Web Services For Human Membrane Receptor Interactome (HMRI)

Web Service for Human Membrane Receptor Interactome (HMRI)

Services:

Help:

Membrane receptor-activated signal transduction pathways are critical to cellular functions and disease mechanisms in human.

To fully understand these pathways, the identification of the repertoire of all proteins that interact with membrane receptors is urgently needed. We apply a computational learning approach to derive these protein interactions by combining evidences from multiple biological data sets. Interaction confidence score was evaluated between each human receptor to all possible human proteins.

Here we provide a web server to contain these predicted interactions and the score confidence, to let users be able to search these interactions. There are four basic functions in our service. For each of them, we give an example in the following.

1. Check input query

This service would perform a check on the input query gene / protein to see if the query is a human receptor [1] or not. If yes, we further check if the input belongs to the GPCR family or not.

Input: the input query would be either NCBI Entrez gene ID or gene Name. For example as :

Output: the output would be as following: (The query is a receptor and not in GPCR family. Its gene ID is ‘1956’). The URLs links directly to the page about this query in NCBI [2] and HPMR [1] database. )

2. Search interaction partners for the query protein

This service would search on the whole predicted receptor interactome to find interaction partners of the query. The returned pairs are those whose interaction scores are higher than an input score threshold. The confidence score range is [-1.5, 5], with default as 2.5.

Input: the input query would be either NCBI Entrez gene ID or gene Name. Also a score threshold needs to be specified by the users. For example as: looking for partners for ‘EGFR’ and those partners should have interaction score (with EGFR) higher than ‘3.8’.

Output: the part of the output would be as following: (The URLs links directly to the page about this query in NCBI [2]). The retrieved pairs could be downloaded in text file format. And they are also displayed in the tabular format and provided extra information (if in HPRD or not.) as well. The features to each pair could also be accessed through the provided links.

3. Search interaction pairs among the set of input proteins

This service would search the potential pairs among a group of input proteins. The returned pairs’ interaction scores are higher than an input score threshold. The confidence score range is [-1.5, 5], with default as 2.5.

Input: the input query proteins would be either NCBI Entrez gene ID or gene Name. For example as :

Output: the output would be as following: (The URLs links directly to the page about this query in NCBI [2]). The retrieved pairs could be downloaded in text file format. And they are also displayed in the tabular format and provided extra information (if in HPRD or not.) as well. The features to each pair could also be accessed through the provided links. In addition, a graph representation about the retrieved pairs is provided.

4. Check predicted scores for a pair of input proteins

This service would return the predicted score for a pair of input proteins. We check if this pair existed in HPRD (2006 version) or not. In addition, we also provide the features of this requested pair.

Input: the input two proteins would be either NCBI Entrez gene ID or gene Name. For example as :

Output: the output would be as following: (The URLs links directly to the page about this query in NCBI [2] database.)

…….

Reference:

Ben-Shlomo, I., Yu Hsu, S., Rauch, R., Kowalski, H. W. & Hsueh, A. J. Signaling receptome: a genomic and evolutionary perspective of plasma membrane receptors involved in signal transduction. Sci STKE 17, RE9 (2003).
NCBI: http://www.ncbi.nlm.nih.gov/sites/entrez