Open Access Research article

MMP1 bimodal expression and differential response to inflammatory mediators is linked to promoter polymorphisms

Muna Affara1, Benjamin J Dunmore2, Deborah A Sanders2, Nicola Johnson1, Cristin G Print13 and D Stephen Charnock-Jones124*

  • * Corresponding author: D S Charnock-Jones

  • † Equal contributors

Author Affiliations

1 Department of Pathology, University of Cambridge. Tennis Court Road, Cambridge, CB2 1QP, UK

2 Department of Obstetrics and Gynaecology, University of Cambridge. The Rosie Hospital, Robinson Way, Cambridge CB2 0SW, UK

3 Department of Molecular Medicine and Pathology, School of Medical Sciences, University of Auckland, Private bag 92019, Auckland, New Zealand

4 National Institute for Health Research, Cambridge Comprehensive Biomedical Centre, Box 277, Hills Road, Cambridge, CB2 0QQ, UK

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BMC Genomics 2011, 12:43  doi:10.1186/1471-2164-12-43

Published: 19 January 2011

Additional files

Additional file 1:

R-script: Source code to identify and visualise bimodally expressed transcripts from a microarray expression dataset.

Format: R Size: 8KB Download file

Open Data

Additional file 2:

Clustering results: Clustering results for both the un-treated (UT) and IM-treated (IM) HUVEC data set are shown for 10531 RNA transcripts. "OGS" is the official human gene symbol. "max_height" denotes the greatest distance (maximum cluster branch height) between the any two clusters of individuals, and is used a surrogate marker for the degree of bimodal expression. "p_max_height" denotes, for this transcript, the frequency with which this maximum cluster branch height is exceeded in clustering of 1,000 simulated data sets generated by aprametric bootstrapping (an estimate of the probability of each transcripts appearing to be bimodally expressed due to chance alone).

Format: XLSX Size: 1.3MB Download file

Open Data

Additional file 3:

R-script: To plot histograms.

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Additional file 4:

Table of 21 short listed RNA transcripts: Table of features for each of the 21 RNA transcripts to help determine selection

Format: XLSX Size: 1KB Download file

Open Data