PosMed: ranking genes and bioresources based on Semantic Web Association Study

ABSTRACT Positional MEDLINE (PosMed; http://biolo

Gateways to the FANTOM5 promoter level mammalian expression atlas

The FANTOM5 project investigates transcription initiation activities in more than 1,000 human and mouse primary cells, cell lines and tissues using CAGE. Based on manual curation of sample information and development of an ontology for sample classification, we assemble the resulting data into a centralized data resource (http://fantom.gsc.riken.jp/5/). This resource contains web-based tools and data-access points for the research community to search and extract data related to samples, genes, promoter activities, transcription factors and enhancers across the FANTOM5 atlas. Electronic supplementary material The online version of this article (doi:10.1186/s13059-014-0560-6) contains supplementary material, which is available to authorized users

Comparative Simulations of the Ground State and the M-Intermediate State of the Sensory Rhodopsin II–Transducer Complex with a HAMP Domain Model

The complex of sensory rhodopsin II (SRII) and its cognate transducer HtrII (2:2 SRII–HtrII complex) consists of a photoreceptor and its signal transducer, respectively, associated with negative phototaxis in extreme halophiles. In this study to investigate how photoexcitation in SRII affects the structures of the complex, we conducted two series of molecular dynamics simulations of the complex of SRII and truncated HtrII (residues 1–136) of <i>Natronomonas pharaonis</i> linked with a modeled HAMP domain in the lipid bilayer using the two crystal structures of the ground state and the M-intermediate state as the starting structures. The simulation results showed significant enhancements of the structural differences observed between the two crystal structures. Helix F of SRII showed an outward motion, and the C-terminal end of transmembrane domain 2 (TM2) in HtrII rotated by ∼10°. The most significant structural changes were observed in the overall orientations of the two SRII molecules, closed in the ground state and open in the M-state. This change was attributed to substantial differences in the structure of the four-helix bundle of the HtrII dimer causing the apparent rotation of TM2. These simulation results established the structural basis for the various experimental observations explaining the structural differences between the ground state and the M-intermediate state

Database Construction for PromoterCAD: Synthetic Promoter Design for Mammals and Plants

Synthetic promoters can control a gene’s timing, location, and expression level. The PromoterCAD web server (http://promotercad.org) allows the design of synthetic promoters to control plant gene expression, by novel arrangement of <i>cis</i>-regulatory elements. Recently, we have expanded PromoterCAD’s scope with additional plant and animal data: (1) PLACE (Plant <i>Cis</i>-acting Regulatory DNA Elements), including various sized sequence motifs; (2) PEDB (Mammalian Promoter/Enhancer Database), including gene expression data for mammalian tissues. The plant PromoterCAD data now contains 22 000 <i>Arabidopsis thaliana</i> genes, 2 200 000 microarray measurements in 20 growth conditions and 79 tissue organs and developmental stages, while the new mammalian PromoterCAD data contains 679 <i>Mus musculus</i> genes and 65 000 microarray measurements in 96 tissue organs and cell types (http://promotercad.org/mammal/). This work presents step-by-step instructions for adding both regulatory motif and gene expression data to PromoterCAD, to illustrate how users can expand PromoterCAD functionality for their own applications and organisms