Open Access Research article

Genome-wide analysis uncovers high frequency, strong differential chromosomal interactions and their associated epigenetic patterns in E2-mediated gene regulation

Junbai Wang1*, Xun Lan2, Pei-Yin Hsu3, Hang-Kai Hsu3, Kun Huang2, Jeffrey Parvin2, Tim H-M Huang3 and Victor X Jin2*

Author Affiliations

1 Department of Pathology, Oslo University Hospital – Norwegian Radium Hospital, Montebello, 0310 Oslo, Norway

2 Department of Biomedical Informatics, The Ohio State University, 460 W 12th Ave., 212 BRT, Columbus, OH 43210, USA

3 Department of Molecular Medicine, Institute of Biotechnology, University of Texas Health Science Center, San Antonio, TX, 78245, USA

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BMC Genomics 2013, 14:70  doi:10.1186/1471-2164-14-70

Published: 31 January 2013

Additional files

Additional file 1:

Additional Figures and Tables. Contains all additional tables and figures.

Format: DOCX Size: 4.7MB Download file

Open Data

Additional file 2:

DAVID results for genes in chromosomal interaction hot regions. Contains DAVID results of 69 genes located in the top 10 chromosomal interaction hot regions.

Format: XLSX Size: 49KB Download file

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Additional file 3:

DAVID results for genes in chromosomal interaction cold regions. Contains DAVID results of 45 genes located in the top 10 chromosomal interaction cold regions.

Format: XLSX Size: 17KB Download file

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Additional file 4:

DAVID results for genes in chromosomal interaction hot regions. Contains DAVID results of 280 genes located in the top 50 chromosomal interaction hot regions.

Format: XLS Size: 227KB Download file

This file can be viewed with: Microsoft Excel Viewer

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Additional file 5:

DAVID results for genes in chromosomal interaction cold regions. Contains DAVID results of 500 genes located in the top 50 chromosomal interaction cold regions.

Format: XLS Size: 142KB Download file

This file can be viewed with: Microsoft Excel Viewer

Open Data

Additional file 6:

Comparing 69 genes at interaction hot regions with Fullwood’s results. Contains a comparison between 69 genes at the top 10 chromosomal interaction hot regions and Fullwood’s results.

Format: XLS Size: 27KB Download file

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Additional file 7:

Strong chromosomal interaction changes. Contains chromosome regions with strong interaction changes under the E2 treated condition (e.g. Zscore > 1 and Relative ratios = 2).

Format: XLSX Size: 1.1MB Download file

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Additional file 8:

Additional Figure. Contains an additional figure that shows the correlation between histone modification and chromosomal interaction frequency for all interaction regions in 1Mbp resolution. The order of chromosome regions is sorted by their interaction frequency at the control condition.

Format: XLSX Size: 8.1MB Download file

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Additional file 9:

Genes of top 10 regions with the most gained and lost interactions according to four types of strong chromosomal interaction changes. Contains results of functional annotation of genes in the top 10 most frequent dynamical chromosomal interaction regions. The regions are estimated from four types of strong chromosomal interaction changes.

Format: XLS Size: 153KB Download file

This file can be viewed with: Microsoft Excel Viewer

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