Computation method to identify differential allelic gene expression and novel imprinted genes

MOTIVATION: Genomic imprinting plays an important role in both normal development and diseases. Abnormal imprinting is strongly associated with several human diseases including cancers. Most of the imprinted genes were discovered in the neighborhood of the known imprinted genes. This approach is difficult to extend to analyze the whole genome. We have decided to take a computational approach to systematically search the whole genome for the presence of mono-allelic expressed genes and imprinted genes in human genome. RESULTS: A computational method was developed to identify novel imprinted or mono-allelic genes. Individuals represented in human cDNA libraries were genotyped using Bayesian statistics, and differential expression of polymorphic alleles was identified. A significant reduction in the number of libraries that expressed both alleles, measured by Z-statistics, is a strong indicator for an imprinted or a mono-allelic gene. AVAILABILITY: The data sets are available at http://leelab.nci.nih.gov/leelab/jsp/IGDM/IGDM.html     

In vivo expression technology (IVET) selection of genes of Rhizobium leguminosarum biovar viciae A34 expressed in the rhizosphere

IVET was used to identify genes that are specifically expressed in the rhizosphere of the pea-nodulating bacterium Rhizobium leguminosarum A34. A library of R. leguminosarum A34 cloned in the integration vector pIE1, with inserts upstream of a promoter-less purN:gfp:gusA, was conjugated into purN host RU2249 and recombined into the genome. After removal of colonies that expressed the reporter genes of the vector under laboratory conditions, the library was inoculated into a nonsterile pea rhizosphere. The key result is that 29 rhizosphere-induced loci were identified. Sequence analysis of these clones showed that a wide variety of R. leguminosarum A34 genes are expressed specifically in the rhizosphere including those encoding proteins involved in environmental sensing, control of gene expression, metabolic reactions and membrane transport. These genes are likely to be important for survival and colonization of the pea rhizosphere.     

Determination of stable housekeeping genes, differentially regulated target genes and sample integrity: BestKeeper – Excel-based tool using pair-wise correlations

The stability of standard gene expression is an elementary prerequisite for internal standardisation of target gene expression data and many so called housekeeping genes with assumed stable expression can exhibit either up- or down-regulation under some experimental conditions. The developed, and herein presented, software called BestKeeper determines the best suited standards, out of ten candidates, and combines them into an index. The index can be compared with further ten target genes to decide, whether they are differentially expressed under an applied treatment. All data processing is based on crossing points. The BestKeeper software tool was validated on four housekeeping genes and 10 members of the somatotropic axis differentially expressed in bovine corpora lutea total RNA. The BestKeeper application and necessary information about data processing and handling can be downloaded on http://www.wzw.tum.de/gene-quantification/bestkeeper.html.     

Gene selection using a two-level hierarchical Bayesian model

SUMMARY: The fundamental problem of gene selection via cDNA data is to identify which genes are differentially expressed across different kinds of tissue samples (e.g. normal and cancer). cDNA data contain large number of variables (genes) and usually the sample size is relatively small so the selection process can be unstable. Therefore, models which incorporate sparsity in terms of variables (genes) are desirable for this kind of problem. This paper proposes a two-level hierarchical Bayesian model for variable selection which assumes a prior that favors sparseness. We adopt a Markov chain Monte Carlo (MCMC) based computation technique to simulate the parameters from the posteriors. The method is applied to leukemia data from a previous study and a published dataset on breast cancer. SUPPLEMENTARY INFORMATION: http://stat.tamu.edu/people/faculty/bmallick.html.     

A renewed approach to the nonparametric analysis of replicated microarray experiments

DNA-microarrays find broad employment in biochemical research. This technology allows the monitoring of the expression levels of thousands of genes at the same time. Often, the goal of a microarray study is to find differentially expressed genes in two different types of tissue, for example normal and cancerous. Multiple hypothesis testing is a useful statistical tool for such studies. One approach using multiple hypothesis testing is nonparametric analysis for replicated microarray experiments. In this paper we present an improved version of this method. We also show how p-values are calculated for all significant genes detected with this testing procedure. All algorithms were implemented in an R-package, and instructions on it's use are included. The package can be downloaded at http://www.statistik.unidortmund.de/de/content/einrichtungen/lehrstuehle/personen/jung.html     

DiffCoEx: a simple and sensitive method to find differentially coexpressed gene modules

Background  

Large microarray datasets have enabled gene regulation to be studied through coexpression analysis. While numerous methods have been developed for identifying differentially expressed genes between two conditions, the field of differential coexpression analysis is still relatively new. More specifically, there is so far no sensitive and untargeted method to identify gene modules (also known as gene sets or clusters) that are differentially coexpressed between two conditions. Here, sensitive and untargeted means that the method should be able to construct de novo modules by grouping genes based on shared, but subtle, differential correlation patterns.     

运用差异展示分离特异性表达的基因

在高等生物中含有约100000个不同的基因,其中仅有15％的基因在任何个体细胞中均表达．因此分离特异的目的基因便显得十分重要.差异展示是通过部分扩增mRNA的逆转录产物、经测序胶电泳,分离到差异性表达的基因.它与消减杂交相比是分离特异表达基因的更有效的手段．虽然这种方法在实际运用中存在着这样或那样的困难,但随着对这种技术的不断改进,它将会有越来越广泛的用途．     

ESTminer: a suite of programs for gene and allele identification

SUMMARY: ESTminer is a collection of programs that use expressed sequence tag (EST) data from inbred genomes to identify unique genes within gene families. The algorithm utilizes Cap3 to perform an initial clustering of related EST sequences to produce a consensus sequence of a gene family. These consensus sequences are then used to collect all ESTs in the original EST library that are related using BLAST. A redundancy based criterion is applied to each EST to identify reliable unique gene-sequences. Using a highly inbred genome as a source of ESTs eliminates the necessity of computing covariance on each polymorphism to identify alleles of the same gene, thus making this algorithm more streamlined than other alternatives which must computationally attempt to distinguish genes from alleles. AVAILABILITY: The programs were written in PERL and are freely available at http://www.soybase.org/publication_data/Nelson/ESTminer/ESTminer.html CONTACT: nelsonrt@iastate.edu SUPPLEMENTARY INFORMATION: Figures and dataset can be obtained from: http://www.soybase.org/publication_data/Nelson/ESTminer/ESTminer.html.     

Differential expression of retinoic acid-inducible (Stra) genes during mouse placentation

Several retinoid binding proteins and nuclear receptors are specifically expressed in murine placenta. However, little is known about molecular events and target genes regulated by retinoids during placentation. Here, we report that several retinoic acid-inducible (Stra) genes, originally isolated by a differential screening procedure, exhibit specific expression patterns in mouse placental tissues. Three Stra genes, including the ephrinB1 receptor tyrosine kinase ligand, are prominently expressed in the regions of exchanges between maternal and embryonic circulations, i.e. the yolk sac and/or the labyrinthine zone of the mature placenta. The Meis2 homeobox gene appears to be specifically expressed in maternally-derived cell populations. Three other Stra genes, including the AP-2-related gene AP-2gamma, are differentially expressed in the trophoblastic cell lineage. Thus, retinoids may regulate various signaling pathways in specific placental cell-types.     

A Non-transformation Method for Identifying Differentially Expressed Genes from cDNA Microarrays

cDNA microarray data are subject to many sources of variation that have to be removed before statistical tests can be applied for identifying genes that are expressed differentially. Background correction, log-ratio transformation, and normalization, referred as the log-ratio approach, have been widely used for this purpose. However, there are some problems associated with this procedure. In this study, we proposed an alternative approach that obviates the log-ratio transformation step and goes directly to normalization after background correction. The method can estimate the “noise” effect by utilizing the information more effectively. Simulation studies were carried out to compare the feasibility and efficiency of this approach for detecting the specifically and differentially expressed genes under various conditions with the log-ratio approach. The results showed that our approach worked well and was more robust and powerful than the log-ratio approach.     

cDNA芯片差异表达基因检测的非转换方法

cDNA微阵列数据中包含许多变异因素,用于检测差异表达基因和其它统计分析前,必须将这些“噪音”剔除。对数比法（背景校正、对数比转换和数据标准化）已经被广泛应用于cDNA微阵列数据分析中,然而这种方法却存在着一些亟待解决的缺陷。对此,该文提出一种非转换方法,它可免去对数比的转化过程,直接在背景校正后进行数据标准化,可以有效剔除实验“噪音”。研究结果表明：在检测差异表达基因的效率方面,非转换方法比常规的对数比法具有更好的稳健性和更高的检测功效,基因检出率和准确性大大提高。     

Identification of Botrytis cinerea genes up-regulated during infection and controlled by the Galpha subunit BCG1 using suppression subtractive hybridization (SSH)

The Galpha subunit BCG1 plays an important role during the infection of host plants by Botrytis cinerea. Delta bcg1 mutants are able to conidiate, penetrate host leaves, and produce small primary lesions. However, in contrast to the wild type, the mutants completely stop invasion of plant tissue at this stage; secondary lesions have never been observed. Suppression subtractive hybridization (SSH) was used to identify fungal genes whose expression on the host plant is specifically affected in bcg1 mutants. Among the 22 differentially expressed genes, we found those which were predicted to encode proteases, enzymes involved in secondary metabolism, and others encoding cell wall-degrading enzymes. All these genes are highly expressed during infection in the wild type but not in the mutant. However, the genes are expressed in both the wild type and the mutant under certain conditions in vitro. Most of the BCG1-controlled genes are still expressed in adenylate cyclase (bac) mutants in planta, suggesting that BCG1 is involved in at least one additional signaling cascade in addition to the cAMP-depending pathway. In a second SSH approach, 1,500 clones were screened for those that are specifically induced by the wild type during the infection of bean leaves. Of the 22 BCG1-controlled genes, 11 also were found in the in planta SSH library. Therefore, SSH technology can be successfully applied to identify target genes of signaling pathways and differentially expressed genes in planta.     

Analysis of expressed sequence tags from the antarctic psychrophilic green algae, Pyramimonas gelidicola

Expressed sequence tags (ESTs) from the Antarctic green algae Pyramimonas gelidicola were analyzed to obtain molecular information on cold acclimation of psychrophilic microorganisms. A total of 2,112 EST clones were sequenced, generating 222 contigs and 219 singletons, and 200 contigs and 391 singletons from control (4 degrees C) and cold-shock conditions (-2 degrees C), respectively. The complete EST sequences were deposited to the DDBJ EST database (http:// www.ddbj.nig.ac.jp/index-e.html) and the nucleotide sequences reported in this study are available in the DDBJ/EMBL/ GenBank. These EST databases of Antarctic green algae can be used in a wide range of studies on psychrophilic genes expressed by polar microorganisms.