Wavelet-domain elastic net for clustering on genomes strains

Ferreira, Leila Maria; Sáfadi, Thelma; Ferreira, Juliano Lino

doi:10.1590/1678-4685-GMB-2018-0035

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Genomics and Bioinformatics • Genet. Mol. Biol. 41 (4) • Oct-Dec 2018 • https://doi.org/10.1590/1678-4685-GMB-2018-0035 copy

Wavelet-domain elastic net for clustering on genomes strains

Authorship SCIMAGO INSTITUTIONS RANKINGS

Abstract

We propose to evaluate genome similarity by combining discrete non-decimated wavelet transform (NDWT) and elastic net. The wavelets represent a signal with levels of detail, that is, hidden components are detected by means of the decomposition of this signal, where each level provides a different characteristic. The main feature of the elastic net is the grouping of correlated variables where the number of predictors is greater than the number of observations. The combination of these two methodologies applied in the clustering analysis of the Mycobacterium tuberculosis genome strains proved very effective, being able to identify clusters at each level of decomposition.

Keywords:
Elastic net; genome; GC-content; cluster analysis; wavelet transform

Sequences	Descriptions of the strains
Seq1_DS	Strain was isolated in Russia belonging to the AI family (according to RFLP genotyping) and it is sensitive to all common drugs used in the treatment of tuberculosis.
Seq2_DS	Susceptible strain representing the largest portion of tuberculosis isolates recovered during an epidemic in the Western Cape of South Africa.
Seq3_DS	Susceptible strain belonging to the Beijing family, sequenced for comparative genomic studies.
Seq4_DR	Resistant strain isolated in 2004, referring to a patient with secondary pulmonary tuberculosis, sequenced for comparative genomic studies.
Seq5_DR	Drug-resistant strain, having an accelerated rate of transmission between humans under agglomeration conditions.
Seq6_MDR	Strain from a single patient in KwaZulu-Natal, South Africa.
Seq7_XDR	Strain from a single patient in KwaZulu-Natal, South Africa.
Seq8_DS	Susceptible strain used for comparative genomic studies.
Seq9_DS	Susceptible strain derived from the original human lung H37, isolated in 1934. It has been widely used all over the world in biomedical research. Unlike some clinical isolates, it retains total virulence in animals with tuberculosis and is susceptible to drugs and receptive to genetic manipulation.
Seq10_DS	A virulent susceptible strain derived from its virulent parent strain H37 (isolated from a 19-year-old male patient with chronic pulmonary tuberculosis, named Edward R. Baldwin in 1905). This strain was obtained through an aging and dissociation process of an in vitro culture in 1935.

Sequence number	NCBI Access number	Resistance type	Total Rate of GC-content	Infraspecific name
Seq1	CP002992.1	DS	0.6560	CTRI-2
Seq2	CP000717.1	DS	0.6562	F11
Seq3	CP001641.1	DS	0.6561	CCDC5079
Seq4	CP001642.1	DR	0.6559	CCDC5180
Seq5	CP001664.1	DR	0.6563	str. Haarlem
Seq6	CP001658.1	MDR	0.6561	KZN 1435
Seq7	CP001976.1	XDR	0.6561	KZN 605
Seq8	CP002884.1	DS	0.6561	CCDC5079
Seq9	AL123456.3	DS	0.6561	H37Rv
Seq10	CP000611.1	DS	0.6561	H37Ra

Levels	Groups
	1	2	3	4	5
1	DS{1}	DS{2, 3} DR{4, 5}	DS{8, 9, 10}{6-MDR, 7-XDR}
2	DS{2}	DS{3, 10}	DR{4}	{6-MDR, 7-XDR}	DS{1, 8, 9} DR{5}
3	DS{2}	DS{3, 10} {6-MDR, 7-XDR}	DS{1, 8, 9} DR{4, 5}
4	{6-MDR, 7-XDR}	DS{1, 2, 3, 8, 9, 10} DR{4, 5}
5	{6-MDR, 7-XDR}	DS{1, 2, 3, 8, 9, 10} DR{4, 5}

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E-mail: editor@gmb.org.br

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[1] Send correspondence to Leila Maria Ferreira. Departamento de Estatística, Universidade Federal de Lavras (UFLA), P.O. Box 3037, 37200-000 Lavras, MG, Brazil. E-mail: leilamaria2003@yahoo.com.br.