The Comparison of Gene Expression from Multiple cDNA Libraries

Stekel, Dov J.; Git, Yoav; Falciani, Francesco

doi:10.1101/gr.gr-1325rr

Cited by 228 publications

(317 citation statements)

References 21 publications

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“…We set this threshold so as to give ∼500 genes in every tissue. 28 for each gene. We selected the genes according to two criteria: (i) representation in testis cDNA libraries (pool A) was two times higher than representation in the other libraries (pool B) and (ii) the R likelihood score was above a preset limit.…”

Section: Methodsmentioning

confidence: 99%

The mouse X chromosome is enriched for sex-biased genes not subject to selection by meiotic sex chromosome inactivation

et al. 2004

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Sex chromosomes are subject to sex-specific selective evolutionary forces 1,2 . One model predicts that genes with sexbiased expression should be enriched on the X chromosome 2-5 . In agreement with Rice's hypothesis 3 , spermatogonial genes are over-represented on the X chromosome of mice 6 and sex-and reproduction-related genes are over-represented on the human X chromosome 7,8 . Male-biased genes are under-represented on the X chromosome in worms and flies 9-11 , however. Here we show that mouse spermatogenesis genes are relatively underrepresented on the X chromosome and female-biased genes are enriched on it. We used Spo11 -/-mice blocked in spermatogenesis early in meiosis 12 to evaluate the temporal pattern of gene expression in sperm development. Genes expressed before the Spo11 block are enriched on the X chromosome, whereas those expressed later in spermatogenesis are depleted. Inactivation of the X chromosome in male meiosis may be a universal driving force for X-chromosome demasculinization.To investigate the genomic distribution of mouse genes with patterns of sex-biased expression, we analyzed the chromosomal distribution of genes expressed in sexually dimorphic tissues. We consider genes that are preferentially expressed in such tissues as testis, ovary and placenta to be sex-biased genes. We used two approaches to define the tissue specificity of genes expressed in mice: analysis of large-scale microarray-based gene expression data and analysis of the distribution of expressed-sequence tags (ESTs) in different cDNA libraries. Instead of focusing on transcripts restricted to a single tissue, our analysis targeted the identification of tissue-enriched transcripts using a 'preferential expression measure' (PEM) 13 . As an uniform source of expression data, we used publicly available data sets of mouse RNA samples representing 49 tissues hybridized to Affymetrix mouse U74A microarrays (GNF data set) 14 and 20 tissues analyzed with RIKEN cDNA microarrays (RIKEN data set) 15 .In the GNF data set 14 , expression of 624 genes (∼7% of all analyzed) in testis was three times greater than the median expression in other tissues, and expression of 361 genes in testis was five times greater (PEM values >1.58 and >2.32, respectively). These genes are considered testis-enriched genes. The chromosomal distribution of testisenriched genes was significantly different from uniform (χ 2 = 30.8, P = 0.05; Fig. 1a and Supplementary Table 1 online). The most significant deviation from the average gene density was on the X chromosome, where testis-enriched genes were 2.5 times less dense (the ratio of the density of testis-enriched genes on the X chromosome to the average density on all chromosomes, ρ X , was 0.40; χ 2 = 7.7, P = 0.006). The depletion of testis-enriched genes on the X chromosome was independent of the cut-off (three or five times greater expression) used in the selection process (Table 1). In addition, genes that were expressed most highly in testis and all the genes detected in testis were underrepresen...

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Section: Methodsmentioning

confidence: 99%

The mouse X chromosome is enriched for sex-biased genes not subject to selection by meiotic sex chromosome inactivation

et al. 2004

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“…In addition to a comparison between gene expression from sweet orange flavedo and other tissues (flower, bark and leaf), an analysis of differential gene expression among each of the six flavedo libraries corresponding to various fruit developmental stages was also performed adopting the likelihood R-statistics proposed by Stekel et al (2000). Significance (R > 8.0) of a given cluster was an indication of differential expression of its corresponding sequence, at least in one of the distinct sampled fruit stages, and interpreted as a suggestion that the transcript is under developmental regulation.…”

Section: Methodsmentioning

confidence: 99%

“…A double in silico hybridization strategy, combining the likelihood method (R-statistics) proposed by Stekel et al (2000) to compare multiple libraries all at once and the P-statistics described by Audic and Claverie (1997), was used to identify differentially expressed clusters (or tentative consensi -TCs) among Citrus tissues. All of the statistically significant TCs from the R-statistics (R > 8.0) were submitted to additional 2x2 P-statistics.…”

Section: Methodsmentioning

confidence: 99%

“…A global assembly of flavedo (51,729), leaf (34,957), flower (9,082) and bark (7,952) derived ESTs from healthy tissues of C. sinensis was performed (Reis et al, this issue) Berger et al 753 to generate a single pool of clusters and run the in silico hybridization likelihood method proposed by Stekel et al (2000). This resulted in 232 differentially abundant clusters (R > 8.0).…”

Section: Flavedo Differentially Expressed Sequencesmentioning

confidence: 99%

“…This includes identification of the most probable candidates to flavedo-specific genes and the ones that are of clear preferential expression in this tissue and, finally, considerations regarding the possible regulation of some genes during fruit development. In order to accomplish this, we propose a combination of two statistical methods, the likelihood R-statistics (Stekel et al, 2000) and the P-statistics (Audic and Claverie, 1997), resulting in a double in silico hybridization strategy to be used for multiple library comparison.…”

Section: Introductionmentioning

confidence: 99%

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In silico prediction of gene expression patterns in Citrus flavedo

et al. 2007

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Out of the 18,942 flavedo expressed sequences (clusters plus singletons) in Citrus sinensis from the Citrus EST Project (CitEST), 25 were statistically supported to be differentially expressed in this tissue after a double in silico hybridization strategy against leaf-, flower-, and bark-derived ESTs. Five of them, two terpene synthases and three O-methyltransferases, are absent in the other citrus tissues with concomitant 2x2 statistics, supporting the hypothesis that they are putative flavedo-specific expressed sequences. The pattern of these differentially expressed sequences during fruit development suggests that most of them are developmentally regulated. Some expressed gene products, including a putative germin-like protein highly expressed in flavedo, are shown to be promising candidates for further characterization. In addition to promoter seeking, this kind of analysis can lead to gene discovery, tissue-specific and tissue-enriched expression pattern predictions (as shown herein) and can also be adopted as an in silico first, and probably reliable approach, for detecting expression profiles from EST sequencing efforts before experimental validation is available or for heuristically guiding that validation.

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Using the TIGR Gene Index Databases for Biological Discovery

Lee¹,

Quackenbush²

2003

CP in Bioinformatics

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The TIGR Gene Index web pages provide access to analyses of ESTs and gene sequences for nearly 60 species, as well as a number of resources derived from these. Each species‐specific database is presented using a common format with a homepage. A variety of methods exist that allow users to search each species‐specific database. Methods implemented currently include nucleotide or protein sequence queries using WU‐BLAST, text‐based searches using various sequence identifiers, searches by gene, tissue and library name, and searches using functional classes through Gene Ontology assignments. This protocol provides guidance for using the Gene Index Databases to extract information.

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The Comparison of Gene Expression from Multiple cDNA Libraries

Cited by 228 publications

References 21 publications

The mouse X chromosome is enriched for sex-biased genes not subject to selection by meiotic sex chromosome inactivation

The mouse X chromosome is enriched for sex-biased genes not subject to selection by meiotic sex chromosome inactivation

In silico prediction of gene expression patterns in Citrus flavedo

Using the TIGR Gene Index Databases for Biological Discovery

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