PDQ_MED Example

As an example, we have analyzed a set of 50 known genes randomly selected from a liver EST library. MEDLINE contains nearly 50,000 abstracts for these 50 genes. This is an intractable quantity of data for traditional text browsing methods. A PDQ_MED analysis of this set of 50 genes identifies a subset of 16 genes which co-occur in the literature, suggesting various of inter-relationships including regulatory, metabolic, and signaling pathways.

Tree Analysis:

PDQ_MED provides the user with a hierarchical tree analysis of the co-occurrence of the terms within a given set. In the tree below, closely related terms are connected in the hierarchy. The numbers in parenthesis represent the inverse of the degree of co-occurrence. Individual terms and term-pairs are linked back to the MEDLINE abstract.

Graph Analysis:

PDQ_MED also provides a graphical analysis of the co-occurrence of the terms within the set.  In the graph at right, the complete set of linkages between terms is shown.  The lengths of the interconnecting lines represent the inverse of the frequency of co-occurrence.

Other Output:

Key Sentences (more than two query or pharma terms):

10753589  The results demonstrate that IGF-I regulates IGFBP-4 post-trancriptionally 
and post-translationally, whereas IGFBP-3 is only affected post-translationally.

Pharma Sentences (query plus a pharma term):

10389993  Cytosolic determinations of cathepsin-D (cath-D), urokinase plasminogen
activator (uPA) and its specific inhibitor PAI-1 have shown an association with 
adverse prognosis in breast cancer.

Proximity Sentences (two query terms):

7538844  The chymotryptic activity of PSA was further confirmed by the ability of 
alpha-1-antichymotrypsin and chymostatin to block PSA cleavage of radiolabeled 
IGFBP-3.