IRView: a database and viewer for protein interacting regions.

UNLABELLED: Protein-protein interactions (PPIs) are mediated through specific regions on proteins. Some proteins have two or more protein interacting regions (IRs) and some IRs are competitively used for interactions with different proteins. IRView currently contains data for 3417 IRs in human and mouse proteins. The data were obtained from different sources and combined with annotated region data from InterPro. Information on non-synonymous single nucleotide polymorphism sites and variable regions owing to alternative mRNA splicing is also included. The IRView web interface displays all IR data, including user-uploaded data, on reference sequences so that the positional relationship between IRs can be easily understood. IRView should be useful for analyzing underlying relationships between the proteins behind the PPI networks. AVAILABILITY: IRView is publicly available on the web at http://ir.hgc.jp/

New parameter that supports speculation on the possible mechanism of hypothyroidism induced by chemical substances in repeated-dose toxicity studies.

Hypothyroidism induced by xenobiotic treatment was analyzed for possible underlying mechanism(s) on the basis of different responses of the thyroid gland and the liver, using a newly-created database of repeated-dose toxicity of 500 chemicals. Two mechanisms are proposed: direct inhibition of thyroid hormone biosynthesis in the thyroid gland, and stimulated degradation of thyroid hormone by induction of hepatic drug-metabolizing enzymes. In the database there were 10 chemicals inducing hypertrophy/hyperplasia of follicular cells in the thyroid gland and having data on thyroid glands. On the basis of the chemical structure and information available in the literature, we judged three chemicals to be typical thioamide derivatives that act directly on the thyroid gland, and the others as non-thioamide derivatives that were unlikely to have any direct action on the thyroid gland. All these chemicals were classified into two groups using the ratios of relative weight increase rate of thyroid gland versus that of the liver. These values were at least 1.7, but 3.2 or more in the most of the cases for thioamide derivatives, and 1.2 or less for non-thioamide derivatives. This background analysis suggests the feasibility of parameter-supported speculation on the possible underlying mechanism when new repeated-dose toxicity data on hypothyroidism becomes available.

Next-generation sequencing coupled with a cell-free display technology for high-throughput production of reliable interactome data.

Next-generation sequencing (NGS) has been applied to various kinds of omics studies, resulting in many biological and medical discoveries. However, high-throughput protein-protein interactome datasets derived from detection by sequencing are scarce, because protein-protein interaction analysis requires many cell manipulations to examine the interactions. The low reliability of the high-throughput data is also a problem. Here, we describe a cell-free display technology combined with NGS that can improve both the coverage and reliability of interactome datasets. The completely cell-free method gives a high-throughput and a large detection space, testing the interactions without using clones. The quantitative information provided by NGS reduces the number of false positives. The method is suitable for the in vitro detection of proteins that interact not only with the bait protein, but also with DNA, RNA and chemical compounds. Thus, it could become a universal approach for exploring the large space of protein sequences and interactome networks.

Erratum : Thesaurus for histopathological findings in publically available reports of repeated-dose oral toxicity studies in rats for 156 chemicals.

Because histopathological findings are often conclusive indicators of the toxicities of chemicals, standardization of nomenclature and construction of a thesaurus for histopathological findings are important for the comparative evaluation of histopathological data from repeated-dose toxicity studies (RTS). however, terms for histopathological findings have not been standardized and different technical terms are used to indicate almost the same things in RTS. The present study was conducted to construct and easy-to-use thesaurus for histopathological findings in order to facilitate hazard assessments of untested chemicals by the category approach using knowledge of the toxicity of analogue chemicals. We used reports of 28-day RTS, conducted on rats by gavage, which were posted on the websites of the National Institute of health Sciences (NIHS) and the National Institute of Technology and Evaluation (NITE). The histopathological data were from 156 reports on RTS conducted by 13 institutions in Japan. As a result of this study, major parts of the thesaurus were devoted to the findings in the liver, kidney, stomach, adrenal, thyroid and testis; the first three organs are known to be the main targets of chemicals. We also decided that findings such as swelling and enlargement of hepatocytes should be categorized as synonyms for terms meaning hypertrophy. Our thesaurus will be helpful in assessing or screening new untested chemical by the category approach using knowledge of the toxicities of analogues of the new chemical. The RTS database with this thesaurus will be made publically available in 2010.

Thesaurus for histopathological findings in publically available reports of repeated-dose oral toxicity studies in rats for 156 chemicals.

Because histopathological findings are often conclusive indicators of the toxicities of chemicals, standardization of nomenclature and construction of a thesaurus for histopathological findings are important for the comparative evaluation of histopathological data from repeated-dose toxicity studies (RTS). However, terms for histopathological findings have not been standardized and different technical terms are used to indicate almost the same thing in RTS. The present study was conducted to construct an easy-to-use thesaurus for histopathological findings in order to facilitate hazard assessments of untested chemicals by the category approach using knowledge of the toxicity of analogue chemicals. We used reports of 28-day RTS, conducted on rats by gavage, which were posted on the websites of the National Institute of Health Sciences (NIHS) and the National Institute of Technology and Evaluation (NITE). The histopathological data were from 156 reports on RTS conducted by 13 institutions in Japan. As a result of this study, major parts of the thesaurus were devoted to the findings in the liver, kidney, stomach, adrenal, thyroid and testis; the first three organs are known to be the main targets of chemicals. We also decided that findings such as swelling and enlargement of hepatocytes should be categorized as synonyms for terms meaning hypertrophy. Our thesaurus will be helpful in assessing or screening new untested chemicals by the category approach using knowledge of the toxicities of analogues of the new chemical. The RTS database with this thesaurus will be made publically available in 2012.

A comprehensive resource of interacting protein regions for refining human transcription factor networks.

Large-scale data sets of protein-protein interactions (PPIs) are a valuable resource for mapping and analysis of the topological and dynamic features of interactome networks. The currently available large-scale PPI data sets only contain information on interaction partners. The data presented in this study also include the sequences involved in the interactions (i.e., the interacting regions, IRs) suggested to correspond to functional and structural domains. Here we present the first large-scale IR data set obtained using mRNA display for 50 human transcription factors (TFs), including 12 transcription-related proteins. The core data set (966 IRs; 943 PPIs) displays a verification rate of 70%. Analysis of the IR data set revealed the existence of IRs that interact with multiple partners. Furthermore, these IRs were preferentially associated with intrinsic disorder. This finding supports the hypothesis that intrinsically disordered regions play a major role in the dynamics and diversity of TF networks through their ability to structurally adapt to and bind with multiple partners. Accordingly, this domain-based interaction resource represents an important step in refining protein interactions and networks at the domain level and in associating network analysis with biological structure and function.