Resolution:
## Figure 1.
Transcriptome analyses of the . (a) Transcriptomes of the ex vivo cultured P. falciparum parasitesex-vivo IDC of 6 field isolates (representative set of total 11 transcriptomes generated in
this study; Additional file 3) from the 3 geographical locations over 48 hour sampling time. The heat maps represent
the mean-centered log_{2 }microarray expression ratios for the P. falciparum genes that were ordered according to the phase calculated by the Fast Fourier Transformation
for the reference in vitro IDC transcriptome. (b) Age estimate of the ex vivo culture time points for all 11 field isolates. Each colored box represents age estimate
(hpi; shown by numbers outside the circle) of the isolate sample relative to the in vitro reference IDC transcriptome calculated as a best fit Correlation (Spearman rank, see
materials and methods). Indicated within each box is the sampling collection time
with respect to the first sampling time denoted by 0 h that correspond to the initial
sample collection from the infected patients prior to culturing. Sampling times with
* represent Spearman Rank correlation value less than 0.35 which indicates a deteriorating
synchronicity in the later IDC time points and were excluded from the analysis. Time
points included in 3 windows (yellow frame) corresponding to rings at 12-16 hpi, trophozoites
at 24 to 28 hpi and schizonts at 32 to 36 hpi were selected for further analysis.
(c) Clusters of genes with significant differential expression (p-value < 0.01) between
the resistant (grey) and susceptible (orange) parasites at ring (14 hpi), trophozoite
(26 hpi) and schizont (34 hpi) stages. Shown are the mean-centered expression log_{2 }ratios for these genes ranked by the z-score based on the differential expression
between the resistant and susceptible isolates. Graphs represent the frequency distribution
of the peak abundance time in the IDC transcriptome for each group of genes: over-expressed
(red bars), under-expressed (green bars) or no significant change in expression (yellow
bars). The grey lines represent the middle of the time IDC interval used for the analysis
(e.g. ring, (14 hpi), trophozoite (26 hpi) and schizonts (34 hpi).
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