Melina II: a web tool for comparisons among several predictive algorithms to find potential motifs from promoter regions

We present the second version of Melina, a web-based tool for promoter analysis. Melina II shows potential DNA motifs in promoter regions with a combination of several available programs, Consensus, MEME, Gibbs sampler, MDscan and Weeder, as well as several parameter settings. It allows running a maximum of four programs simultaneously, and comparing their results with graphical representations. In addition, users can build a weight matrix from a predicted motif and apply it to upstream sequences of several typical genomes (human, mouse, S. cerevisiae, E. coli, B. subtilis or A. thaliana) or to public motif databases (JASPAR or DBTBS) in order to find similar motifs. Melina II is a client/server system developed by using Adobe (Macromedia) Flash and is accessible over the web at http://melina.hgc.jp

GEM-TREND: a web tool for gene expression data mining toward relevant network discovery

<p>Abstract</p> <p>Background</p> <p>DNA microarray technology provides us with a first step toward the goal of uncovering gene functions on a genomic scale. In recent years, vast amounts of gene expression data have been collected, much of which are available in public databases, such as the Gene Expression Omnibus (GEO). To date, most researchers have been manually retrieving data from databases through web browsers using accession numbers (IDs) or keywords, but gene-expression patterns are not considered when retrieving such data. The Connectivity Map was recently introduced to compare gene expression data by introducing gene-expression signatures (represented by a set of genes with up- or down-regulated labels according to their biological states) and is available as a web tool for detecting similar gene-expression signatures from a limited data set (approximately 7,000 expression profiles representing 1,309 compounds). In order to support researchers to utilize the public gene expression data more effectively, we developed a web tool for finding similar gene expression data and generating its co-expression networks from a publicly available database.</p> <p>Results</p> <p>GEM-TREND, a web tool for searching gene expression data, allows users to search data from GEO using gene-expression signatures or gene expression ratio data as a query and retrieve gene expression data by comparing gene-expression pattern between the query and GEO gene expression data. The comparison methods are based on the nonparametric, rank-based pattern matching approach of Lamb et al. (Science 2006) with the additional calculation of statistical significance. The web tool was tested using gene expression ratio data randomly extracted from the GEO and with in-house microarray data, respectively. The results validated the ability of GEM-TREND to retrieve gene expression entries biologically related to a query from GEO. For further analysis, a network visualization interface is also provided, whereby genes and gene annotations are dynamically linked to external data repositories.</p> <p>Conclusion</p> <p>GEM-TREND was developed to retrieve gene expression data by comparing query gene-expression pattern with those of GEO gene expression data. It could be a very useful resource for finding similar gene expression profiles and constructing its gene co-expression networks from a publicly available database. GEM-TREND was designed to be user-friendly and is expected to support knowledge discovery. GEM-TREND is freely available at <url>http://cgs.pharm.kyoto-u.ac.jp/services/network</url>.</p

Squamous Cell Carcinoma Arising from Abdominal Wall Defect Lesion Complicated with Cloacal Exstrophy

Summary: Cloacal exstrophy is an extremely rare congenital complex deformity that is associated with anterior abdominal wall defects, reflex and exposure of the cloaca (uninterrupted ureter and bowel), aproctia, a widely separated pubic bone, and defects or dysplasia of external genital organs. Here, we present the case of a 42-year-old man with squamous cell carcinoma arising from an abdominal wall defect complicated by cloacal exstrophy. He was successfully treated with excision of the skin lesion with the bowel and reconstruction using a pedicled anterolateral thigh flap combined with a tensor fasciae latae flap. To our knowledge, this is the first report of squamous cell carcinoma arising from an abdominal wall defect complicated by cloacal exstrophy

遊走腎を合併した腎血管性高血圧の一例

雑誌掲載版28歳女.平成10年産婦人科に入院中,血圧上昇,頭痛,右側腰背部痛を主訴とし,本態性高血圧症として外来経過観察されていたが,第二子を希望し,降圧薬の妊娠への影響を懸念して精査目的で入院した.諸検査により遊走腎に合併した腎血管性高血圧(RVH)と診断し,腎動脈狭窄の原因は,その形態から線維筋性異型性が疑われた.経皮的腎動脈拡張術も考慮したが,腎動脈の解剖学的走行と遊走腎の症状を考慮し,腎動脈グラフト術,腎固定術を施行した.術後経過は良好で,降圧薬中止後も血圧は正常化し,右腰部痛も消失した.カプトプリル負荷レノグラムで典型的所見を呈しており,RVHの疑診例に対し負荷レノグラムは確定診断に有用であった.遊走腎に合併したRVHの治療法の選択としては,バイパス術と腎固定術の一期的手術も考慮すべきと考えられるが,遊走腎の固定術自体が一般的でなく有用性に関しては今後の検討が必要であ