Category Cross-Omics>Pathway Analysis/Gene Regulatory Networks/Tools

Abstract PIMRider® is a web-based application dedicated to the exploration of Protein-protein Interaction Maps (PIM®).

Fed by the manufacturer’s reliable interaction data, PIMRider allows the exploration of biological functions and the understanding of pathways.

PIMRider is composed of several Viewers, which may be grouped in two (2) classes:

1) The first class of viewers consists of a group of classical HTML viewers that give access to annotations of proteins and genes such as normalized names and ids, annotations, sequences, bibliographical references, and database entries.

2) The second class of viewers comprises specific graphical viewers (‘JAVA Applets’), each of these being specialized in one aspect of proteomics using 2-Hybrid technology (2H).

Two (2) search tools were developed to explore network contents in terms of genes / proteins.

1) The Basic search tool seeks genes / proteins in the network on the basis of simple text criteria such as ‘names’ and ‘annotations’.

2) The Advanced search tool seeks genes / proteins on the basis of more sophisticated criteria such as ‘functional category’, ‘functional domains’, ‘bibliographical references’, etc. that can be combined using logical operators.

The Basic search tool is embedded within the HTML classical viewers as the ‘Advanced search tool’ is an HTML viewer in itself.

PIMRider General Concepts --

PIMRider basically gives access to a Protein-protein Interaction Map (PIM) built from a series of experiments made using 2H technology.

In a 2H experiment a proteic fragment of interest (BAIT) is screened against a prey library, e.g. a proteome, for interacting partners.

In a PIM program, a set of Baits is screened against one given prey proteome. PIMRider can access a PIM that was made from a maximum of eight (8) PIM programs.

A PIM program can involve one or two Proteomes (two proteomes meaning that the Bait proteins and the interacting partners are separated).

Therefore, PIMRider can access a PIM involving a maximum of 16 different proteomes.

A protein can belong to more than one proteome. Within the PIM and for two given interacting proteins, more than one interaction can be detected. But within the whole PIM, each ‘atomic’ interaction that was detected belongs to one and only one PIM program.

PIMRider Specific concepts --

SID® (Selected Interacting Domain) -

SID corresponds to the smallest identified protein domain necessary for a particular protein-protein interaction.

PBS® (PIM Biological Score) -

PBS is a score that quantifies the reliability of each interaction and allows the filtering of interactions based on their reliability.

The aim of the PBS computation is to add value to the generated Protein Interaction Maps by allowing the rescue of false negatives while efficiently filtering out false positives.

PBS represents a confidence number assigned to each interaction identified. The PBS score (the result of Hybrigenics’ bioinformatics algorithms) takes into account the characteristics of the libraries screened and the target organism as well as the results of the screens.

The current PBS score is displayed as the probability that the interaction is found by chance, as a result of a two-hybrid artifact.

The PBS score ranges from 0 (best) to 1 (worst).

For practical use, the PBS score is displayed by four (4) main categories:

A (best), B, C, and D (worst), and two special distinct categories E and ‘N/A’. Each PBS category possesses its own color to emphasize its meaning and enhance its visualization in the different viewers.

PIMRider Basic Search Tool --

Purpose - To select proteins within the PIM, corresponding to the given criteria.

Features -

PIMRider Advanced Search Tool --

Purpose - To select proteins within the PIM via a composite request that may include the following criteria:

Features -

PIMRider PIM Viewer® - Ride the interactions --

Features -

PIMRider Interaction Viewer® - Review details of experimental data --

Features -

PIMRider Domain Viewer® - Ride the interactions --

Features -

System Requirements

PIMRider has been tested and is fully operational with the following configurations:


Manufacturer Web Site PIMRider

Price Contact manufacturer.

G6G Abstract Number 20649

G6G Manufacturer Number 104247