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PubMed2007

Global analysis of chromosome X gene expression in primary cultures of normal ovarian surface epithelial cells and epithelial ovarian cancer cell lines.

The interpretation of loss of heterozygosity (LOH) in cancers is complicated as genes that map to LOH regions may be transcriptionally active (Xa) or inactive (Xi) due to X chromosome inactivation (XCI). We have analyzed the chromosome X transcriptome in four epithelial ovarian cancer (EOC) cell lines (TOV21G, TOV81D, TOV112D, and OV90) and 12 primary cultures of normal ovarian surface epithelial (NOSE) cells in relation to chromosome X integrity. Two-way comparative analysis using HuGeneFL Affymetrix GeneChips of TOV21G, TOV81D and OV90 relative to the NOSE samples was highly correlated (> 89%) in contrast to that of TOV112D (56-69%). TOV112D, followed by TOV21G, exhibited the largest number of up-regulated genes. XIST expression by RT-PCR was not detectable in TOV112D or TOV21G. Allele-specific transcription by cDNA sequence analysis of genes known to be subjected to XCI revealed maintenance of XCI in TOV81D and OV90, but not TOV21G. Biallelic expression could not be assessed in TOV112D due to reduction to hemizygosity of chromosome X. Chromosome X rearrangements were observed in FISH analysis of TOV112D and TOV21G, and both of these EOC cell lines were negative for Barr body analysis. The differentially expressed genes did not appear to map to any particular region of the X chromosome in any EOC cell line. The absence of XIST expression is consistent with Barr body loss in TOV112D and TOV21G. The combined evidence is consistent with two proposed mechanisms to account for absence of Xi in female cancers: Xi loss followed by Xa duplication (exemplified by TOV112D) and transcriptional reactivation of Xi (exemplified by TOV21G). Despite an alteration in XIST expression and differences in allelic content in the EOC cell lines, the chromosome X transcriptome was modified modestly when compared with that of NOSE samples.

Cell Line, Tumor↗

PubMed2006

Analysis of the wheat endosperm transcriptome.

Among the cereals, wheat is the most widely grown geographically and is part of the staple diet in much of the world. Understanding how the cereal endosperm develops and functions will help generate better tools to manipulate grain qualities important to end-users. We used a genomics approach to identify and characterize genes that are expressed in the wheat endosperm. We analyzed the 17,949 publicly available wheat endosperm EST sequences to identify genes involved in the biological processes that occur within this tissue. Clustering and assembly of the ESTs resulted in the identification of 6,187 tentative unique genes, 2,358 of which formed contigs and 3,829 remained as singletons. A BLAST similarity search against the NCBI non-redundant sequence database revealed abundant messages for storage proteins, putative defense proteins, and proteins involved in starch and sucrose metabolism. The level of abundance of the putatively identified genes reflects the physiology of the developing endosperm. Half of the identified genes have unknown functions. Approximately 61% of the endosperm ESTs has been tentatively mapped in the hexaploid wheat genome. Using microarrays for global RNA profiling, we identified endosperm genes that are specifically up regulated in the developing grain.

Expressed Sequence Tags↗

PubMed2006

Transcriptome analysis reveals the population of dendritic RNAs and their redistribution by neural activity.

Subcellular localization of RNA is an efficient way to localize proteins to a specific region of a cell. The dendritic localization of RNAs underlies the establishment and maintenance of the synaptic functions of neuronal cells. A requirement for dendritic RNA localization and subsequent local translation has been demonstrated in several forms of experience-dependent synaptic plasticity. In spite of several attempts to identify these RNAs, the population of RNA species present in dendrites as a whole has not been well described. Here we show the results of microarray analyses with RNAs isolated from heavy portion of polysome (HP) fraction where RNA granules are enriched in and synaptosome fraction, prepared from the rat brain. These analyses revealed the complex nature of the dendritic RNA population, which included RNAs that were not expected to be in the dendrites. Neural activity caused by an electroconvulsive shock triggered a redistribution of the population of dendritic transcriptome towards the area of overlap between the HP and the synaptosome, which is assumed to be neck of spine. This redistribution may accompany some changes in the translatability of those transcriptome, which suggests complex mechanisms of local translation in response to synaptic inputs.

Animals↗

PubMed2026

Wound healing in Atlantic spiny dogfish sharks.

Field observations and limited experimental studies indicate that elasmobranchs can repair substantial skin injuries, but the temporal course and cellular composition of wound healing in Atlantic spiny dogfish remain poorly characterized. We conducted an exploratory laboratory study in 20 female Atlantic spiny dogfish (Squalus acanthias) using standardized full-thickness skin wounds monitored by serial photography for 35 days, histological analysis at defined post-injury time points, and pooled single-nucleus RNA sequencing of intact and wounded skin. A continuous neoepithelial layer covered all examined wound beds by Day 1, whereas macroscopic wound area decreased progressively over 35 days and dermal denticles remained absent from the repaired surface. Histological examination showed progressive neoepidermal maturation, basement-membrane reformation, collagen deposition, and granulation-tissue organization, indicating that epithelial coverage preceded restoration of normal skin architecture. Single-nucleus RNA sequencing identified epithelial, stromal, vascular, pigment, neural, and immune-cell populations. T and B cells were detected in intact skin, and their relative abundance, together with that of several other leukocyte populations, increased at Day 1 and generally declined by Day 14. Because samples were pooled by time point, these transcriptomic changes are descriptive. These findings characterize rapid early reepithelialization followed by slower tissue remodeling in Atlantic spiny dogfish and provide a foundation for future comparative studies of elasmobranch skin repair.

Animals↗

PubMed2004

Simulated annealing of microarray data reduces noise and enables cross-experimental comparisons.

Microarrays are a powerful tool for assessing the genome-wide induction of a transcriptional response to internal or external stimuli, but are not considered quantitatively rigorous (i.e., the signal intensity of hybridized probe is normally used to quantify relative transcript abundance). Thus, it is difficult, if not impossible, to accurately compare separate microarray experiments without a reference standard. However, even among replicated microarray experiments, each gene varies significantly in the amount of signal detected, suggesting no single gene would be appropriate as a standard. We propose and test a method to "align" experimental transcription profiles to a set of reference experiments using simulated annealing (SA), essentially using the relative positions of all genes as a reference standard. SA attempts to find a globally optimal adjustment factor for the relative expression level of each experimental gene expression signal, given a previously observed range of gene expression measurements. By defining a relative dynamic range of gene expression under control conditions for all genes, we can more accurately compare transcription profiles between separate experiments and, potentially, between species--enabling comparative transcriptomics. Testing SA on a published dataset, we find that it significantly reduces interexperimental variation, suggesting it holds promise to accomplish this goal.

Oligonucleotide Array Sequence Analysis↗

PubMed2003

A novel family in Medicago truncatula consisting of more than 300 nodule-specific genes coding for small, secreted polypeptides with conserved cysteine motifs.

Transcriptome analysis of Medicago truncatula nodules has led to the discovery of a gene family named NCR (nodule-specific cysteine rich) with more than 300 members. The encoded polypeptides were short (60-90 amino acids), carried a conserved signal peptide, and, except for a conserved cysteine motif, displayed otherwise extensive sequence divergence. Family members were found in pea (Pisum sativum), broad bean (Vicia faba), white clover (Trifolium repens), and Galega orientalis but not in other plants, including other legumes, suggesting that the family might be specific for galegoid legumes forming indeterminate nodules. Gene expression of all family members was restricted to nodules except for two, also expressed in mycorrhizal roots. NCR genes exhibited distinct temporal and spatial expression patterns in nodules and, thus, were coupled to different stages of development. The signal peptide targeted the polypeptides in the secretory pathway, as shown by green fluorescent protein fusions expressed in onion (Allium cepa) epidermal cells. Coregulation of certain NCR genes with genes coding for a potentially secreted calmodulin-like protein and for a signal peptide peptidase suggests a concerted action in nodule development. Potential functions of the NCR polypeptides in cell-to-cell signaling and creation of a defense system are discussed.

Amino Acid Sequence↗

PubMed2006

Inactivation of the Pseudomonas putida cytochrome o ubiquinol oxidase leads to a significant change in the transcriptome and to increased expression of the CIO and cbb3-1 terminal oxidases.

Pseudomonas putida KT2440 contains a branched aerobic respiratory chain with several terminal oxidases. Inactivation of the cyo terminal ubiquinol oxidase has little effect on growth rate but is known to relieve the inhibition by global control that modulates induction of genes required to assimilate alkanes in cells growing in the presence of preferred carbon sources. We show that inactivation of other terminal oxidases has no effect on regulation of the alkane degradation pathway, which points to cyo as the oxidase that transmits a regulatory signal related to the activity of the electron transport chain. Using a genome-wide DNA microarray we found that inactivation of cyo has a significant effect on the transcriptome, supporting that it participates in global regulation of gene expression. Among the genes affected stand out those coding for transporters of organic acids, porins, transcriptional regulators and terminal oxidases. Real-time reverse transcription polymerase chain reaction (RT-PCR) showed that, in cells growing exponentially in a complete medium, the absence of cyo was compensated by increased expression of the cyanide-insensitive and cbb3-1 terminal oxidases, while cbb3-2 and aa3 oxidases remained unaffected. When cells enter into stationary phase cyo levels decrease and inhibition of the alkane degradation genes ceases. This was paralleled by upregulation of the cyanide-insensitive, cbb3-1, cbb3-2 and aa3 terminal oxidases. The results suggest that P. putida adapts the composition of the electron transport chain not only to optimize energy generation, but also to influence the transcriptome profile of the cell through global control of gene expression.

Alkanes↗

PubMed2006

Transcriptome analysis of bud burst in sessile oak (Quercus petraea).

Expression patterns of hundreds of transcripts in apical buds were monitored during bud flushing in sessile oak (Quercus petraea), in order to identify genes differentially expressed between the quiescent and active stage of bud development. Different transcriptomic techniques combining the construction of suppression subtractive hybridization (SSH) libraries and the monitoring of gene expression using macroarray and real-time reverse transcriptase polymerase chain reaction (RT-PCR) were performed to dissect bud burst, with a special emphasis on the onset of the process. We generated 801 expressed sequence tags (ESTs) derived from six developmental stages of bud burst. Macroarray experiment revealed a total of 233 unique transcripts exhibiting differential expression during the process, and a putative function was assigned to 65% of them. Cell rescue/defense-, metabolism-, protein synthesis-, cell cycle- and transcription-related transcripts were among the most regulated genes. Macroarray and real-time RT-PCR showed that several genes exhibited contrasted expressions between quiescent and swelling buds, such as a putative homologue of the transcription factor DAG2 (Dof Affecting Germination 2), previously reported to be involved in the control of seed germination in Arabidopsis thaliana. These differentially expressed genes constitute relevant candidates for signaling pathway of bud burst in trees.

Cluster Analysis↗

PubMed2004

Transcriptome analysis of alfalfa glandular trichomes.

Glandular trichomes are a major site of plant natural product synthesis and accumulation for protection against insect predation. However, to date few studies have attempted to obtain a global view of trichome gene expression. Two contrasting approaches have been adopted to investigate genes expressed in glandular trichomes from alfalfa (Medicago sativa L.). In the first approach, 5,674 clones from an alfalfa glandular trichome cDNA library were sequenced. The most highly abundant expressed sequence tag (EST) corresponded to a lipid transfer protein. The presence of ESTs corresponding to enzymes for all steps in the biosynthesis of flavonoids suggests that these are important metabolites in alfalfa trichome biology, as confirmed by histochemistry and metabolite profiling. No ESTs corresponded to enzymes of cyclized terpenoid biosynthesis. In a second approach, microarray analysis was used to compare levels of alfalfa transcripts corresponding to 16,086 Medicago truncatula A17 genes in stems with and without trichomes. This revealed over 1,000 genes with strong preferential expression in the trichome fraction of the stem, 70% of which are of unknown function. These define a class of genes that are not trichome-specific, since M. truncatula A17 does not itself have glandular trichomes, but has potential importance for trichome function within the stem.

Base Sequence↗

PubMed2005

A comparative analysis by SAGE of gene expression profiles of Barrett's esophagus, normal squamous esophagus, and gastric cardia.

BACKGROUND & AIMS: The metaplastic process in which the normal squamous epithelium of the distal esophagus is replaced by columnar-lined epithelium, known as Barrett's esophagus (BE), is poorly understood. The aim of this study was to define, analyze, and compare transcription profiles of BE, normal cardia epithelium, and squamous epithelium to gain more insight into the process of metaplasia and to identify uniquely expressed genes in these epithelia. METHODS: Serial analysis of gene expression was applied for obtaining transcription libraries of biopsy specimens taken from a BE-affected patient with intestinal type of metaplasia and from normal squamous and gastric cardia epithelia. Validation of results by reverse-transcription polymerase chain reaction and immunoblotting was performed using tissues of 20 patients with BE. RESULTS: More than 120,000 tags were sequenced. Between BE and squamous 776, and between BE and gastric cardia 534 tags were significantly differentially expressed (P < .05, pairwise comparison). In contrast, squamous compared with gastric cardia epithelia showed significant differential expression of 1316 tags. The most up-regulated genes in BE compared with squamous epithelium were trefoil factors, annexin A10, and galectin-4. Each of the epithelia showed a unique cytokeratin expression profile. CONCLUSIONS: This study provides a comparison of the transcriptomes of BE, squamous epithelium, and gastric cardia epithelium. BE proves to be an incompletely differentiated type of epithelium that shows similarities to both normal squamous and gastric cardia epithelia. In addition, several uniquely expressed genes are identified. These results are a major advancement in understanding the process of metaplasia that leads to BE.

Adult↗

PubMed2006

Bioinformatic screening of human ESTs for differentially expressed genes in normal and tumor tissues.

BACKGROUND: Owing to the explosion of information generated by human genomics, analysis of publicly available databases can help identify potential candidate genes relevant to the cancerous phenotype. The aim of this study was to scan for such genes by whole-genome in silico subtraction using Expressed Sequence Tag (EST) data. METHODS: Genes differentially expressed in normal versus tumor tissues were identified using a computer-based differential display strategy. Bcl-xL, an anti-apoptotic member of the Bcl-2 family, was selected for confirmation by western blot analysis. RESULTS: Our genome-wide expression analysis identified a set of genes whose differential expression may be attributed to the genetic alterations associated with tumor formation and malignant growth. We propose complete lists of genes that may serve as targets for projects seeking novel candidates for cancer diagnosis and therapy. Our validation result showed increased protein levels of Bcl-xL in two different liver cancer specimens compared to normal liver. Notably, our EST-based data mining procedure indicated that most of the changes in gene expression observed in cancer cells corresponded to gene inactivation patterns. Chromosomes and chromosomal regions most frequently associated with aberrant expression changes in cancer libraries were also determined. CONCLUSION: Through the description of several candidates (including genes encoding extracellular matrix and ribosomal components, cytoskeletal proteins, apoptotic regulators, and novel tissue-specific biomarkers), our study illustrates the utility of in silico transcriptomics to identify tumor cell signatures, tumor-related genes and chromosomal regions frequently associated with aberrant expression in cancer.

Algorithms↗

PubMed2026

The Small Noncoding RNA, RsaC, Is Essential for Staphylococcus aureus Virulence.

BACKGROUND: Bacterial small noncoding RNAs (sRNAs) play critical roles in virulence, stress adaptation, and host-pathogen interactions. Transcriptomic analyses during infection can help reveal pathogen-derived sRNAs required for pathogenesis, providing valuable insights for the development of novel therapeutic strategies. However, the low abundance of pathogen biomass within the host tissues poses a significant challenge for such analyses. METHODS: We employed 2-step cell disruption to enrich Staphylococcus aureus cells from infected mouse organs and conducted RNA sequencing (RNA-seq) analysis to examine staphylococcal sRNAs expressed during infection. qRT-PCR was used to confirm the gene expression. A knockout mutant of highly expressed sRNA, RsaC, was generated, and RNA-seq under in vivo as well as in vitro aerobic and anaerobic conditions were compared between the wild-type and ΔrsaC strains. Virulence of S. aureus was assessed using both mouse and silkworm survival assays. RESULTS: We identified RsaC as one of the most highly expressed sRNAs in mouse organs with consistent increment over time postinfection. Through gene disruption and complementation, we demonstrated that RsaC is an independent virulence determinant required for full pathogenicity of S. aureus in a murine infection model. In addition, RsaC influenced gene expression in response to oxygen availability and host-associated stress. Further analysis revealed that mutation of 2 genes downregulated in ΔrsaC in vivo, NWMN_RS03420 (sodium: proton antiporter) and NWMN_RS12015 (hypothetical protein), reduced S. aureus virulence in a silkworm model. CONCLUSIONS: These findings identify RsaC as a novel independent virulence determinant that supports S. aureus adaptation within the host.

Animals↗

PubMed2005

Serial analysis of gene expression in adrenocortical hyperplasia caused by a germline PRKAR1A mutation.

CONTEXT: Adrenocortical tumors have been studied at the molecular genetic and cytogenetic levels, but the gene expression profiles of normal and tumor adrenal tissue have not been extensively investigated. OBJECTIVE: The objective of this study was to obtain information about transcriptome differences in hyperplastic adrenal cells. DESIGN AND PATIENTS: We performed serial analysis of gene expression (SAGE) on control adrenal tissue and primary pigmented nodular adrenocortical disease (PPNAD) tissue from two adolescent female patients. MAIN OUTCOME MEASURE: The main outcome measure was to provide quantitative datasets of the vast majority of the transcripts implicated in normal and pathogenic adrenal functioning. RESULTS: The libraries of 28,705 and 31,278 tags represented 14,846 and 16,698 unique mRNAs from the control and PPNAD tissue, respectively. A total of 842 tags from the two libraries did not match any known sequences. We found 127 tags, including 70 no-match tags, to be expressed almost exclusively in control and/or PPNAD adrenals and to be absent or very rare in other human tissues. Examples of well-characterized genes expressed at significantly higher levels in PPNAD included steroidogenic acute regulator, chromogranin A, and those coding for the steroidogenic enzymes P450 cytochromes CYP17A1 and CYP21A2. Pathway analysis revealed Wnt signaling as the most up-regulated in PPNAD. These data were confirmed for selected genes by quantitative RT-PCR and/or immunohistochemistry. CONCLUSIONS: This study was the first of its kind for adrenal tissue and provides important information about the adrenal transcriptome and aberrant signaling in an inherited form of adrenocortical hyperplasia.

Adrenal Cortex Neoplasms↗

PubMed2025

Fine mapping of the dominant female sterility gene and novel model of hybrid seed production in cabbage (Brassica oleracea L. var. capitata).

Hybrid breeding based on male sterility requires the removal of male parents, which is time- and labor-intensive; however, the use of female sterile male parent can solve this problem. In the offspring of distant hybridization between Brassica oleracea and Brassica napus, we obtained a mutant, 5GH12-279, which not only fails to generate gynoecium (thereby causing female sterility) but also has serrated leaves that could be used as a phenotypic marker in seedling screening. Genetic analysis revealed that this trait was controlled by a single dominant gene. Further analysis revealed that Bo2g005230, an orthologous gene of LATE MERISTEM IDENTITY1 (LMI1) in Arabidopsis, was predicted as the candidate gene and was renamed BoLMI1c. Sequence analysis revealed that homoeologous exchange (HE) occurred within the BoLMI1c gene body of 5GH12-279, which resulted in the generation of a novel fusion transcript. Two pairs of primers, N5230-1F/1R and N5230-2F/2R, were designed and successfully used for the identification of different genotypes of BoLMI1c. Transcriptome analysis revealed that BoLMI1c orchestrates the expression of several related biological processes and transcription factors. Furthermore, we found that self-pollination with mason bees produced no seeds in 5GH12-279, whereas the near-isogenic line 5GH12-170 produced seeds that were normal. Therefore, a new labor-saving hybrid seed production system with no need to remove the male parents, which is especially important for mechanized harvest in the future, has been proposed. Our study provides a valuable source of dominant female sterility and suggests the potential utilization of the female sterile line in hybrid breeding for mechanized harvest.

Plant Infertility↗

PubMed2026

Insights into the regulation of the HOTAIR proximal promoter.

HOTAIR (HOX transcript antisense RNA) is a HOXC-cluster long intervening non-coding RNA (lincRNA) whose cancer relevance is tightly coupled to how its transcription is wired into hormone, hypoxia, inflammatory, and developmental signaling. HOTAIR is known to associate with cancer cell proliferation, motility, tumor invasion, and metastasis. The present mini-review focuses on the regulatory architecture and mechanistic complexity of HOTAIR transcriptional regulation, with emphasis on three organizing principles. First, we consider the impact of promoter choice between a canonical proximal promoter (P1), which supports the 2.2-2.4 kb transcript, and an alternative upstream promoter/TSS (P2), which contributes to context-dependent transcription initiation. Second, we examine the long-distance enhancer-promoter communication between HOTAIR distal enhancer and P1/P2. Third, we summarize the recent epigenetic and epi-transcriptomic mechanisms involved in HOTAIR transcript initiation and elongation. A combination of these events determines isoform-specific transcription to govern cell-type-, context-, and cancer specific modulation of HOTAIR expression that promotes tumor formation and cancer progression. Finally, the review proposes how large-scale RNA datasets, long-read sequencing, and isoform-specific studies can refine our understanding of this versatile lincRNA's regulation.

Humans↗

PubMed2006

CovR activation of the dipeptide permease promoter (PdppA) in Group A Streptococcus.

CovR, the two-component response regulator of Streptococcus pyogenes (group A streptococcus [GAS]) directly or indirectly represses about 15% of the genome, including genes encoding many virulence factors and itself. Transcriptome analyses also showed that some genes are activated by CovR. We asked whether the regulation by CovR of one of these genes, dppA, the first gene in an operon encoding a dipeptide permease, is direct or indirect. Direct regulation by CovR was suggested by the presence of five CovR consensus binding sequences (CBs) near the putative promoter. In this study, we identified the 5' end of the dppA transcript synthesized in vivo and showed that the start of dppA transcription in vitro is the same. We found that CovR binds specifically to the dppA promoter region (PdppA) in vitro with an affinity similar to that at which it binds to other CovR-regulated promoters. Disruption of any of the five CBs by a substitution of GG for TT inhibited CovR binding to that site in vitro, and binding at two of the CBs appeared cooperative. In vivo, CovR activation of transcription was not affected by individual mutations of any of the four CBs that we could study. This suggests that the binding sites are redundant in vivo. In vitro, CovR did not activate transcription from PdppA in experiments using purified GAS RNA polymerase and either linear or supercoiled DNA template. Therefore, we propose that in vivo, CovR may interfere with the binding of a repressor of PdppA.

Bacterial Proteins↗

PubMed2025

Insights into dill (Anethum graveolens) flavor formation via integrative analysis of chromosomal-scale genome, metabolome and transcriptome.

INTRODUCTION: Dill (Anethum graveolens) is a significant medicinal herb belonging to the Apiaceae family. Owing to its high levels of volatile organic compounds (VOCs), dill is commonly utilized for essential oil extraction and medicine purpose. However, the biosynthesis of the crucial VOC in dill remains obscure. OBJECTIVES: Identify the key VOCs related to the flavor formation in dill and dissect the regulatory mechanism of their synthesis. METHODS: The dill chromosomal-level genome was constructed by PacBio HiFi, Hi-C, and BGISEQ second generation sequencing and assembly. The VOCs in dill leaves were identified through GC-MS. The potential mechanism involved in regulating the VOC accumulation in dill flavor formation was analyzed by multi-omics analysis. RESULTS: A 1.17 Gb chromosome-scale genome of dill with a contig N50 of 10.78 Mb was constructed. A total of 46,538 genes were annotated across 11 assembled chromosomes. Comparative genomics analysis suggested that transposable element insertions, especially LTR-Gypsy, have contributed to the evolution and expansion of the dill genome. The flavor formation of dill was mainly attributed to terpenoids, especially α-phellandrene, β-ocimene, and o-cymene. The contribution of expansion and replication of terpenoid synthesis pathway genes, especially terpene synthase (TPS), to the abundant terpenoid production of dill was identified. Differential gene expression patterns observed at various developmental stages and tissues provided key candidate genes for the regulation of terpenoid synthesis, as well as transcription factors. The different accumulation of esters and aromatics also affected the flavor formation of dill. The key genes implicated in the synthesis of anethole, namely AIS and AMT were further identified. CONCLUSION: This study constructed the chromosome level genome and identified the main VOCs and related key genes in flavor formation of dill, shedding lights on our understanding of terpenoid biosynthesis but also offered guidance for future genetic research on molecular breeding in Anethum graveolens.

Transcriptome↗

PubMed2004

The operons, a criterion to compare the reliability of transcriptome analysis tools: ICA is more reliable than ANOVA, PLS and PCA.

The number of statistical tools used to analyze transcriptome data is continuously increasing and no one, definitive method has so far emerged. There is a need for comparison and a number of different approaches has been taken to evaluate the effectiveness of the different statistical tools available for microarray analyses. In this paper, we describe a simple and efficient protocol to compare the reliability of different statistical tools available for microarray analyses. It exploits the fact that genes within an operon exhibit the same expression patterns. In order to compare the tools, the genes are ranked according to the most relevant criterion for each tool; for each tool we look at the number of different operons represented within the first twenty genes detected. We then look at the size of the interval within which we find the most significant genes belonging to each operon in question. This allows us to define and estimate the sensitivity and accuracy of each statistical tool. We have compared four statistical tools using Bacillus subtilis expression data: the analysis of variance (ANOVA), the principal component analysis (PCA), the independent component analysis (ICA) and the partial least square regression (PLS). Our results show ICA to be the most sensitive and accurate of the tools tested. In this article, we have used the protocol to compare statistical tools applied to the analysis of differential gene expression. However, it can also be applied without modification to compare the statistical tools developed for other types of transcriptome analyses, like the study of gene co-expression.

Bacillus subtilis↗