The MUSMIRSUS (Mus miRNA susceptibility loci) database was created to compare the positions of microRNA (miRNA) genes with the positions of solid tumor susceptibility and modifier loci in the mouse. The chromosomal locations of 438 mouse miRNAs were downloaded from the miRNA registry website (Version 10.1, December 2007) (microrna.sanger.ac.uk) (1-2). The positions of mouse miRNAs were compared with susceptibility loci for eight types of solid tumors (www.ensembl.org) (December 2007) (3); this ordered list was used to identify miRNAs that mapped at or near the peak of tumor loci (4). The "length" of a susceptibility region was ±0.5 Mb if the gene is known, or estimated as ±5 Mb from the peak marker if the gene is unknown. The peak marker is defined as a position which has the peak probability for the specified trait. Although a quantitative trait locus (QTL) need not be at the peak marker, the critical distance selected here covers the most likely interval. A miRNA was considered within a tumor susceptibility region if it was located <5 Mb from the peak marker of a given locus. "Telomere" shows the length of each chromosome (www.ensembl.org).
Column A lists the names of mouse tumor susceptibility and modifier loci for 8 different solid tumors and the 438 miRNAs (5). MiRNA gene symbols are shown in white. The tumor susceptibility loci are color coded by tissue type:
Bladder = yellow
Colon = red
Liver = brown
Lung = blue
Mammary = green
Ovary = purple
Skin = pink
Small intestine = orange
Column B shows either the peak marker for each tumor susceptibility locus or the two markers that define the boundaries of a susceptibility locus.
Column C lists the mouse chromosomal location of each susceptibility locus and miRNA gene.
Column D lists the tissue types for each solid tumor.
Column E shows the resistant inbred strains of mice.
Column F shows susceptible inbred strains of mice.
Column G reports the midpoint position (bp) for the peak marker or the midpoint position (bp) between two markers, and the midpoint position (bp) for each miRNA stem-loop sequence. The bp positions of miRNAs <5 Mb from tumor susceptibility loci are shown in beige.
Column H reports the distance (bp) of miRNAs that are located <5 Mb proximal to a locus.
Column J reports the distance (bp) of miRNAs that are located <5 Mb distal to a locus.
Columns I and K list the number of loci that are located <5 Mb from a miRNA gene.
Column L shows the human fragile site (FRA) and/or human cancer associated genomic regions (CAGR) that contain the homologous human miRNA (6).
Column M lists the human chromosome bands for FRA or CAGR.
Column N lists the citations evaluated from PubMed (www.pubmed.gov) to determine the average position for the peak marker in combination with the Mouse Genome Informatics Database
(www.informatics.jax.org) (7).
The MUSMIRSUS database is maintained by Dr. Linda D. Siracusa, Dr. Cinzia Sevignani, and Stephanie Nnadi at Thomas Jefferson University, 233 South 10th Street, Philadelphia, PA 19107. Comments, corrections, or suggestions are welcomed and should be emailed to Siracusa@mail.jci.tju.edu
References:
| 1. |
Griffiths-Jones S. 2004 The microRNA Registry. NAR 32, Database Issue, D109-D111. |
| 2. |
Griffiths-Jones S, Grocock RJ, van Dongen S, Bateman A, Enright AJ. 2006 miRBase: microRNA sequences, targets and gene nomenclature. NAR 34, Database Issue, D140-D144. |
| 3. |
Hubbard T, Andrews D, Caccamo M, Cameron G, Chen Y, Clamp M, Clarke L, Coates G, Cox T, Cunningham F, Curwen V, Cutts T, Down T, Durbin R, Fernandez-Suarez XM, Gilbert J, Hammond M, Herrero J, Hotz H, Howe K, Iyer V, Jekosch K, Kahari A, Kasprzyk A, Keefe D, Keenan S, Kokocinsci F, London D, Longden I, McVicker G, Melsopp C, Meidl P, Potter S, Proctor G, Rae M, Rios D, Schuster M, Searle S, Severin J, Slater G, Smedley D, Smith J, Spooner W, Stabenau A, Stalker J, Storey R, Trevanion S, Ureta-Vidal A, Vogel J, White S, Woodwark C, Birney E. 2005 Ensembl 2005. Nucleic Acids Res. Jan 1; 33(Database issue):D447-53. |
| 4. |
Sevignani C, Calin GA, Nnadi S, Shimizu M, Davaluri RV, Hyslop T, Demant P, Croce CM, Siracusa L. 2007 MicroRNA genes are frequently located near mouse cancer susceptibility loci. Proc Natl Acad Sci USA May 8; 104(19):017-8022. |
| 5. |
Rossi S, Sevignani C, Nnadi SC, Siracusa LD, Calin GA. 2008 Cancer-associated genomic regions (CAGRs) and noncoding RNAs: bioinformatics and therapeutic implications. Mamm Genome. Aug; 19(7-8):526-40. |
| 6. |
Calin GA, Sevignani C, Dumitro CD, Hyslop T, Noch E, Yendamuri S, Shimizu M, Rattan S, Bulrich F, Negrini M, Croce CM. 2004 Human microRNA genes are frequently located at fragile sites and genomic regions involved in cancers. Proc Natl Acad Sci USA Mar 2; 101(9):2999-3004.(See Supplemental Tables 5 and 6). |
| 7. |
Eppig Jt, Bult Cj, Kadin JA, Richardson JE, Blake JA, and the members of the mouse genome database group. 2005 The mouse database (MGD): from genes to mice -a community resource for mouse biology. Nucleic Acids Res. 32:D471-D475. |