Name
Title | ||
|---|---|---|
Using affinity propagation for identifying subspecies among clonal organisms: lessons from M. tuberculosis. |
Abstract | ||
|---|---|---|
Background Classification and naming is a key step in the analysis, understanding and adequate management of living organisms. However,
where to set limits between groups can be puzzling especially in clonal organisms. Within the Mycobacterium tuberculosis complex (MTC), the etiological agent of tuberculosis (TB), experts have first identified several groups according to their
pattern at repetitive sequences, especially at the CRISPR locus (spoligotyping), and to their epidemiological relevance. Most
groups such as "Beijing" found good support when tested with other loci. However, other groups such as T family and T1 subfamily
(belonging to the "Euro-American" lineage) correspond to non-monophyletic groups and still need to be refined. Here, we propose
to use a method called Affinity Propagation that has been successfully used in image categorization to identify relevant patterns
at the CRISPR locus in MTC.
Results To adequately infer the relative divergence time between strains, we used a distance method inspired by the recent evolutionary
model by Reyes et al. We first confirm that this method performs better than the Jaccard index commonly used to compare spoligotype patterns.
Second, we document the support of each spoligotype family among the previous classification using affinity propagation on
the international spoligotyping database SpolDB4. This allowed us to propose a consensus assignation for all SpolDB4 spoligotypes.
Third, we propose new signatures to subclassify the T family.
Conclusion Altogether, this study shows how the new clustering algorithm Affinity Propagation can help building or refining clonal organims
classifications. It also describes well-supported families and subfamilies among M. tuberculosis complex, especially inside the modern "Euro-American" lineage. |
Year | DOI | Venue |
|---|---|---|
2011 | 10.1186/1471-2105-12-224 | BMC Bioinformatics |
Keywords | Field | DocType |
bioinformatics,indexation,microarrays,algorithms,affinity propagation | Mycobacterium tuberculosis,Affinity propagation,Biology,Mycobacterium tuberculosis complex,Bioinformatics,Subspecies,Locus (genetics),Genetics,CRISPR,Subfamily,Tuberculosis | Journal |
Volume | Issue | ISSN |
12 | 1 | 1471-2105 |
Citations | PageRank | References |
1 | 0.38 | 5 |
Authors | ||
5 | ||
Name | Order | Citations | PageRank |
|---|---|---|---|
| Claudio Borile | 1 | 1 | 0.38 |
| Mathieu Labarre | 2 | 1 | 0.38 |
| Silvio Franz | 3 | 9 | 1.57 |
| Christophe Sola | 4 | 15 | 2.72 |
| Guislaine Refrégier | 5 | 1 | 0.38 |