Open Access Research article

A predictive signature gene set for discriminating active from latent tuberculosis in Warao Amerindian children

Lilly M Verhagen12, Aldert Zomer13, Mailis Maes2, Julian A Villalba24, Berenice del Nogal56, Marc Eleveld1, Sacha AFT van Hijum37, Jacobus H de Waard26 and Peter WM Hermans1*

Author Affiliations

1 Laboratory of Pediatric Infectious Diseases, Radboud University Medical Centre, PO Box 9101 (internal post 224), Nijmegen, 6500 HB, The Netherlands

2 Laboratorio de Tuberculosis, Instituto de Biomedicina, Caracas, Venezuela

3 Centre for Molecular and Biomolecular Informatics, Nijmegen Centre for Molecular Life Sciences, Radboud University Medical Centre, Nijmegen, The Netherlands

4 Lovelace Respiratory Research Institute, Albuquerque, USA

5 Departamento de Pediatría, Hospital de Niños J.M. de los Ríos, Caracas, Venezuela

6 Facultad de Medicina, Universidad Central de Venezuela, Caracas, Venezuela

7 NIZO food research, Kluyver Centre for Genomics of Industrial Fermentation, Ede, The Netherlands

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BMC Genomics 2013, 14:74  doi:10.1186/1471-2164-14-74

Published: 1 February 2013

Additional files

Additional file 1: Table S1:

Detailed characteristics of 27 children with TB, LTBI and HC in which microarray analyses were performed.

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Additional file 2: Table S2:

Enriched gene sets in the 116 gene set.

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Additional file 3: Table S3:

Sheet 1. Minimal discriminatory gene set to discriminate between TB and LTBI. Sheet 2. Minimal discriminatory gene set to discriminate between TB, LTBI and HC. Sheet 3. Variable frequencies estimated by the bootstrapping procedure implemented in VarSelRF (1). Sheet 4. Variable frequencies estimated by the bootstrapping procedure implemented in VarSelRF (2).

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Additional file 4: Figure S1:

qRT-PCR cycle threshold (delta Ct) values in TB, LTBI, HC and non-TB pneumonia subjects for each of the ten signature genes. The delta Ct was calculated as Ct value (number of cycles required for the fluorescent signal to exceed the background level) of the target gene – Ct value of the reference gene (GAPDH). The boxplots show the median delta Ct values and the interquartile ranges. The whiskers represent the highest and lowest values that are not outliers. Dots represent outliers and squares in the boxes indicate mean delta Ct values. The p-values for each gene (in parentheses) are the outcomes of the one-way analyses of variance comparing TB, LTBI, HC and non-TB pneumonia. The asterisks indicate statistically significant differences (p < 0.05) between TB and other groups as found by an unpaired Student’s t test.

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Additional file 5: Table S4:

qRT-PCR cycle threshold (delta Ct) values in TB, LTBI, HC and non-TB pneumonia subjects for each of the ten signature genes. The delta Ct was calculated as Ct value (number of cycles required for the fluorescent signal to exceed the background level, a lower Delta Ct value indicates a higher expression) of the target gene – Ct value of the reference gene (GAPDH).

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