Category Cross-Omics>Data/Text Mining Systems/Tools

Abstract PubGene is a tool for researchers, physicians and the general public. Graphic networks provide an overview of how genes and their proteins relate to each other and to important concepts.

These networks are a product of the manufacturer’s algorithms, which constantly search scientific texts and sequence data to extract information relevant to specific genes.

Searches are performed in the context of specific gene symbols, their corresponding proteins and associated synonyms.

Results are cross-referenced - gene to gene as well as to terms describing diseases, chemicals, cellular components, biological functions and processes - to build data bases that allow you to quickly visualize and navigate to the information you need.

PubGene currently consists of multiple products:

1) PubGene Public -- provides cutting-edge technology to the scientific community, physicians and the public at large. The public service includes the core, advanced text-mining technologies and network presentations that made PubGene famous.

PubGene can also present networks based on comparisons of protein sequences, and includes a sequence homology interface to query databases using PARALIGN.

My Workspace lets users save results of queries and to build gene lists. Users can also e-mail results to colleagues - making PubGene part of the interactive exchange of knowledge.

In addition, the manufacturers have introduced a regimen of weekly data updates - scouring MEDLINE for new references to genes, their protein products and terms relevant to these - such that searches performed in PubGene give you current information.

2) PubGene Analysis Online -- is an ideal package for interpreting microarray results. Subscribers to PubGene Analysis can upload their "short list" of implicated genes and visualize these as networks.

Networks can be annotated with keywords of relevance to help build an understanding of individual gene importance and interactions with other genes.

In addition, the Analysis package allows users to visualize information on published mutations, and to create networks based on literature or sequence similarity through searches of chromosomal regions.

A subscriber can access PubGene Analysis Online from any computer through the Internet on a secure and encrypted connection to PubGene's server. Products features/capabilities include:

What PubGene does -- PubGene helps you retrieve information on genes and proteins. The underlying structure of PubGene can be viewed as a "gene-centric" database.

Gene and protein names are cross-referenced to each other and to terms that are relevant to understanding their biological function, importance in disease and relationship to chemical substances.

The result is a "literature network" organizing information in a form that is easy to navigate.

PubGene Text Mining -- PubGene targets information on genes and proteins in the MEDLINE database.

Specially developed algorithms mine the abstract texts of Millions of PubMed articles for co-citation of multiple genes or proteins and display them as "Literature Networks", where nodes represent each gene or protein and the 'connecting lines' represents the number of articles in which each gene or protein pair is co-cited.

The list of articles can be retrieved by clicking on the number along the lines.

PubGene "Bio Networks" -- Bio Networks show how gene or protein names are co-cited in the literature. That is, names that appear in the same text form a pair and are said to be neighbors in the network.

When a gene or protein is studied, there is a good chance its name (or a synonym for that name) will appear in articles together with other gene or protein names.

One can visualize how most genes that have been studied will be connected either directly or indirectly to each other in a Bio Network.

Connections in the literature are a strong indicator of biological interaction. Networks can also be annotated with Gene Ontology (GO), Medical Subject Heading (MeSH) or chemical keywords.

By organizing genes and proteins into networks PubGene helps you visualize and navigate information to gain an understanding.

Finding out what a gene (or protein) "does" via PubGene -- PubGene extracts information associated with individual genes and proteins from MEDLINE records and metadata.

In this way, genes and proteins are linked to "keywords" such as Gene Ontology (GO), Medical Subject Heading (MeSH), drugs, toxins and other chemicals or compounds (Chem).

The options within the BioAssociations tool allow you to view lists of such terms associated with individual genes or proteins.

Using these options from the BioAssociations tool, you can find out what is known about the processes, function, cellular compartmentalization, pathologies and behavior in response to chemical treatment associated with a gene or protein.

DNA- and Protein sequences via PubGene -- PubGene can draw networks based on sequence similarity. This function is available under Advanced Options in Bio Networks. PubGene 'sequence networks' are based on the pair-wise alignment of reference sequences in a pre- compiled database.

By viewing a ‘sequence network’ you can quickly see if other genes with similar sequence have been described in terms of their biological or medical importance.

You can also perform searches of sequence databases with the PubGene Sequence Homology tool. This tool aligns a DNA or protein sequence against the entries in one of several databases using the Smith-Waterman algorithm.

PubGene employs the advanced PARALIGN method. This makes it possible to return the highly accurate and sensitive Smith-Waterman alignments in a matter of minutes.

Finding Genes using Keywords via PubGene -- PubGene tools are designed to allow you to find gene (protein) to gene as well as keyword to gene (protein) connections.

A "keyword" submitted to the PubGene Bio Networks will show a literature (or sequence) network of genes associated with that keyword. BioAssociations can generate lists of keywords associated with a gene (protein). Or, BioAssociations can do the opposite: find a list of genes (proteins) relevant to a keyword.

In both cases the entries in the list are ranked by the significance of the association.

Finding a connection between specific genes via PubGene -- Some genes are Not co-cited (mentioned together) in any MEDLINE record. But you can submit both gene names simultaneously to PubGene Bio Networks.

Networks produced by submitting two (or more) genes simultaneously may show indirect connections between genes (via a neighbor).

System Requirements

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Manufacturer Web Site PubGene SA

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G6G Abstract Number 20251

G6G Manufacturer Number 102233