FragIdent - Automatic identification and characterisation of cDNA-fragments

Background

The ubiquitin 26S/proteasome system (UPS), a serial cascade process of protein ubiquitination and degradation, is the last step for most cellular proteins. There are many genes involved in this system, but are not identified in many species. The accumulating availability of genomic sequence data is generating more demands in data management and analysis. Genomics data of plants such as Populus trichocarpa, Medicago truncatula, Glycine max and others are now publicly accessible. It is time to integrate information on classes of genes for complex protein systems such as UPS.

Results

We developed a database of higher plants' UPS, named 'plantsUPS'. Both automated search and manual curation were performed in identifying candidate genes. Extensive annotations referring to each gene were generated, including basic gene characterization, protein features, GO (gene ontology) assignment, microarray probe set annotation and expression data, as well as cross-links among different organisms. A chromosome distribution map, multi-sequence alignment, and phylogenetic trees for each species or gene family were also created. A user-friendly web interface and regular updates make plantsUPS valuable to researchers in related fields.

Conclusion

The plantsUPS enables the exploration and comparative analysis of UPS in higher plants. It now archives > 8000 genes from seven plant species distributed in 11 UPS-involved gene families. The plantsUPS is freely available now to all users at http://bioinformatics.cau.edu.cn/plantsUPS.     

Non-sex specific genes associated with the secondary mitotic period of primordial germ cell proliferation in the gonads of embryonic rainbow trout (Oncorhynchus mykiss)

The purposes of this study were to quantify the secondary proliferation of primordial germ cells (PGCs) in both sexes of rainbow trout, determine if a sex difference in the timing of PGC proliferation and eventual pre‐meiotic number exists, and use microarray data collected during this period to identify genes that are associated with PGC mitosis. The experiments used vasa‐green fluorescent protein (vasa‐GFP) transgenic rainbow trout of known genetic sex that allowed for the identification and collection of PGCs in vivo. An increase was observed in the number of PGCs counted in the gonads of both female and male embryonic vasa‐GFP rainbow trout, from 300 to 700° days (water temperature in °C × days post‐fertilization). For both sexes, a statistically significant (P < 0.05) increase in the PGC number was first noted at either 350 or 400° days of development. By 700° days, a 20–50‐fold increase in germ cell number was apparent. No sex‐specific differences in the timing of PGC proliferation or number were notable in any of the families until 700° days. In conjunction, a custom microarray based on cDNA libraries from embryonic rainbow trout gonads was used to identify genes involved in PGC mitosis. Five genes were discovered: guanine nucleotide binding protein, integral membrane protein 2B, transmembrane protein 47, C‐src tyrosine‐protein kinase, and the decorin precursor protein. All the genes identified have not been previously associated with germ cell mitosis, but are known to be involved with the cell plasma membrane and/or cell signaling pathways. Mol. Reprod. Dev. 78:181–187, 2011. © 2011 Wiley‐Liss, Inc.     

Construction of a polycystic ovarian syndrome (PCOS) pathway based on the interactions of PCOS-related proteins retrieved from bibliomic data

Polycystic ovary syndrome (PCOS) is a complex but frequently occurring endocrine abnormality. PCOS has become one of the leading causes of oligo-ovulatory infertility among premenopausal women. The definition of PCOS remains unclear because of the heterogeneity of this abnormality, but it is associated with insulin resistance, hyperandrogenism, obesity and dyslipidaemia. The main purpose of this study was to identify possible candidate genes involved in PCOS. Several genomic approaches, including linkage analysis and microarray analysis, have been used to look for candidate PCOS genes. To obtain a clearer view of the mechanism of PCOS, we have compiled data from microarray analyses. An extensive literature search identified seven published microarray analyses that utilized PCOS samples. These were published between the year of 2003 and 2007 and included analyses of ovary tissues as well as whole ovaries and theca cells. Although somewhat different methods were used, all the studies employed cDNA microarrays to compare the gene expression patterns of PCOS patients with those of healthy controls. These analyses identified more than a thousand genes whose expression was altered in PCOS patients. Most of the genes were found to be involved in gene and protein expression, cell signaling and metabolism. We have classified all of the 1081 identified genes as coding for either known or unknown proteins. Cytoscape 2.6.1 was used to build a network of protein and then to analyze it. This protein network consists of 504 protein nodes and 1408 interactions among those proteins. One hypothetical protein in the PCOS network was postulated to be involved in the cell cycle. BiNGO was used to identify the three main ontologies in the protein network: molecular functions, biological processes and cellular components. This gene ontology analysis identified a number of ontologies and genes likely to be involved in the complex mechanism of PCOS. These include the insulin receptor signaling pathway, steroid biosynthesis, and the regulation of gonadotropin secretion among others.     

Gene expression patterns define pathways correlated with loss of differentiation in lung adenocarcinomas

An analysis of microarray data from 86 lung adenocarcinomas reveals hundreds of genes significantly correlated with tumor cell differentiation. A bioinformatics approach of linking these genes to public information from the Locuslink and KEGG databases yields evidence for a loss of tumor cell differentiation being associated with biological processes of cell division, protein degradation, pyrimidine and purine metabolism, oxidative phosphorylation, glyoxylate and dicarboxylate metabolism, folate biosynthesis, and glutamate metabolism. The increased expression of genes involved in these processes is consistent with increased proliferation and metabolism characteristics of poorly differentiated tumors. The complete results of this analysis are available at http://dot.ped.med.umich.edu:2000/pub/diff/index.htm.     

Clustering microarray gene expression data using weighted Chinese restaurant process

MOTIVATION: Clustering microarray gene expression data is a powerful tool for elucidating co-regulatory relationships among genes. Many different clustering techniques have been successfully applied and the results are promising. However, substantial fluctuation contained in microarray data, lack of knowledge on the number of clusters and complex regulatory mechanisms underlying biological systems make the clustering problems tremendously challenging. RESULTS: We devised an improved model-based Bayesian approach to cluster microarray gene expression data. Cluster assignment is carried out by an iterative weighted Chinese restaurant seating scheme such that the optimal number of clusters can be determined simultaneously with cluster assignment. The predictive updating technique was applied to improve the efficiency of the Gibbs sampler. An additional step is added during reassignment to allow genes that display complex correlation relationships such as time-shifted and/or inverted to be clustered together. Analysis done on a real dataset showed that as much as 30% of significant genes clustered in the same group display complex relationships with the consensus pattern of the cluster. Other notable features including automatic handling of missing data, quantitative measures of cluster strength and assignment confidence. Synthetic and real microarray gene expression datasets were analyzed to demonstrate its performance. AVAILABILITY: A computer program named Chinese restaurant cluster (CRC) has been developed based on this algorithm. The program can be downloaded at http://www.sph.umich.edu/csg/qin/CRC/.     

Global gene expression profile of Orientia tsutsugamushi

Orientia tsutsugamushi, an obligate intracellular bacterium, is the causative agent of Scrub typhus. The control mechanisms for bacterial gene expression are largely unknown. Here, the global gene expression of O. tsutsugamushi within eukaryotic cells was examined using a microarray and proteomic approaches for the first time. These approaches identified 643 genes, corresponding to approximately 30% of the genes encoded in the genome. The majority of expressed genes belonged to several functional categories including protein translation, protein processing/secretion, and replication/repair. We also searched the conserved sequence blocks (CSBs) in the O. tsutsugamushi genome which is unique in that up to 40% of its genome consists of dispersed repeated sequences. Although extensive shuffling of genomic sequences was observed between two different strains, 204 CSBs, covering 48% of the genome, were identified. When combining the data of CSBs and global gene expression, the CSBs correlates well with the location of expressed genes, suggesting the functional conservation between gene expression and genomic location. Finally, we compared the gene expression of the bacteria‐infected fibroblasts and macrophages using microarray analysis. Some major changes were the downregulation of genes involved in translation, protein processing and secretion, which correlated with the reduction in bacterial translation rates and growth within macrophages.