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This article is part of the supplement: The International Conference on Intelligent Biology and Medicine (ICIBM) – Genomics

Open Access Research

GLAD4U: deriving and prioritizing gene lists from PubMed literature

Jérôme Jourquin12, Dexter Duncan1, Zhiao Shi34 and Bing Zhang12*

Author Affiliations

1 Department of Biomedical Informatics, Vanderbilt University School of Medicine, 400 Eskind Biomedical Library, 2209 Garland Avenue, Nashville, TN 37232, USA

2 Department of Cancer Biology, Vanderbilt University School of Medicine, 2220 Pierce Avenue, PRB771, Nashville, TN 37232, USA

3 Advanced Computing Center for Research & Education, Vanderbilt University, Nashville, TN 37240, USA

4 Department of Electrical Engineering and Computer Science, Vanderbilt University, Nashville, TN 37240, USA

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BMC Genomics 2012, 13(Suppl 8):S20  doi:10.1186/1471-2164-13-S8-S20

Published: 17 December 2012

Additional files

Additional file 1:

False-positive genes retrieved by querying "apoptosis" with GLAD4U. This table shows all genes retrieved by GLAD4U with the query "apoptosis" that were not among the gold standards. The table presents the rank and score of these genes and all the retrieved supporting publications.

Format: XLSX Size: 349KB Download file

Open Data

Additional file 2:

False-positive genes retrieved by querying "hypertension" with GLAD4U. This table shows all genes retrieved by GLAD4U with the query "hypertension" that were not among the gold standards. The table presents the rank and score of these genes and all the retrieved supporting publications.

Format: XLSX Size: 151KB Download file

Open Data

Additional file 3:

GLAD4U prioritization of disease candidate genes. This table shows the number of genes associated with each GeneWanderer hereditaty disease, retrieved by GLAD4U and overlapping between the two lists before and after thresholding. F-measure fold change between the GLAD4U prioritized list before and after thresholding, as well as the actual F-measures are also displayed in the table.

Format: XLSX Size: 11KB Download file

Open Data