Literature Lab: a method of automated literature interrogation to infer biology from microarray analysis

doi:10.1186/1471-2164-8-461

BMC Genomics

Volume 8

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Febbo PG
Mulligan MG
Slonina DA
Stegmaier K
Di Vizio D
Martinez PR
Loda M
Taylor SC

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Mulligan MG
Slonina DA
Stegmaier K
Di Vizio D
Martinez PR
Loda M
Taylor SC
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Literature Lab: a method of automated literature interrogation to infer biology from microarray analysis

Phillip G Febbo¹^,2^,3 , Mike G Mulligan⁴ , David A Slonina⁴ , Kimberly Stegmaier⁵ , Dolores Di Vizio⁶ , Paul R Martinez⁴ , Massimo Loda⁶ and Stephen C Taylor⁴

¹Institute for Genome Science and Policy, Duke University, Durham, North Carolina, USA

²Department of Medicine, Duke University School of Medicine, Durham, North Carolina, USA

³Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, North Carolina, USA

⁴Acumenta Corporation, Boston, Massachusetts, USA

⁵Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts, USA

⁶Department of Pathology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts, USA

author email corresponding author email

BMC Genomics 2007, 8:461doi:10.1186/1471-2164-8-461


Published:	18 December 2007

Additional files

Additional file 1:

Supplemental Methods.

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Additional file 2:

Term Lists. Excel spreadsheet of term lists used for physiology, metabolism, and pathway domains.

Format: XLS Size: 40KB Download file

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Additional file 3:

Gene Thesaurus. Excel spreadsheet of all genes with all aliases used for all experiments in this manuscript.

Format: XLS Size: 4.5MB Download file

This file can be viewed with: Microsoft Excel Viewer

Additional file 4:

Excluded Terms. Excel spreadsheet of terms excluded from search due to ambiguity or limited associated information.

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This file can be viewed with: Microsoft Excel Viewer

Additional file 5:

Effects of Time Frame. Standard Literature Lab interrogations performed on the HL60 gene set for key term lists for metabolism, pathways, and physiology. The only difference between the two interrogations involved time frame: One search included citations from the first 5 years of the standard 10 year interval (12/31/93 and 12/30/98, "1^st5 yr") and the other the latter 5 years (12/31/98–12/31/03, "2^nd5 yr"). Log₁₀(PF) ("Score") was used to order key terms and standard heuristics were applied to identify associations as "strong" or "moderate".

Format: JPEG Size: 605KB Download file

Additional file 6:

Effects of Gene Set Size. Standard Literature Lab interrogations performed on the HL60 gene set for key term lists for metabolism with increasing size of the gene set. "Metabolism-X" where X equals 10, 25, 50, 100, 150, 200, 250, and 300 and represents the number of genes in the gene set.. Log₁₀(PF) ("Score") was used to order key terms and standard heuristics were applied to identify associations as "strong" or "moderate".

Format: JPEG Size: 671KB Download file

Additional file 7:

Results of Breast Cancer Gene Set. The 70-genes associated with outcome for localized breast cancer were used as a gene set and interrogated by Literature Lab for associations between members of the gene set and key terms included on the lists of Physiology, Metabolizm, and Pathways. Log₁₀(PF) ("Score") was used to order key terms and standard heuristics were applied to identify associations as "strong" or "moderate".

Format: JPEG Size: 284KB Download file

Additional file 8:

GOMiner. Excel spreadsheet of results from GOMiner using gene list from MPAKT experiment annotated for overlap with Literature Lab.

Format: XLS Size: 31KB Download file

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Additional file 9:

Mesher. Excel spreadsheet of results from MESHer using gene list from MPAKT experiment annotated for overlap with Literature Lab.

Format: XLS Size: 30KB Download file

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Additional file 10:

GeneCite MPAKT. Excel spreadsheet of results from GeneCite using gene list from MPAKT experiment annotated for overlap with Literature Lab.

Format: XLS Size: 1.2MB Download file

This file can be viewed with: Microsoft Excel Viewer

Additional file 11:

GeneCite Metastatic Prostate Cancer. Excel spreadsheet of results from GeneCite using gene list from local v metastatic prostate cancer experiment annotated for overlap with Literature Lab.

Format: XLS Size: 1.6MB Download file

This file can be viewed with: Microsoft Excel Viewer