Detecting differentially expressed genes in multiple tag sampling experiments: comparative evaluation of statistical tests

Romualdi, Chiara; Bortoluzzi, Stefania; Danieli, Gian Antonio

doi:10.1093/hmg/10.19.2133

Cited by 56 publications

(68 citation statements)

References 22 publications

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“…Digital analyses of gene expression were performed based on AC statistics (Audic and Claverie, 1997) for pairwise comparisons and general chi-square tests for multiple cDNA library comparisons (Romualdi et al, 2001). P values for the statistical tests were calculated using IDEG6 (Romualdi et al, 2001).…”

Section: Digital Expression Analysismentioning

confidence: 99%

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Identification of Genes with Potential Roles in Apple Fruit Development and Biochemistry through Large-Scale Statistical Analysis of Expressed Sequence Tags

Sugimoto²,

et al. 2006

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Advanced studies of apple (Malus domestica Borkh) development, physiology, and biochemistry have been hampered by the lack of appropriate genomics tools. One exception is the recent acquisition of extensive expressed sequence tag (EST) data. The entire available EST dataset for apple resulted from the efforts of at least 20 contributors and was derived from more than 70 cDNA libraries representing diverse transcriptional profiles from a variety of organs, fruit parts, developmental stages, biotic and abiotic stresses, and from at least nine cultivars. We analyzed apple EST sequences available in public databanks using statistical algorithms to identify those apple genes that are likely to be highly expressed in fruit, expressed uniquely or preferentially in fruit, and/or temporally or spatially regulated during fruit growth and development. We applied these results to the analysis of biochemical pathways involved in biosynthesis of precursors for volatile esters and identified a subset of apple genes that may participate in generating flavor and aroma components found in mature fruit.Cultivated apple (Malus domestica Borkh) is among the most diverse and ubiquitously cultivated fruit species. Apple is a member of the Rosaceae family, which includes many commercial fruit (e

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Section: Digital Expression Analysismentioning

confidence: 99%

“…P values for the statistical tests were calculated using IDEG6 (Romualdi et al, 2001). To select genes potentially enriched in fruit tissues, we applied an AC test statistic of P , 0.005 and a proportional frequency difference of at least 2-fold between the pooled libraries.…”

Section: Digital Expression Analysismentioning

confidence: 99%

Identification of Genes with Potential Roles in Apple Fruit Development and Biochemistry through Large-Scale Statistical Analysis of Expressed Sequence Tags

Sugimoto²,

et al. 2006

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“…The IDEG.6 software (Romualdi et al, 2001) was used to calculate the values of six different statistical tests aiming to identify differentially expressed genes in multiple tag sampling experiments. The AC, R and GT statistics (Audic and Claverie, 1997;Stekel et al, 2000;Greller and Tobin, 1999), the Fisher's 2X2 exact test, the 2X2 c 2 test…”

Section: Identification Of Gene Expression Patternsmentioning

confidence: 99%

“…The use of robust statistical tests is essential in the identification of differentially expressed genes in EST projects. In the past few years several statistical approaches have been described (Audic and Claverie, 1997;Stekel et al, 2000;Greller and Tobin, 1999;Romualdi et al, 2001).…”

Section: Introductionmentioning

confidence: 99%

In silico evaluation of the Eucalyptus transcriptome

et al. 2005

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The expressed sequence tags (ESTs) produced in the Forests project provide an invaluable opportunity to assess the Eucalyptus transcriptome. Besides providing information on the different proteins produced by this plant, it is possible to infer gene expression profiles because non-normalized cDNA libraries were used. The EST frequency from any gene is correlated to the transcript levels in the tissues from which the cDNA libraries were constructed. The goal of this work was to identify Eucalyptus genes that showed either differential expression pattern or were ubiquitously expressed in the tissues sampled in the Forests project. Six robust statistical tests and very restrictive rules were applied to gain confidence in the in silico data aiming to avoid false positives. Several genes with interesting expression profiles were identified and some of them were validated by RT-PCR.

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“…In a recent work we applied a simulation approach to verify which tests are more sensitive and are able to detect a larger number of true positive in different conditions (7). General 2 test was shown to be fairly efficient in multiple tag sampling experiments, especially when dealing with variations affecting weakly expressed genes, whereas the method of Audic and Claverie was shown to be the most adequate for detecting differences in gene expression in pairwise comparisons.…”

mentioning

confidence: 99%

IDEG6: a web tool for detection of differentially expressed genes in multiple tag sampling experiments

Romualdi

Bortoluzzi

d’Alessi

et al. 2003

Physiological Genomics

338

282

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Here we present a novel web tool for the statistical analysis of gene expression data in multiple tag sampling experiments. Differentially expressed genes are detected by using six different test statistics. Result tables, linked to the GenBank, UniGene, or LocusLink database, can be browsed or searched in different ways. Software is freely available at the site: http://telethon.bio.unipd.it/bioinfo/IDEG6_form/, together with additional information on statistical methodologies

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Detecting differentially expressed genes in multiple tag sampling experiments: comparative evaluation of statistical tests

Cited by 56 publications

References 22 publications

Identification of Genes with Potential Roles in Apple Fruit Development and Biochemistry through Large-Scale Statistical Analysis of Expressed Sequence Tags

Identification of Genes with Potential Roles in Apple Fruit Development and Biochemistry through Large-Scale Statistical Analysis of Expressed Sequence Tags

In silico evaluation of the Eucalyptus transcriptome

IDEG6: a web tool for detection of differentially expressed genes in multiple tag sampling experiments

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