SNPs of genes associated with drug-resistant TB.

<p>SNPs of genes associated with drug-resistant TB.</p

Genotypes of drug resistant <i>M</i>. <i>tuberculosis</i> based on spoligotpying and 24 loci MIRU-VNTR.

<p>Genotypes of drug resistant <i>M</i>. <i>tuberculosis</i> based on spoligotpying and 24 loci MIRU-VNTR.</p

Venn diagram comparing the number of SNPs shared by serially isolated <i>M</i>. <i>tuberculosis</i> isolates.

<p>Venn diagram comparing the number of SNPs shared by serially isolated <i>M</i>. <i>tuberculosis</i> isolates.</p

Drug susceptibility profile based on phenotype and whole-genome sequencing analysis of serially isolated <i>M</i>. <i>tuberculosis</i>.

<p>Drug susceptibility profile based on phenotype and whole-genome sequencing analysis of serially isolated <i>M</i>. <i>tuberculosis</i>.</p

Phylogenetic analysis of serially isolated <i>M</i>. <i>tuberculosis</i> isolates.

<p><b>(A)</b> Phylogenetic tree based on maximum likelihood method using 1,890 high-confidence SNPs and compared to the H37Rv reference genome. The scale bar length represents 0.2 nucleotide substitutions per site. <b>(B)</b> The large sequence polymorphism analysis showing the presence/absence of RDs in each isolate.</p

Demographic and Characteristics of the Participants.

<p>Demographic and Characteristics of the Participants.</p

Genes whose differential transcription for gestational age was replicated across the qPCR groups, also containing CpGs whose methylation levels correlated with gestational age.

<p>Genes whose differential transcription for gestational age was replicated across the qPCR groups, also containing CpGs whose methylation levels correlated with gestational age.</p

Expression signature for gestational age organises samples into gestational age groups.

<p>Hierarchical clustering of samples (columns) by the expression levels of the 64 probes (rows) significantly associated with gestational age (adjusted p-value&lt;0.05), organises normal birth weight samples perfectly by gestational age group (A) and organises all samples into two clusters with significantly different gestational ages (B). Z-score normalised logged expression levels are denoted in the heat map (green for low, red for high, white for intermediate). X-axis colour bars denote sample classification: high birth weight group (&gt;3700 g) in orange; low birthweight group (&lt;2500 g) in green; normal birthweight and gestational age less than or equal to 37 weeks in blue; or normal birthweight and gestational age more than 37 weeks in red. Gestational age is also represented as a continuous variable in the x-axis colour bar in (B) green for low, red for high, white for intermediate.</p

Twelve transcripts have differential expression levels in gestational age groups across the 120 sample replication set.

<p>Fold change with regard to the median sample of the more than 37 weeks gestation group, is shown on the y-axis. Gene names are shown above each panel. P-values from the 2 group tests are shown within each panel. Data is represented as a box plot where the 2–3 quartile range is within the box, the median is denoted by a horizontal line within the box, the min and max are denoted by horizontal lines outside of the box and single outliers are represented by crosses.</p

RNA Expression Microarray Study Design.

<p>Gestational age in weeks (y-axis) and birth-weight in grams (x-axis) of the samples analysed by expression microarrays are symmetrical to allow somewhat independent comparisons for birth-weight and gestational age. Samples are classified into high birth weight group (&gt;3700 g) in orange; low birthweight group (&lt;2500 g) in green; normal birthweight and gestational age less than or equal to 37 weeks in blue; or normal birthweight and gestational age more than 37 weeks in red. Two samples that failed QC are shown as non-filled circles.</p