, Global tuberculosis report, 2015.

, World Health Organization. Global TB facts, 2015.

P. Glaziou, C. Sismanidis, K. Floyd, and M. Raviglione, Global epidemiology of tuberculosis. Cold Spring Harbor perspectives in medicine 5, pp.445-461, 2015.

G. Sotgiu, R. Centis, L. Migliori, and G. B. , Tuberculosis treatment and drug regimens. Cold Spring Harbor perspectives in medicine 5, pp.505-516, 2015.

K. J. Seung, S. Keshavjee, and M. L. Rich, Multidrug-resistant tuberculosis and extensively drug-resistant tuberculosis. Cold Spring Harbor perspectives in medicine 5, pp.579-598, 2015.

L. Muñoz, H. R. Stagg, and I. Abubakar, Diagnosis and management of latent tuberculosis infection. Cold Spring Harbor perspectives in medicine 5, pp.517-529, 2015.

R. J. North and Y. Jung, Immunity to tuberculosis, Annual review of immunology, vol.22, pp.599-623, 2004.

A. O'garra, The immune response in tuberculosis, Annual review of immunology, vol.31, pp.475-527, 2013.

F. J. Kallmann and D. Reisner, Twin studies on genetic variations in resistance to tuberculosis, Journal of Heredity, vol.34, pp.269-276, 1943.

G. W. Comstock, Tuberculosis in twins: a re-analysis of the Prophit survey. The American review of respiratory disease, vol.117, pp.621-625, 1978.

A. Cobat, High heritability of antimycobacterial immunity in an area of hyperendemicity for tuberculosis disease, The Journal of infectious diseases, vol.201, pp.15-24, 2010.

M. Möller and E. G. Hoal, Current findings, challenges and novel approaches in human genetic susceptibility to tuberculosis, Tuberculosis, vol.90, pp.71-83, 2010.

T. Thye, Genome-wide association analyses identifies a susceptibility locus for tuberculosis on chromosome 18q11.2, Nature genetics, vol.42, pp.739-780, 2010.

S. Mahasirimongkol, Genome-wide association studies of tuberculosis in Asians identify distinct at-risk locus for young tuberculosis, Journal of human genetics, vol.57, pp.363-370, 2012.

T. Thye, Common variants at 11p13 are associated with susceptibility to tuberculosis, Nature genetics, vol.44, pp.257-266, 2012.

E. Png, A genome wide association study of pulmonary tuberculosis susceptibility in Indonesians, BMC medical genetics, vol.13, pp.1-9, 2012.

E. R. Chimusa, Genome-wide association study of ancestry-specific TB risk in the South African Coloured population, Human molecular genetics, vol.23, pp.796-809, 2014.

J. Curtis, Susceptibility to tuberculosis is associated with variants in the ASAP1 gene encoding a regulator of dendritic cell migration, Nature genetics, vol.47, pp.523-530, 2015.

R. S. Sobota, A locus at 5q33.3 confers resistance to tuberculosis in highly susceptible individuals, American journal of human genetics, vol.98, pp.514-538, 2016.

N. T. Thuong, Identification of tuberculosis susceptibility genes with human macrophage gene expression profiles, PLoS pathogens, vol.4, p.1000229, 2008.

P. A. Bryant, Susceptibility to acute rheumatic fever based on differential expression of genes involved in cytotoxicity, chemotaxis, and apoptosis, Infection and immunity, vol.82, pp.753-61, 2014.

R. Loddenkemper, M. Lipman, and A. Zumla, Clinical aspects of adult tuberculosis. Cold Spring Harbor perspectives in medicine, vol.6, p.17848, 2016.

A. M. Cooper, Cell-mediated immune responses in tuberculosis, Annual review of immunology, vol.27, pp.393-422, 2009.

L. B. Barreiro, Deciphering the genetic architecture of variation in the immune response to Mycobacterium tuberculosis infection, Proceedings of the National Academy of Sciences of the United States of America, vol.109, pp.1204-1213, 2012.

H. Lango-allen, Hundreds of variants clustered in genomic loci and biological pathways affect human height, Nature, vol.467, pp.832-840, 2010.
URL : https://hal.archives-ouvertes.fr/cea-00904990

L. Tailleux, Probing host pathogen cross-talk by transcriptional profiling of both Mycobacterium tuberculosis and infected human dendritic cells and macrophages, PloS one, vol.3, p.1403, 2008.

V. Deretic, Autophagy in tuberculosis. Cold Spring Harbor Perspectives in Medicine, vol.4, pp.53-67, 2014.

N. S. Castrejón-jiménez, K. Leyva-paredes, J. C. Hernández-gonzález, J. Luna-herrera, and B. E. García-pérez, The role of autophagy in bacterial infections, Bioscience trends, vol.9, pp.149-59, 2015.

N. Spang, RAB3GAP1 and RAB3GAP2 modulate basal and rapamycin-induced autophagy, Autophagy, vol.10, pp.2297-309, 2014.
DOI : 10.4161/15548627.2014.994359
URL : http://europepmc.org/articles/pmc4502700?pdf=render

S. Sturgill-koszycki, Lack of acidification in mycobacterium phagosomes produced by exclusion of the vesicular proton-atpase, Science, vol.263, pp.678-81, 1994.

M. W. Hornef, M. J. Wick, M. Rhen, and S. Normark, Bacterial strategies for overcoming host innate and adaptive immune responses, Nature immunology, vol.3, pp.1033-1073, 2002.
DOI : 10.1038/ni1102-1033

A. L. Hestvik, Z. Hmama, and Y. Av-gay, Mycobacterial manipulation of the host cell, FEMS microbiology reviews, vol.29, pp.1041-50, 2005.

J. L. Flynn, M. M. Goldstein, K. J. Triebold, B. Koller, and B. R. Bloom, Major histocompatibility complex class I-restricted T cells are required for resistance to Mycobacterium tuberculosis infection, Proceedings of the National Academy of Sciences of the United States of America, vol.89, pp.12013-12020, 1992.
DOI : 10.1073/pnas.89.24.12013
URL : http://www.pnas.org/content/89/24/12013.full.pdf

J. E. Grotzke, The Mycobacterium tuberculosis phagosome is a HLA-I processing competent organelle, PLoS pathogens, vol.5, p.1000374, 2009.
DOI : 10.1371/journal.ppat.1000374
URL : https://journals.plos.org/plospathogens/article/file?id=10.1371/journal.ppat.1000374&type=printable

J. E. Grotzke, A. C. Siler, D. A. Lewinsohn, and D. M. Lewinsohn, Secreted immunodominant Mycobacterium tuberculosis antigens are processed by the cytosolic pathway, Journal of immunology, vol.185, pp.4336-4379, 1950.
DOI : 10.4049/jimmunol.1000801
URL : http://www.jimmunol.org/content/185/7/4336.full.pdf

C. S. Lindestam-arlehamn, D. Lewinsohn, A. Sette, and D. Lewinsohn, Antigens for CD4 and CD8 T cells in tuberculosis. Cold Spring Harbor perspectives in medicine 4, pp.89-103, 2014.

M. D. Miller and M. S. Krangel, The human cytokine I-309 is a monocyte chemoattractant, Proceedings of the National Academy of Sciences of the United States of America, vol.89, pp.2950-2954, 1992.

J. D. Blischak, L. Tailleux, A. Mitrano, L. B. Barreiro, and Y. Gilad, Mycobacterial infection induces a specific human innate immune response, Scientific reports, vol.5, p.16882, 2015.
DOI : 10.1101/017483
URL : https://www.biorxiv.org/content/biorxiv/early/2015/04/03/017483.full.pdf

T. C. Sudhof, The synaptic vesicle cycle, Annual review of neuroscience, vol.27, pp.509-556, 2004.

M. P. Berry, An interferon-inducible neutrophil-driven blood transcriptional signature in human tuberculosis, Nature, vol.466, pp.973-980, 2010.

S. Blankley, The application of transcriptional blood signatures to enhance our understanding of the host response to infection: the example of tuberculosis, Philosophical transactions of the Royal Society of London. Series B, Biological sciences, vol.369, p.20130427, 2014.

J. Maertzdorf, S. H. Kaufmann, and J. Weiner, Toward a unified biosignature for tuberculosis, Cold Spring Harbor Perspectives in Medicine, vol.5, pp.183-95, 2015.
DOI : 10.1101/cshperspect.a018531
URL : http://perspectivesinmedicine.cshlp.org/content/5/1/a018531.full.pdf

M. Coscolla and S. Gagneux, Does M. tuberculosis genomic diversity explain disease diversity? Drug discovery today, Disease mechanisms, vol.7, pp.43-59, 2010.

R. Ostuni, Latent enhancers activated by stimulation in differentiated cells, Cell, vol.152, pp.157-71, 2013.
DOI : 10.1016/j.cell.2012.12.018
URL : https://doi.org/10.1016/j.cell.2012.12.018

M. G. Netea, Trained immunity: A program of innate immune memory in health and disease, Science, vol.352, p.1098, 2016.

Y. Lavin, Tissue-resident macrophage enhancer landscapes are shaped by the local microenvironment, Cell, vol.159, pp.1312-1338, 2014.

C. I. Bloom, Detectable changes in the blood transcriptome are present after two weeks of antituberculosis therapy, PloS one, vol.7, p.46191, 2012.

D. Chaussabel, Unique gene expression profiles of human macrophages and dendritic cells to phylogenetically distinct parasites, Blood, vol.102, pp.672-81, 2003.

Y. Liao, G. K. Smyth, and W. Shi, The Subread aligner: fast, accurate and scalable read mapping by seed-and-vote, Nucleic acids research, vol.41, p.108, 2013.

A. Yates, Nucleic acids research, vol.44, pp.710-716, 2016.

W. Huber, Orchestrating high-throughput genomic analysis with Bioconductor, Nature methods, vol.12, pp.115-136, 2015.

S. Durinck, BioMart and Bioconductor: a powerful link between biological databases and microarray data analysis, Bioinformatics, vol.21, pp.3439-3479, 2005.

S. Durinck, P. T. Spellman, E. Birney, and W. Huber, Mapping identifiers for the integration of genomic datasets with the R/ Bioconductor package biomaRt, Nature protocols, vol.4, pp.1184-91, 2009.

Y. Liao, G. K. Smyth, and W. Shi, featureCounts: an efficient general purpose program for assigning sequence reads to genomic features, Bioinformatics, vol.30, pp.923-953, 2014.

G. K. Smyth, Linear models and empirical bayes methods for assessing differential expression in microarray experiments, Statistical applications in genetics and molecular biology, vol.3, p.3, 2004.

C. W. Law, Y. Chen, W. Shi, and G. K. Smyth, Voom: Precision weights unlock linear model analysis tools for RNA-seq read counts, Genome biology, vol.15, p.29, 2014.

M. E. Ritchie, limma powers differential expression analyses for RNA-sequencing and microarray studies, Nucleic acids research, vol.43, p.47, 2015.

G. K. Smyth, J. Michaud, and H. S. Scott, Use of within-array replicate spots for assessing differential expression in microarray experiments, Bioinformatics, vol.21, pp.2067-75, 2005.

R. Liu, Why weight? modelling sample and observational level variability improves power in RNA-seq analyses, Nucleic acids research, vol.43, p.97, 2015.

M. Stephens, False discovery rates: a new deal, Biostatistics, pp.1-20, 2016.

M. Lawrence, Software for computing and annotating genomic ranges, PLoS computational biology, vol.9, p.1003118, 2013.

G. Jurasinski, F. Koebsch, A. Guenther, S. Beetz, and . Flux, Flux rate calculation from dynamic closed chamber measurements, 2014.

M. Kuhn, Building predictive models in R using the caret package, Journal of Statistical Software, vol.28, pp.1-26, 2008.

J. Friedman, T. Hastie, and R. Tibshirani, Regularization paths for generalized linear models via coordinate descent, Journal of Statistical Software, vol.33, 2008.

A. Karatzoglou, A. Smola, K. Hornik, and A. Zeileis, kernlab-an S4 package for kernel methods in R, Journal of Statistical Software, vol.11, pp.1-20, 2004.

A. Liaw and M. Wiener, Classification and regression by randomForest, R News, vol.2, pp.18-22, 2002.

J. Köster and S. Rahmann, Snakemake-a scalable bioinformatics workflow engine, Bioinformatics, vol.28, pp.2520-2522, 2012.

P. Ewels, M. Magnusson, S. Lundin, and M. Käller, MultiQC: summarize analysis results for multiple tools and samples in a single report, Bioinformatics, p.354, 2016.

H. Li, The sequence alignment/map format and samtools, Bioinformatics, vol.25, pp.2078-2087, 2009.

. R-core-team, R: A Language and Environment for Statistical Computing. R Foundation for Statistical Computing, 2015.

D. Sulakhe, Lynx: a knowledge base and an analytical workbench for integrative medicine, Nucleic acids research, vol.44, pp.882-889, 2016.

R. Edgar, M. Domrachev, and A. E. Lash, Gene Expression Omnibus: NCBI gene expression and hybridization array data repository, Nucleic acids research, vol.30, pp.207-217, 2002.