Research article
Genes involved in complex adaptive processes tend to have highly conserved upstream regions in mammalian genomes
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* Corresponding author: Simon Kasif kasif@bu.edu
1 Bioinformatics Program, Boston University, Boston, MA 02215, USA
2 Department of Biomedical Engineering, Boston University, Boston, MA 02215, USA
3 Center for Advanced Genomic Technology,. Boston University, Boston, MA 02215, USA
4 Children's Hospital Informatics Program at Harvard-MIT Health Sciences and Technology, Boston, MA 02215, USA
BMC Genomics 2005, 6:168 doi:10.1186/1471-2164-6-168
Published: 27 November 2005Additional files
Additional File 1:
Table 1 GO terms significantly correlated with upstream alignment scores. The table lists all the GO terms significantly correlated with 1 kb, 2 kb and 5 kb upstream alignment scores in the human-mouse analysis.
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Additional File 2:
Table 2 GO terms significantly correlated with upstream alignment scores in the analysis using dog. The table lists all the GO terms significantly correlated with 1 kb, 2 kb and 5 kb upstream alignment scores in the human-dog analysis.
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Additional File 3:
Table 3 List of Hox and Hox homolog genes. List of Hox and Hox homolog genes used in the analysis, with their 1 kb, 2 kb and 5 kb upstream alignment scores.
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Additional File 4:
Table 4 GO terms significantly correlated with upstream alignment scores after partialling out G+C%. The table lists all the GO terms significantly correlated with 1 kb, 2 kb and 5 kb upstream alignment scores in the human-mouse analysis after controlling G+C% using partial rank correlation.
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Additional File 5:
Table 5 GO terms significantly correlated with CpG dinucleotide frequency in the human upstream sequence. The table lists all the GO terms significantly correlated with CpG dinucleotide frequency in the 1 kb, 2 kb and 5 kb human upstream sequences. Genes are sorted by 1 kb upstream alignment score.
Format: XLS Size: 56KB Download file
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Additional File 6:
Table 6 Human genes with their upstream alignment scores and Gene Ontology annotations. The 1 kb, 2 kb and 5 kb upstream alignment scores based on human-mouse comparison and Gene Ontology annotations of human genes.
Format: XLS Size: 2.4MB Download file
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