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CIDeR: multifactorial interaction networks in human diseases

Martin Lechner1, Veit Höhn1, Barbara Brauner1, Irmtraud Dunger1, Gisela Fobo1, Goar Frishman1, Corinna Montrone1, Gabi Kastenmüller1, Brigitte Waegele12 and Andreas Ruepp1*

Author Affiliations

1 Institute for Bioinformatics and Systems Biology (MIPS), Helmholtz Center Munich - German Research Center for Environmental Health (GmbH), Ingolstädter Landstraße 1, D-85764 Neuherberg, Germany

2 Department of Genome-oriented Bioinformatics, Life and Food Science Center Weihenstephan, Technische Universität München, Alte Akademie 1, 85354 Freising, Germany

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Genome Biology 2012, 13:R62  doi:10.1186/gb-2012-13-7-r62

Published: 18 July 2012

Additional files

Additional file 1:

Supplementary figures. Figure s1: Go to the CIDeR homepage: Focus topics in diseases => mitochondria. Choose 'Mental disorders' and click on 'Graph'. A user who is interested in a research area, such as mitochondria, that is prepared as focus topic has access to this information via links on the CIDeR homepage. In order to obtain more or more specific information on the topic, the user has the option to start an individual search (Figure s2). Figure s2: CIDeR query: mitochondrial respiratory chain complex V. The user starts a survey in CIDeR - for example, with a query for 'Mitochondrial respiratory chain complex V' - and clicks on 'Graphical View'. Knowledge of the precise term is not required as CIDeR makes use of an auto-complementation tool that offers all related terms in the database after a few characters have been filled in. The search for 'Mitochondrial respiratory chain complex V' results in a graph consisting of six elements (nodes). It shows that the mitochondrial respiratory chain complex V is linked to bipolar disorder as well as to two angiotensin receptors (AGTR1 and AGTR2), which are all part of the angiotensin-renin system, which regulates blood pressure but also interacts with insulin signaling and is thus part of the type 2 diabetes network. A double-click on AGTR1 (Figure s3) extends the 'Mitochondrial respiratory chain complex V' for the AGTR1 network. Figure s3: CIDeR query: Mitochondrial respiratory chain complex V and double-click on AGTR1. A double-click on AGTR1 shows relations between AGTR1 and several drugs - for instance, nebivolol, a beta-blocker. Nebivolol interacts with a number of proteins and processes, many of them involved in blood pressure regulation, but also insulin resistance. AGTR1 also shows an interaction with cortisol (Figure s4). Figure s4: CIDeR query: Mitochondrial respiratory chain complex V and double-click on AGTR1 and double-click on cortisol. A double click on cortisol leads to interactions with different diseases (Alzheimer's disease, schizophrenia, insulin resistance) as well as to inflammatory response, a bioprocess that is involved in the etiology of various diseases and is also curated in CIDeR as 'Focus topic'. The figure shows that different diseases, such as bipolar disorder and insulin resistance, can be linked via a few elements ('Mitochondrial respiratory chain complex V'-AGTR1-cortisol) and that a disease network is created that can facilitate the generation of hypotheses - for example, to investigate diseases using drugs that are not ordinarily used for them.

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Additional file 2:

Supplementary tables. Table s1: quantitative comparison of interaction information in different resources - diabetes/metabolic syndrome. The table shows the different types of interactions (process-phenotype, environment-process, microRNA-genes, and so on) and the number of respective interactions for diabetes/metabolic syndrome. Table s2: quantitative comparison of interaction information in different resources - Alzheimer's disease. The table shows the different types of interactions (process-phenotype, environment-process, microRNA-genes, and so on) and the number of respective interactions for Alzheimer's disease. Table s3: quantitative comparison of interaction information in different resources - Parkinson's disease. The table shows the different types of interactions (process-phenotype, environment-process, microRNA-genes, and so on) and the number of respective interactions for Parkinson's disease. Table s4: quantitative comparison of interaction information in different resources - amyotrophic lateral sclerosis. The table shows the different types of interactions (process-phenotype, environment-process, microRNA-genes, and so on) and the number of respective interactions for amyotrophic lateral sclerosis.

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Additional file 3:

Potential side effects of type 2 diabetes drugs on patients affected by Alzheimer's disease or depression.

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