Open Access Research article

The adjacent positioning of co-regulated gene pairs is widely conserved across eukaryotes

James T Arnone1, Adam Robbins-Pianka12, Jeffrey R Arace1, Sara Kass-Gergi1 and Michael A McAlear1*

Author Affiliations

1 Department of Molecular Biology and Biochemistry, Wesleyan University, Middletown, CT 06459, USA

2 Department of Computer Science, University of Colorado Boulder, Boulder, CO, 80309-0430, USA

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BMC Genomics 2012, 13:546  doi:10.1186/1471-2164-13-546

Published: 10 October 2012

Additional files

Additional file 1:

Figure S1. The transcription profiles of the entire set of paired RRB genes throughout a heat shock (A-F). For clarity, a maximum for three sets of pairs are plotted per graph.

Format: TIFF Size: 149KB Download file

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Additional file 2:

Figure S2. The transcription profiles of the entire set of paired RP genes throughout a heat shock (A-C). For clarity, a maximum for three sets of pairs (or two sets of triplets) are plotted per graph.

Format: TIFF Size: 80KB Download file

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Additional file 3:

Figure S3. The transcription profiles of the entire set of paired rRNA and ribosome biosynthesis genes following release from alpha-factor synchronization (A-F). For clarity, a maximum for three sets of pairs are plotted per graph.

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Additional file 4:

Figure S4. The transcription profiles of the entire set of paired ribosomal protein genes following release from alpha-factor synchronization (A-C). For clarity only a maximum for three sets of pairs (or two sets of triplets) are plotted per graph.

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Additional file 5:

Complete list of the S. cerevisiae gene members for the various GO term groupings.

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Additional file 6:

Table S1. No significant gene pair adjacencies were found within the following ontologies.

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Additional file 7:

Figure S5. The transcription profiles of the heat shock genes throughout a heat-shock induction of the budding yeast stress response. The unpaired members of the regulon are show on top (A) and the two sets of pairs are show in (B).(B)

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Additional file 8:

Table S2. The closest homologs (E-value < 10 -9) to members of the paired gene sets are not their immediate, adjacent neighbors.

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Additional file 9:

Figure S6. Adjacently paired RRB and RRP genes are conserved in Saccharomyces sensu strictu species. Paired sets of genes were randomly selected and their conservation was determined by comparing that pairs’ location in S. paradoxus, S. bayanus and S. mikatae. Every gene pairing relationship that is conserved in any of these species was counted and the histogram showing frequency plot is shown for the set of pairs the size of the RRB regulon (n = 282) and for the RP regulon (n = 180) above (A and B, respectively). The actual percentage of conserved RRB (†) genes and RP (‡) genes is highlighted.

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Additional file 10:

List of adjacent members for the RP and RRB gene sets in divergent eukaryotes.

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Additional file 11:

List of expanded RRB gene set membership from  S.cerevisiae.

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