From genes to networks: in systematic points of view

We present a report of the BIOCOMP'10 - The 2010 International Conference on Bioinformatics & Computational Biology and other related work in the area of systems biology

Application of Volcano Plots in Analyses of mRNA Differential Expressions with Microarrays

Volcano plot displays unstandardized signal (e.g. log-fold-change) against noise-adjusted/standardized signal (e.g. t-statistic or -log10(p-value) from the t test). We review the basic and an interactive use of the volcano plot, and its crucial role in understanding the regularized t-statistic. The joint filtering gene selection criterion based on regularized statistics has a curved discriminant line in the volcano plot, as compared to the two perpendicular lines for the "double filtering" criterion. This review attempts to provide an unifying framework for discussions on alternative measures of differential expression, improved methods for estimating variance, and visual display of a microarray analysis result. We also discuss the possibility to apply volcano plots to other fields beyond microarray.Comment: 8 figure

Transcriptomic Response of Karenia brevis to Environmental Stress

Karenia brevis is a toxic, marine phytoplankton that forms harmful algal blooms in the Gulf of Mexico. This toxicity is due to the production of ladder-frame polyketides known as brevetoxins, for which the production pathway and function in the cell are not known. Osmotic stress has been shown to increase the production of brevetoxin in K. brevis, and recent studies implicate the toxin as linked to the function of light harvesting complex II in the thylakoid membrane. Understanding if whether brevetoxin production and photosynthetic stress are linked in an osmotic shock response will shed further light on its function in the cell. Using K. brevis clones with high, average, low, and non-detectable levels of brevetoxin, we explored the response to osmotic stress using analysis of differential gene expression, measurements of PAM fluorometry, and production of the known osmolyte glycerol. Brevetoxin-producing clones of K. brevis showed lower expression in Photosystem II genes, and correspondingly lower photosynthetic efficiencies and intracellular glycerol concentrations in response to stress. In contrast, clones that produce non-detectable and low toxin levels showed no significant stress response, and also showed a deficiency in Non-Photochemical Quenching (NPQ) compared to toxic cultures. This observation supports the potential link between reactive oxygen species and NPQ pathways that is related to the presence of brevetoxin in K. brevis. Further, brevetoxin producing K. brevis clones respond to osmotic stress by utilizing photosynthesis for osmoacclimation and through small molecule degradation, in particular intracellular photosynthetically derived glycerol, whereas the low and non-detectable clones do not

Transcriptomic Response of Karenia brevis to Environmental Stress

Karenia brevis is a toxic, marine phytoplankton that forms harmful algal blooms in the Gulf of Mexico. This toxicity is due to the production of ladder-frame polyketides known as brevetoxins, for which the production pathway and function in the cell are not known. Osmotic stress has been shown to increase the production of brevetoxin in K. brevis, and recent studies implicate the toxin as linked to the function of light harvesting complex II in the thylakoid membrane. Understanding if whether brevetoxin production and photosynthetic stress are linked in an osmotic shock response will shed further light on its function in the cell. Using K. brevis clones with high, average, low, and non-detectable levels of brevetoxin, we explored the response to osmotic stress using analysis of differential gene expression, measurements of PAM fluorometry, and production of the known osmolyte glycerol. Brevetoxin-producing clones of K. brevis showed lower expression in Photosystem II genes, and correspondingly lower photosynthetic efficiencies and intracellular glycerol concentrations in response to stress. In contrast, clones that produce non-detectable and low toxin levels showed no significant stress response, and also showed a deficiency in Non-Photochemical Quenching (NPQ) compared to toxic cultures. This observation supports the potential link between reactive oxygen species and NPQ pathways that is related to the presence of brevetoxin in K. brevis. Further, brevetoxin producing K. brevis clones respond to osmotic stress by utilizing photosynthesis for osmoacclimation and through small molecule degradation, in particular intracellular photosynthetically derived glycerol, whereas the low and non-detectable clones do not

Sample size calculation while controlling false discovery rate for differential expression analysis with RNA-sequencing experiments

This excel file contains comparison of resulting sample size and power between Li et al.’s method [18] and our proposed method for simulation 1, with parameter settings from Table 1 in [18]. The results are obtained under m=200, with Li’s result in the first row from each parameter setting, and our result in the second row. (XLS 49.2 kb

Complex basis of hybrid female sterility and Haldane's rule in Heliconius butterflies: Z-linkage and epistasis

Hybrids between species are often sterile or inviable. Hybrid unfitness usually evolves first in the heterogametic sex—a pattern known as Haldane's rule. The genetics of Haldane's rule have been extensively studied in species where the male is the heterogametic (XX/XY) sex, but its basis in taxa where the female is heterogametic (ZW/ZZ), such as Lepidoptera and birds, is largely unknown. Here, we analyse a new case of female hybrid sterility between geographic subspecies of Heliconius pardalinus. The two subspecies mate freely in captivity, but female F1 hybrids in both directions of cross are sterile. Sterility is due to arrested development of oocytes after they become differentiated from nurse cells, but before yolk deposition. We backcrossed fertile male F1 hybrids to parental females and mapped quantitative trait loci (QTLs) for female sterility. We also identified genes differentially expressed in the ovary as a function of oocyte development. The Z chromosome has a major effect, similar to the ‘large X effect’ in Drosophila, with strong epistatic interactions between loci at either end of the Z chromosome, and between the Z chromosome and autosomal loci on chromosomes 8 and 20. By intersecting the list of genes within these QTLs with those differentially expressed in sterile and fertile hybrids, we identified three candidate genes with relevant phenotypes. This study is the first to characterize hybrid sterility using genome mapping in the Lepidoptera and shows that it is produced by multiple complex epistatic interactions often involving the sex chromosome, as predicted by the dominance theory of Haldane's rule

Provitamin A biofortification of cassava enhances shelf life but reduces dry matter content of storage roots due to altered carbon partitioning into starch

Storage roots of cassava (Manihot esculenta Crantz), a major subsistence crop of sub-Saharan Africa, are calorie rich but deficient in essential micronutrients, including provitamin A β-carotene. In this study, β-carotene concentrations in cassava storage roots were enhanced by coexpression of transgenes for deoxy-d-xylulose-5-phosphate synthase (DXS) and bacterial phytoene synthase (crtB), mediated by the patatin-type 1 promoter. Storage roots harvested from field-grown plants accumulated carotenoids to ≤50 lg/g DW, 15- to 20-fold increases relative to roots from nontransgenic plants. Approximately 85%–90% of these carotenoids accumulated as all-trans-β-carotene, the most nutritionally efficacious carotenoid. β-Carotene-accumulating storage roots displayed delayed onset of postharvest physiological deterioration, a major constraint limiting utilization of cassava products. Large metabolite changes were detected in β-carotene-enhanced storage roots. Most significantly, an inverse correlation was observed between β-carotene and dry matter content, with reductions of 50%–60% of dry matter content in the highest carotenoid-accumulating storage roots of different cultivars. Further analysis confirmed a concomitant reduction in starch content and increased levels of total fatty acids, triacylglycerols, soluble sugars and abscisic acid. Potato engineered to co-express DXS and crtB displayed a similar correlation between β-carotene accumulation, reduced dry matter and starch content and elevated oil and soluble sugars in tubers. Transcriptome analyses revealed a reduced expression of genes involved in starch biosynthesis including ADP-glucose pyrophosphorylase genes in transgenic, carotene-accumulating cassava roots relative to nontransgenic roots. These findings highlight unintended metabolic consequences of provitamin A biofortification of starch-rich organs and point to strategies for redirecting metabolic flux to restore starch production

DREAMSeq: An Improved Method for Analyzing Differentially Expressed Genes in RNA-seq Data

RNA sequencing (RNA-seq) has become a widely used technology for analyzing global gene-expression changes during certain biological processes. It is generally acknowledged that RNA-seq data displays equidispersion and overdispersion characteristics; therefore, most RNA-seq analysis methods were developed based on a negative binomial model capable of capturing both equidispersed and overdispersed data. In this study, we reported that in addition to equidispersion and overdispersion, RNA-seq data also displays underdispersion characteristics that cannot be adequately captured by general RNA-seq analysis methods. Based on a double Poisson model capable of capturing all data characteristics, we developed a new RNA-seq analysis method (DREAMSeq). Comparison of DREAMSeq with five other frequently used RNA-seq analysis methods using simulated datasets showed that its performance was comparable to or exceeded that of other methods in terms of type I error rate, statistical power, receiver operating characteristics (ROC) curve, area under the ROC curve, precision-recall curve, and the ability to detect the number of differentially expressed genes, especially in situations involving underdispersion. These results were validated by quantitative real-time polymerase chain reaction using a real Foxtail dataset. Our findings demonstrated DREAMSeq as a reliable, robust, and powerful new method for RNA-seq data mining. The DREAMSeq R package is available at http://tanglab.hebtu.edu.cn/tanglab/Home/DREAMSeq

Statistical methods on detecting differentially expressed genes for RNA-seq data

BACKGROUND: For RNA-seq data, the aggregated counts of the short reads from the same gene is used to approximate the gene expression level. The count data can be modelled as samples from Poisson distributions with possible different parameters. To detect differentially expressed genes under two situations, statistical methods for detecting the difference of two Poisson means are used. When the expression level of a gene is low, i.e., the number of count is small, it is usually more difficult to detect the mean differences, and therefore statistical methods which are more powerful for low expression level are particularly desirable. In statistical literature, several methods have been proposed to compare two Poisson means (rates). In this paper, we compare these methods by using simulated and real RNA-seq data. RESULTS: Through simulation study and real data analysis, we find that the Wald test with the data being log-transformed is more powerful than other methods, including the likelihood ratio test, which has similar power as the variance stabilizing transformation test; both are more powerful than the conditional exact test and Fisher exact test. CONCLUSIONS: When the count data in RNA-seq can be reasonably modelled as Poisson distribution, the Wald-Log test is more powerful and should be used to detect the differentially expressed genes