Quadratic regression analysis for gene discovery and pattern recognition for non-cyclic short time-course microarray experiments

Liu, Hua; Tarima, Sergey; Borders, Aaron S.; Getchell, Thomas V.; Getchell, Marilyn L.; Stromberg, Arnold J.

doi:10.1186/1471-2105-6-106

Cited by 47 publications

(14 citation statements)

References 20 publications

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“…To get information on the time-course of gene expression, the temporal expression profiles of the DE genes were classified using a quadratic regression method, convenient to analyze time-course microarray data [14] . A large majority (80%) of genes exhibited two patterns characterized by i) a marked increase or decrease in expression occurring between the incubation periods at 30°C and at 4°C, and ii) a limited change in expression over the period at 4°C ( Fig.S2 ).…”

Section: Resultsmentioning

confidence: 99%

A Temporal -omic Study of Propionibacterium freudenreichii CIRM-BIA1T Adaptation Strategies in Conditions Mimicking Cheese Ripening in the Cold

et al. 2012

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Propionibacterium freudenreichii is used as a ripening culture in Swiss cheese manufacture. It grows when cheeses are ripened in a warm room (about 24°C). Cheeses with an acceptable eye formation level are transferred to a cold room (about 4°C), inducing a marked slowdown of propionic fermentation, but P. freudenreichii remains active in the cold. To investigate the P. freudenreichii strategies of adaptation and survival in the cold, we performed the first global gene expression profile for this species. The time-course transcriptomic response of P. freudenreichii CIRM-BIA1T strain was analyzed at five times of incubation, during growth at 30°C then for 9 days at 4°C, under conditions preventing nutrient starvation. Gene expression was also confirmed by RT-qPCR for 28 genes. In addition, proteomic experiments were carried out and the main metabolites were quantified. Microarray analysis revealed that 565 genes (25% of the protein-coding sequences of P. freudenreichii genome) were differentially expressed during transition from 30°C to 4°C (P<0.05 and |fold change|>1). At 4°C, a general slowing down was observed for genes implicated in the cell machinery. On the contrary, P. freudenreichii CIRM-BIA1T strain over-expressed genes involved in lactate, alanine and serine conversion to pyruvate, in gluconeogenesis, and in glycogen synthesis. Interestingly, the expression of different genes involved in the formation of important cheese flavor compounds, remained unchanged at 4°C. This could explain the contribution of P. freudenreichii to cheese ripening even in the cold. In conclusion, P. freudenreichii remains metabolically active at 4°C and induces pathways to maintain its long-term survival.

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Section: Resultsmentioning

confidence: 99%

A Temporal -omic Study of Propionibacterium freudenreichii CIRM-BIA1T Adaptation Strategies in Conditions Mimicking Cheese Ripening in the Cold

et al. 2012

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“…Two statistical approaches were used to identify DEGs. First, RMA matrices were generated for each species and quadratic regression [ 51 ] was used to identify genes that changed as a function of time. This approach also classified genes into nine different temporal profiles based on the values of the estimated regression coefficients (Figure 3 ; see also [ 52 ]).…”

Section: Methodsmentioning

confidence: 99%

Microarray analysis of a salamander hopeful monster reveals transcriptional signatures of paedomorphic brain development

et al. 2010

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BackgroundThe Mexican axolotl (Ambystoma mexicanum) is considered a hopeful monster because it exhibits an adaptive and derived mode of development - paedomorphosis - that has evolved rapidly and independently among tiger salamanders. Unlike related tiger salamanders that undergo metamorphosis, axolotls retain larval morphological traits into adulthood and thus present an adult body plan that differs dramatically from the ancestral (metamorphic) form. The basis of paedomorphic development was investigated by comparing temporal patterns of gene transcription between axolotl and tiger salamander larvae (Ambystoma tigrinum tigrinum) that typically undergo a metamorphosis.ResultsTranscript abundances from whole brain and pituitary were estimated via microarray analysis on four different days post hatching (42, 56, 70, 84 dph) and regression modeling was used to independently identify genes that were differentially expressed as a function of time in both species. Collectively, more differentially expressed genes (DEGs) were identified as unique to the axolotl (n = 76) and tiger salamander (n = 292) than were identified as shared (n = 108). All but two of the shared DEGs exhibited the same temporal pattern of expression and the unique genes tended to show greater changes later in the larval period when tiger salamander larvae were undergoing anatomical metamorphosis. A second, complementary analysis that directly compared the expression of 1320 genes between the species identified 409 genes that differed as a function of species or the interaction between time and species. Of these 409 DEGs, 84% exhibited higher abundances in tiger salamander larvae at all sampling times.ConclusionsMany of the unique tiger salamander transcriptional responses are probably associated with metamorphic biological processes. However, the axolotl also showed unique patterns of transcription early in development. In particular, the axolotl showed a genome-wide reduction in mRNA abundance across loci, including genes that regulate hypothalamic-pituitary activities. This suggests that an axolotls failure to undergo anatomical metamorphosis late in the larval period is indirectly associated with a mechanism(s) that acts earlier in development to broadly program transcription. The axolotl hopeful monster provides a model to identify mechanisms of early brain development that proximally and ultimately affect the expression of adult phenotypes.

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“…We have used a variety of approaches in previous studies to examine gene expression change as a function of time, including t tests, multifactor ANOVA, repeated measures ANOVA, parametric and Bayesian linear and nonlinear modeling, piecewise regression, and clustering (e.g., Huggins et al 2012; Li et al 2004; Liu et al 2005; Page et al 2007, 2008, 2009, 2010, 2013; Monaghan et al 2007, 2009, 2012; Athippozhy et al 2014). These approaches are proven to be effective within the context of experimental designs that sample relatively few points in time.…”

Section: Introductionmentioning

confidence: 99%

Gene expression during the first 28 days of axolotl limb regeneration I: Experimental design and global analysis of gene expression

et al. 2015

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While it is appreciated that global gene expression analyses can provide novel insights about complex biological processes, experiments are generally insufficiently powered to achieve this goal. Here we report the results of a robust microarray experiment of axolotl forelimb regeneration. At each of 20 post-amputation time points, we estimated gene expression for 10 replicate RNA samples that were isolated from 1 mm of heterogeneous tissue collected from the distal limb tip. We show that the limb transcription program diverges progressively with time from the non-injured state, and divergence among time adjacent samples is mostly gradual. However, punctuated episodes of transcription were identified for five intervals of time, with four of these coinciding with well-described stages of limb regeneration—amputation, early bud, late bud, and pallet. The results suggest that regeneration is highly temporally structured and regulated by mechanisms that function within narrow windows of time to coordinate transcription within and across cell types of the regenerating limb. Our results provide an integrative framework for hypothesis generation using this complex and highly informative data set.

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Quadratic regression analysis for gene discovery and pattern recognition for non-cyclic short time-course microarray experiments

Cited by 47 publications

References 20 publications

A Temporal -omic Study of Propionibacterium freudenreichii CIRM-BIA1T Adaptation Strategies in Conditions Mimicking Cheese Ripening in the Cold

A Temporal -omic Study of Propionibacterium freudenreichii CIRM-BIA1T Adaptation Strategies in Conditions Mimicking Cheese Ripening in the Cold

Microarray analysis of a salamander hopeful monster reveals transcriptional signatures of paedomorphic brain development

Gene expression during the first 28 days of axolotl limb regeneration I: Experimental design and global analysis of gene expression

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