Curation of Human Disease Networks

FunCat (The Functional Catalogue)

FunCat is a hierarchically structured, organism-independent, flexible and scalable controlled classification system enabling the functional description of proteins and protein complexes from any organism. The project was performed in collaboration with the ‘Fungal and microbial genomics’ group and the Biomax Informatics AG.

 

Dataset of non-interacting proteins (Negatome)

The Negatome is a collection of protein and domain pairs that are unlikely to be engaged in direct physical interactions. The database currently contains experimentally supported non-interacting protein pairs derived from two distinct sources: by manual curation of literature and by analyzing protein complexes with known 3D structure. The project was performed in collaboration with Philip Pagel and the group of Dmitrij Frishman, both from the Technische Universität München Wissenschaftszentrum Weihenstephan.

 

Protein-protein interactions (yeast, mammalia)

The protein-protein interaction (PPI) dataset from MIPS serves as gold-standard in the field. It has been used in many bioinformatics analyses published in the literature. The MPact dataset containing 4300 PPIs was published in collaboration with the ‘Fungal and microbial genomics’ group.


Analogous to the yeast PPI dataset we generated MPPI, a dataset of 1800 mammalian PPIs. The project was performed in collaboration with the group of Dmitrij Frishman from the Technische Universität München Wissenschaftszentrum Weihenstephan.

 

HSC-Explorer - a curated database for hematopoietic stem cells

HSC-Explorer is a publicly available, integrative database containing detailed information about the early steps of hematopoiesis. It provides structured information on more than 7000 experimentally validated interactions between molecules, bioprocesses and environmental factors. Hematopoiesis-relevant interactions are accompanied with context information such as model organisms and experimental methods for enabling assessment of reliability and relevance of experimental results. Several predefined datasets (Selected topics) offer insights into stem cell behavior, the stem cell niche and signaling processes supporting hematopoietic stem cell maintenance.

 

HoPaCI – Host-pathogen interactions

Bacterial infectious diseases are the result of multifactorial processes affected by the interplay between virulence factors and host targets. The Host-Pathogen Interaction Database (HoPaCI) is a publicly available, manually curated, integrative database of host-pathogen interaction data from Pseudomonas aeruginosa and Coxiella burnetii. The resource provides structured information on 3,585 experimentally validated interactions between molecules, bioprocesses and cellular structures extracted from the scientific literature