PubMatrix: a tool for multiplex literature mining

Abstract

Background: Molecular experiments using multiplex strategies such as cDNA microarrays or proteomic approaches generate large datasets requiring biological interpretation. Text based data mining tools have recently been developed to query large biological datasets of this type of data. PubMatrix is a web-based tool that allows simple text based mining of the NCBI literature search service PubMed using any two lists of keywords terms, resulting in a frequency matrix of term co-occurrence.

Results: For example, a simple term selection procedure allows automatic pair-wise comparisons of approximately 1-100 search terms versus approximately 1-10 modifier terms, resulting in up to 1,000 pair wise comparisons. The matrix table of pair-wise comparisons can then be surveyed, queried individually, and archived. Lists of keywords can include any terms currently capable of being searched in PubMed. In the context of cDNA microarray studies, this may be used for the annotation of gene lists from clusters of genes that are expressed coordinately. An associated PubMatrix public archive provides previous searches using common useful lists of keyword terms.

Conclusions: In this way, lists of terms, such as gene names, or functional assignments can be assigned genetic, biological, or clinical relevance in a rapid flexible systematic fashion. http://pubmatrix.grc.nia.nih.gov/

Figure 1

The PubMatrix Data Input Page

Figure 2

The report page from a simple search of gene names versus neural modifier terms. All reported numbers are hyperlinked and will initiate a de-novo search for that specific term combination.

Figure 3

Gene expression results (Z-ratio) of cisplatin treatment of an ovarian tumor cell line versus keywords relevant to cisplatin resistance. This graph was constructed in MS EXCEL directly from a PubMatrix search result table using the 3D chart view option after adding gene expression values (Z-ratios).

Figure 4

Visual display of chromosomal-band term list versus the term. "autoimmune". Search terms were 313 sequential human chromosomal bands (1pter, 1p36, 1p35, 1p34, etc....Xq26, Xq27, Xq28, Xqter) versus the single modifier term "autoimmune". This graph was constructed in MS EXCEL using 3D chart view option after separating individual chromosome results into individual columns.