Open Access Research article

Genome-wide patterns of promoter sharing and co-expression in bovine skeletal muscle

Quan Gu12, Shivashankar H Nagaraj1, Nicholas J Hudson1, Brian P Dalrymple1 and Antonio Reverter1*

Author Affiliations

1 Computational and Systems Biology, CSIRO Food Futures Flagship and CSIRO Livestock Industries, 306 Carmody Rd. St. Lucia, Brisbane, Queensland 4067, Australia

2 College of Information Sciences and Technology, Donghua University, Shanghai 201620, PR China

For all author emails, please log on.

BMC Genomics 2011, 12:23  doi:10.1186/1471-2164-12-23

Published: 12 January 2011

Additional files

Additional file 1:

Figure S1. Partial view of the Promoterome Matrix (P-matrix). Partial view of the Promoterome Matrix (P-matrix) with 9,242 TG in rows and 333 TF in columns and where the TFs have been rear-ranged according to a hierarchical clustering. The hierarchical tree shows a pattern consistent with the non-random assortment of the connectivity distribution with most TFs having few TGs and few TFs having lots of TGs and consistent with a scale-free power-law distribution.

Format: JPEG Size: 204KB Download file

Open Data

Additional file 2:

Figure S2. Further observation on the linking between co-expression and co-regulation. (A) Log odds ratio (LOD) values as a function of type of transcriptional regulatory motifs (TRM) for absolute correlations (red bars) and positive correlations (green bars) from zero transcription factor (TF) in common (TRM0) to 10 TFs in common (TRM10). LOD values above zero indicate observations that are more common than expected by chance, and vice versa; (B) Difference in LOD-value across the extreme intervals: Extreme positive correlations (i.e. in the {0.8,1.0} interval) and more frequent among high-order TRMs than extreme negative correlations (i.e. in the {-1.0,-0.8} interval); (C) LOD-values for the co-expression as a function of the number of TFs in common for absolute correlations (red bars) and positive correlations (green bars); (D) Empirical density distribution of correlations at three TRM from TRM1 (red) to TRM5 (green) to TRM10 (blue).

Format: JPEG Size: 126KB Download file

Open Data

Additional file 3:

Table S1. Module Genes. Gene content of the six functional modules profiled in this study.

Format: DOC Size: 33KB Download file

This file can be viewed with: Microsoft Word Viewer

Open Data