Research article
Dissecting microregulation of a master regulatory network
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* Corresponding author: Anil G Jegga Anil.Jegga@cchmc.org
- † Equal contributors
1 Department of Computer Science, University of Cincinnati, Ohio, USA
2 Department of Biomedical Engineering, University of Cincinnati, Ohio, USA
3 Department of Pediatrics, University of Cincinnati College of Medicine, Ohio, USA
4 Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Ohio, USA
BMC Genomics 2008, 9:88 doi:10.1186/1471-2164-9-88
Published: 23 February 2008Additional files
Additional File 1:
Systematic break-down of the putative p53-regulated miRNAs (p53-miRs). Schematic classification of putative p53 sites and p53-miRs based on the miRNA types (intragenic or intergenic).
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Additional File 2:
Genomic coordinates of putative p53 sites within 10 kb flanking regions of human miRNAs. Chromosome cooridnates (based on Human Mar. 2006 – hg18 – assembly) of putative p53 sites in the flanking 10 kb regions of human microRNAs.
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Additional File 3:
Putative miRNAs regulating known 23 upstream regulators and 48 downstream TFs of p53. For the known 23 upstream regulators and 48 downstream TFs of p53 (based on p53 Knowledgebase; http://p53.bii.a-star.edu.sg webcite), putative miRs regulating them were extracted using MAMI server and the database http://mami.med.harvard.edu/ webcite.
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Additional File 4:
Functional enrichment (based on GO and pathways) in target genes of 143 p53-miRs. Results of functional over-representation analysis, performed to objectively identify biological processes potentially affected by p53-miR target genes.
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Additional File 5:
Details of Fisher's exact test used to test whether p53-miRs tend to target p53-interactants. Fisher's exact test was used to calculate the probability of p53-miRs regulating the p53 interactants (downloaded from the BioGRID database).
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Additional File 6:
Systematic break-down of the 474 human miRNAs based on their genomic location. Classification of the known 474 human miRNAs based on their genomic location (intergenic or intragenic/intronic).
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Additional File 7:
Details of the 474 human miRNAs analyzed. Additional details of genomic locations of the 474 human miRNAs analyzed (whether part of a cluster, i.e., 2 or more miRNAs occurring together on the genome; or located in the intergenic or intragenic/intronic regions of known genes).
Format: PDF Size: 154KB Download file
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Additional File 8:
Manually compiled list of miRNAs that are reported in the literature as either up or down regulated in various human cancers or cancer cell lines. This file has a list of miRNAs that are reported in the literature as either up or down regulated in various human cancers or cancer cell lines. These "cancer-associated" miRNAs were used to prioritize putative p53-miR targets.
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