thiamine triphosphatase and CyaB-like adenylyl cyclase define a novel superfamily of domains that bind organic phosphates

The CyaB protein from Aeromonas hydrophila has been shown to possess adenylyl cyclase activity. While orthologs of this enzyme have been found in some bacteria and archaea, it shows no detectable relationship to ...

Authors: Lakshminarayan M Iyer and L Aravind

Domain-oriented functional analysis based on expression profiling

Co-regulation of genes may imply involvement in similar biological processes or related function. Many clusters of co-regulated genes have been identified using microarray experiments. In this study, we examin...

Authors: Wei Ding, Luquan Wang, Ping Qiu, Mitchel Kostich, Jonathan Greene and Marco Hernandez

Optimization and evaluation of T7 based RNA linear amplification protocols for cDNA microarray analysis

T7 based linear amplification of RNA is used to obtain sufficient antisense RNA for microarray expression profiling. We optimized and systematically evaluated the fidelity and reproducibility of different ampl...

Authors: Hongjuan Zhao, Trevor Hastie, Michael L Whitfield, Anne-Lise Børresen-Dale and Stefanie S Jeffrey

Mutation screening of two candidate genes from 13q32 in families affected with Bipolar disorder: human peptide transporter (SLC15A1) and human glypican5 (GPC5)

Multiple candidate regions as sites for Schizophrenia and Bipolar susceptibility genes have been reported, suggesting heterogeneity of susceptibility genes or oligogenic inheritance. Linkage analysis has sugge...

Authors: Manjula Maheshwari, SL Christian, C Liu, JA Badner, S Detera-Wadleigh, ES Gershon and Richard A Gibbs

A reference database for tumor-related genes co-expressed with interleukin-8 using genome-scale in silico analysis

The EST database provides a rich resource for gene discovery and in silico expression analysis. We report a novel computational approach to identify co-expressed genes using EST database, and its application to I...

Authors: Lawrence Benbow, Lynn Wang, Maureen Laverty, Suxing Liu, Ping Qiu, Richard W Bond, Eric Gustafson, Joseph A Hedrick, Mitchell Kostich, Jonathan R Greene and Luquan Wang

Assessment of differential gene expression in human peripheral nerve injury

Microarray technology is a powerful methodology for identifying differentially expressed genes. However, when thousands of genes in a microarray data set are evaluated simultaneously by fold changes and signif...

Authors: Yuanyuan Xiao, Mark R Segal, Douglas Rabert, Andrew H Ahn, Praveen Anand, Lakshmi Sangameswaran, Donglei Hu and C Anthony Hunt

Cross-species hybridisation of pig RNA to human nylon microarrays

The objective of this research was to investigate the reproducibility of cross-species microarray hybridisation. Comparisons between same- and cross-species hybridisations were also made. Nine hybridisations b...

Authors: DE Moody, Z Zou and L McIntyre

Mouse ribonuclease III. cDNA structure, expression analysis, and chromosomal location

Members of the ribonuclease III superfamily of double-stranded(ds)-RNA-specific endoribonucleases participate in diverse RNA maturation and decay pathways in eukaryotic and prokaryotic cells. A human RNase III...

Authors: Kristine R Fortin, Rhonda H Nicholson and Allen W Nicholson

In silico and in situ characterization of the zebrafish (Danio rerio) gnrh3 (sGnRH) gene

Gonadotropin releasing hormone (GnRH) is responsible for stimulation of gonadotropic hormone (GtH) in the hypothalamus-pituitary-gonadal axis (HPG). The regulatory mechanisms responsible for brain specificity ...

Authors: Jacob Torgersen, Rasoul Nourizadeh-Lillabadi, Harald Husebye and Peter Aleström

High-resolution physical map for chromosome 16q12.1-q13, the Blau syndrome locus

The Blau syndrome (MIM 186580), an autosomal dominant granulomatous disease, was previously mapped to chromosome 16p12-q21. However, inconsistent physical maps of the region and consequently an unknown order o...

Authors: Xiaoju Wang, Helena Kuivaniemi, Gina Bonavita, Charlene J Williams and Gerard Tromp

Pervasive properties of the genomic signature

The dinucleotide relative abundance profile can be regarded as a genomic signature because, despite diversity between species, it varies little between 50 kilobase or longer windows on a given genome. Both the...

Authors: Robert W Jernigan and Robert H Baran

Multigene family isoform profiling from blood cell lineages

Analysis of cell-selective gene expression for families of proteins of therapeutic interest is crucial when deducing the influence of genes upon complex traits and disease susceptibility. Presently, there is n...

Authors: Grant Dewson, Edward C Conley and Peter Bradding

Comparative analysis of somitogenesis related genes of the hairy/Enhancer of split class in Fugu and zebrafish

Members of a class of bHLH transcription factors, namely the hairy (h), Enhancer of split (E(spl)) and hairy-related with YRPW motif (hey) (h/E(spl)/hey) genes are involved in vertebrate somitogenesis and some of...

Authors: Martin Gajewski and Chris Voolstra

"In-gel" purified ditags direct synthesis of highly efficient SAGE Libraries

SAGE (serial analysis of gene expression) is a recently developed technique for systematic analysis of eukaryotic transcriptomes. The most critical step in the SAGE method is large scale amplification of ditag...

Authors: Saroj P Mathupala and Andrew E Sloan

Defining signal thresholds in DNA microarrays: exemplary application for invasive cancer

Genome-wide or application-targeted microarrays containing a subset of genes of interest have become widely used as a research tool with the prospect of diagnostic application. Intrinsic variability of microar...

Authors: M Bilban, LK Buehler, S Head, G Desoye and V Quaranta

Expression and genomic analysis of midasin, a novel and highly conserved AAA protein distantly related to dynein

The largest open reading frame in the Saccharomyces genome encodes midasin (MDN1p, YLR106p), an AAA ATPase of 560 kDa that is essential for cell viability. Orthologs of midasin have been identified in the geno...

Authors: Joan E Garbarino and I R Gibbons

GPR99, a new G protein-coupled receptor with homology to a new subgroup of nucleotide receptors

Based on sequence similarity, the superfamily of G protein-coupled receptors (GPRs) can be subdivided into several subfamilies, the members of which often share similar ligands. The sequence data provided by t...

Authors: Timo Wittenberger, Susanne Hellebrand, Antonia Munck, Hans-Jürgen Kreienkamp, H Chica Schaller and Wolfgang Hampe

Obtaining reliable information from minute amounts of RNA using cDNA microarrays

High density cDNA microarray technology provides a powerful tool to survey the activity of thousands of genes in normal and diseased cells, which helps us both to understand the molecular basis of the disease ...

Authors: Limei Hu, Jing Wang, Keith Baggerly, Hua Wang, Gregory N Fuller, Stanley R Hamilton, Kevin R Coombes and Wei Zhang

Complete genome sequence of a novel extrachromosomal virus-like element identified in planarian Girardia tigrina

Freshwater planarians are widely used as models for investigation of pattern formation and studies on genetic variation in populations. Despite extensive information on the biology and genetics of planaria, th...

Authors: Denis V Rebrikov, Maria E Bulina, Ekaterina A Bogdanova, Loura L Vagner and Sergey A Lukyanov

Erratum to: The cloning, genomic organization and tissue expression profile of the human DLG5 gene: Correction

Authors: Gopi Shah, Ramon Brugada, Oscar Gonzalez, Grazyna Czernuszewicz, Richard A Gibbs, Linda Bachinski and Robert Roberts