Human promoter CTAG1A and modified constructs.

<p>(<b>a</b>) The 535 base pair long promoter region of human gene CTAG1A is rich in CpGs and exhibits α-scores higher than the genomic distribution with pronounced peaks. Shown are the composite α_k-scores (top), the individual α_k-scores for different sizes of <i>k</i> in the middle graph (colour coded, blue = negative, red/orange = positive), and CpGs in yellow (bottom). The three strongest regions are marked by red bars. (<b>b</b>) In-vitro activity of the original CTAG1A promoter (hCTAG1A Promoter), the three strongest α-score regions deleted (hCTAG1A delta), the three strongest α-score regions replaced with sequences from the genomic concatomer (hCTAG1A replace), and the three strongest α-score regions replaced with sequences from the promoter-like concatomer (hCTAG1A UP). Also shown are results without any promoter (Negative CO) and the SV40 core promoter (SV40 Promoter AVG).</p

Calculation of the binding constants <i>k</i>_on, <i>k</i>_off, and <i>K_D</i> for the TFIIB binding assays.

<p>Calculation of the binding constants <i>k</i>_on, <i>k</i>_off, and <i>K_D</i> for the TFIIB binding assays.</p

<i>In-vitro</i> promoter activity driven by artificial constructs.

<p>Artificial constructs ArS110, ArS300, ArS201 and ArS232 exhibit strong promoter activity driving a reporter gene (firefly luciferase, internally normalized by renilla luciferase) in mammalian cell lines: (<b>a</b>) CHO/hamster, (<b>b</b>) P19/mouse, (<b>c</b>) VERO/monkey, (<b>d</b>) HEK293/human, but not in (<b>e</b>) the insect cell line Sf9/army worm. Also shown are the negative control (−) and the SV40 core promoter activity (+). (<b>f</b>) TATA-boxes 1 (left) and 2 (right) were deleted from construct ArS232: deletion of TATA-box 1 only (dT1) results in lack of activity, deletion of TATA-box 2 (dT2) does not change expression levels, while deletion of both (dT1&2) results in slightly increased expression levels.</p

Binding affinity of artificial promoter constructs to the transcription factors TFIIB and TBP.

<p>The binding expressed as Δnm on the y-axis was monitored in real time as sec (x-axis), using the ForteBio Octet QK instrument. Binding was conducted in four phases: (i) loading of biotinylated DNA fragments to the streptavidin biosensor tip, (ii) washing in Kinetics Buffer, (iii) association of the transcription factor and (iii) dissociation of the transcription factor. (<b>a</b>) The promoter constructs ArS110, ArS201, ArS232 and ArS300 show similar binding affinities to the TFIIB protein. (<b>b</b>) The promoter constructs ArS232, ArS232 dT1, ArS232 dT2 and ArS232 dT12 exhibit sequence-specific binding to the TBP protein. ArS232 dT12 lacking two TATA-Boxes shows the lowest binding affinity compared to the other constructs. (<b>c</b>) TFIIB binding vs. a negative control, for which we chose a 85 bp long sequence from inside the coding region of the luciferase gene (pGL3-Basic Promoter Promega: 1314 bp–1399 bp).</p

Effect of down-sampling Illumina coverage on true positive and false positive rates.

<p>Plots are of the median true positive and false positive minority variant detection rates of the control library with the standard deviation shown as error bars from 10 iterations of random sampling from all reads to generate each coverage depth.</p

Measured versus expected minority variant percentages detected in the control library by Illumina and 454 sequencing.

<p>(A) Nucleotide percentages are plotted with linear regression line and 95% confidence intervals. (B) Amino acid percentages are plotted with 95% confidence intervals. MV, minority variant.</p

Minority variants detected by Illumina and/or 454 sequencing in the 5 patient samples combined.

<p>(A) Nucleotide minority variants categorized by platform (Illumina vs. 454) and whether the minority variants were detected by both Illumina and 454 or by one platform only. The “Illumina (w/454)” category refers to the Illumina minority variant calls that are also detected by 454 and the “454 (w/Illumina)” category refers to the 454 calls that are also detected by Illumina. (B) Pearson correlation of the nucleotide minority variants detected by both Illumina and 454. (C) Amino acid minority variants categorized by platform and whether the variants were detected by both Illumina and 454 or by one platform only. (D) Pearson correlation of the amino acid minority variants detected by both Illumina and 454. MV, minority variant.</p

Performance of Illumina and 454 sequencing for the detection of amino acid minority variants within the control library.

<p>Expected variant percentages include positions where a MV is present on more than one clone. Median variant % reflects only the minority variants detected by each platform and does not include the undetected variants. N represents the number of nucleotide positions in the control library where the variant frequency is expected. Illumina detected 1 false positive minority variant present at 0.7% of the viral population and 454 detected 5 false positive minority variants ranging from 0.09% to 0.6%. FN, false negative.</p

NQS filtering improves fit of probability model to data.

<p>(<b>A</b>) Quantile-quantile (q-q) plots under NQS filtering show good fit of the probability model to the observed distribution of errors. Since the probability model is discrete, p values are projected onto a uniform distribution, and the distribution of projected p values is compared with the expected null distribution. See <a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1002417#s4" target="_blank">Materials and Methods</a> section for details. (<b>B</b>) In contrast, q-q plots under no filtering show that no filtering skews the calibration of the probability model used by <i>V-Phaser</i>. Q-q plots of models based on subsets of the reads demonstrate that this effect becomes more pronounced with increasing coverage (see <a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1002417#pcbi.1002417.s001" target="_blank">Figure S1</a>). Q-q plots are scaled to fit curve, so y = x line is not at a 45 degree angle.</p

Two-point linkage analysis of the <i>Rose-comb</i> locus using 11 markers on chicken chromosome 7.

1<p>SNP markers are defined in <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1002775#pgen.1002775.s010" target="_blank">Table S2</a>.</p