Inforsense meaning

FAQ about GeneSense

1. What is about GeneSense?

GeneSense is a web-based platform that allows users to construct, visualize, manipulate and analyze gene information. It aims to assist researchers to find the optimal gene regulatory factors by associated networks, such as the obesity related gene MAPK8. Users can expect the following benefits using GeneSense:
(i) To gain an accurate overview of genes information of interest;
(ii) To build different models to highlight understudied molecular interactions of proteins coded by user-entered genes.

2. How to use GeneSense?

GeneSense allows users to enter the database via a gene of interest using its approved symbol, alias names, approved name or descriptions. Once users submitted the gene of interest, they retrieve the gene's descriptions and are informed of similarly described genes. Subsequently, the users can choose to continue with a gene summary page (Fig. 1) or abort the process and return to the data entry page. The current results page is divided into five main sections: a search button to search a new gene of interest, the gene summary, the node network for the gene of interest, the leaf network for the gene of interest, and the loop network for the gene of interest.

Fig.1 A screen shot of gene MAPK8 information summary page in GeneSense.
The table is divided into sections that show MAPK8's general information, homologs information, clinical information, gene information, reference information, pathway information, and protein-protein interactions, respectively, with links to additional information.

3. What is the network construction of GeneSense?

GeneSense adopts a number of methods to annotate protein-protein interactions. First, nodenet in GeneSense supports basic queries of PPI network for a single protein (for upstream or downstream proteins analysis), which can be used to rapidly verify whether in-lab generated PPIs are already existed or potentially being novel. Second, GeneSense provides the leafnet network model to visualize the complexity of the queried protein and its upstream or downstream proteins that can be used to find the unique or optimal substrate proteins. Third, GeneSense provides loopnet to visualize the upstream and downstream targets of the queried protein, which reveals biological events in cells at the protein-protein interaction level.

Fig.2A Downstream node network of MAPK8.
MAPK8 and substrate proteins analysis.

Fig.2B Upstream node network of MAPK8.
MAPK8 and upstream proteins analysis.

Fig.2C Downstream leaf network of MAPK8.
Network analysis of MAPK8 substrate proteins.

Fig.2D Upstream leaf network of MAPK8.
Network analysis of MAPK8 upstream proteins.

Fig.2E Loop network of MAPK8.
MAPK8 network analysis.

4. What is the architecture of GeneSense?

GeneSense database contains two parts: the first part consists of gene annotation and the second part consists of PPI database. The gene annotation part includes homologs information, clinical information, and gene related information from HGNC and some other gene related information, such as Pathway information that was integrated from KEGG. PPI databases in GeneSense were integrated from different databases, including a non-redundant database based on integration of data from IntAct, MINT, HPRD and other databases.

5. What is the algorithm of network?

Force-directed algorithm was used to generate graphs and to determine the position of each node. Each node is subject to a repulsive force from every other node, yet constrained by the edges that keep nodes connected together.

6. How should I cite GeneSense?

Authors are requested to cite:
Chen, Z.Z.* et al. GeneSense: a new approach for human gene annotation integrated with protein-protein interaction networks. Sci. Rep. 4, 4474; DOI:10.1038/srep04474 (2014).[PubMed]

7. How to create protein protein interactions using a custom protein list?

The multi-protein search tool allows the user to type or paste a list of proteins to check if there is any interaction existed between them.

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