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Open Access Research article

In Silico discovery of transcription factors as potential diagnostic biomarkers of ovarian cancer

Mandeep Kaur1, Cameron R MacPherson1, Sebastian Schmeier1, Kothandaraman Narasimhan2, Mahesh Choolani3 and Vladimir B Bajic1*

Author Affiliations

1 Computational Bioscience Research Center, King Abdullah University of Science and Technology, Thuwal 23955-6900, Kingdom of Saudi Arabia

2 Centre for Excellence in Genomic Medicine Research, King Abdul Aziz University, PO. Box 80216, Jeddah 21589, Kingdom of Saudi Arabia

3 Diagnostic Biomarker Discovery Laboratory, Department of Obstetrics and Gynaecology, Yong Loo Lin School of Medicine, National University Health System, 5 Lower Kent Ridge Road, 119074, Singapore

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BMC Systems Biology 2011, 5:144  doi:10.1186/1752-0509-5-144

Published: 19 September 2011

Additional files

Additional file 1:

Functional analysis of all four groups of genes using DAVID. Pathway analysis performed on all four groups of genes using DAVID.

Format: XLS Size: 42KB Download file

This file can be viewed with: Microsoft Excel Viewer

Open Data

Additional file 2:

Distribution of TFBSs and EREs in promoters of genes that contain predicted EREs. Details of gene IDs and positions on promoters where TFBSs and EREs were predicted to have binding sites.

Format: XLS Size: 395KB Download file

This file can be viewed with: Microsoft Excel Viewer

Open Data

Additional file 3:

TFs common and unique to gene groups 1 and 3. This file contains list of genes that were found to be common and unique to groups 1 and 3.

Format: TXT Size: 1KB Download file

Open Data

Additional file 4:

TFs common and unique to gene groups 'experimentally controlled genes' and 3. This file contains list of genes that were found to be common and unique to groups 3 and 'experimentally controlled genes'.

Format: TXT Size: 1KB Download file

Open Data

Additional file 5:

TFs common and unique to gene groups 'experimentally controlled genes' and 4. This file contains list of genes that were found to be common and unique to groups 4 and 'experimentally controlled genes'.

Format: TXT Size: 1KB Download file

Open Data

Additional file 6:

TFs with ranks for a set of 323 genes. The list of all TFs with ranks based on number of genes they potentially control from full set of 323 genes.

Format: XLSX Size: 24KB Download file

Open Data

Additional file 7:

Details of primary source of the data for partly validating the biomarkers using CleanEx database. Description of previously published study material that was used for partial validation of biomarkers identified in the current study.

Format: DOCX Size: 34KB Download file

Open Data

Additional file 8:

Functional categorization as identified using Gene/Gene Set overlap matrix with 17 TFs identified as biomarkers for full set of OC genes. The graphical view is a matrix of collections of gene sets, where each colored entry indicates that the two gene sets have a statistically significant overlap. Overlap between gene and gene sets were prominent for cell cycle associated TFs as observed for the first two rows from E2F1, E2F3-4 and TFDP-1 genes). Functional relevance of top ranked 17 biomarkers identified for full set of 323 OC genes in the present investigation.

Format: DOCX Size: 136KB Download file

Open Data

Additional file 9:

Functional categorization as identified using Gene/Gene Set overlap matrix with 17 TFs identified as biomarkers for estrogen-controlled sub-set of 77 OC genes. The graphical view is a matrix of collections of gene sets, where each colored entry indicates that the two gene sets have a statistically significant overlap. Overlap between gene and gene sets were prominent for cell cycle associated TFs. Functional relevance of top ranked 17 biomarkers identified for estrogen-controlled sub-set of 77 OC genes in the present investigation.

Format: DOCX Size: 136KB Download file

Open Data