Per cent improvement in Precision obtained ranking genes and considering increasing percentage of them as belonging to identified modules

<p><b>Copyright information:</b></p><p>Taken from "A quantization method based on threshold optimization for microarray short time series"</p><p></p><p>BMC Bioinformatics 2005;6(Suppl 4):S11-S11.</p><p>Published online 1 Dec 2005</p><p>PMCID:PMC1866397.</p><p></p

Chao1 and Shannon indices of <i>Chd1</i> mutant and wild-type sample replicates.

<p>Three sets of filtering parameters were used to analyse the data.</p

Distribution of bacterial families within the gut microbiome of <i>Chd1</i> mutant and wild-type flies.

<p>Three sets of filtering parameters were used to analyse the data.</p

Time-dependent decrease in supplemented <i>L</i>. <i>plantarum</i> in <i>Chd1</i>^<i>-/-</i> but not <i>Chd1</i>^<i>WT/WT</i> flies.

<p>Flies were fed on <i>L</i>. <i>plantarum</i> overnight, transferred to fresh food vials and collected at the indicated days after inoculation. (A) <i>Lactobacillus</i> load was determined by plating fly homogenates on MRS agar; (B) <i>L</i>. <i>plantarum</i> was detected by real-time PCR. Signals were normalized against the <i>Drosophila</i> GAPDH gene and mean values ±SEM of three biological replicates are shown. Significant differences between the two fly lines were analyzed by t-test (level of significance set to p<0.05) and are marked by (*).</p

Age-related changes of bacterial load and species distribution in <i>Chd1</i> mutant and wild-type flies.

<p>(A) Flies of the indicated ages were surface-sterilized and homogenates were plated on Ace agar (left panel) to select for <i>Acetobacteraceae</i> or on MRS agar (right panel) to select for <i>Lactobacillaceae</i>. CFUs per fly were calculated and mean values from four biological replicates ±SEM were plotted. (B) Semiquantitative PCR was used to determine the relative amounts of <i>Acetobacter</i> “A” and <i>Pseudomonas</i> “P” species in guts of flies of the indicated ages. Band intensities were quantified and P/A ratios were calculated. Mean values ±SEM of three biological replicates are shown.</p

Average Precision at different Recall intensities obtained on 100 simulated data sets, using Reveal (left panel) and DBN (right panel)

<p><b>Copyright information:</b></p><p>Taken from "A quantization method based on threshold optimization for microarray short time series"</p><p></p><p>BMC Bioinformatics 2005;6(Suppl 4):S11-S11.</p><p>Published online 1 Dec 2005</p><p>PMCID:PMC1866397.</p><p></p

The microbiome composition in the gut of <i>Chd1</i>^<i>-/-</i> and <i>Chd1</i>^<i>WT/WT</i> flies is significantly different.

<p>(A) Principal Coordinate Analysis (PCoA) plot depicting β-diversity by jackknifed UniFrac distances (normalized, weighted UniFrac metric) based on 97% similarity OTU assignments. <i>Chd1</i>^<i>WT/WT</i> and <i>Chd1</i>^<i>-/-</i> replicates differ considerably for PC1, which explains 89.1% of the total variation. To estimate the statistical significance of the clustering a two-sample t-test based on distance matrices (distances within all replicates versus distances between all replicates) was performed (P = 4.709 e-5). (B) Rarefaction curves of 97% identity OTUs for <i>Chd1</i>^<i>WT/WT</i> and <i>Chd1</i>^<i>-/-</i> sample replicates show exhaustive sampling depth.</p

Loss of CHD1 causes decreased species diversity in the gut microbiome.

<p>(A) Relative abundance of bacterial families (97% similarity threshold) determined by 16S rDNA sequencing in <i>Chd1</i>^<i>WT/WT</i> and <i>Chd1</i>^<i>-/-</i> samples. Families present at levels less than 1.5% were summarized as “others“. (B) Heatmap of the 25 most abundant 97% identity OTUs within <i>Chd1</i>^<i>WT/WT</i> and <i>Chd1</i>^<i>-/-</i> guts. OTU classification down to the lowest level possible is shown. Color bars denote the relative abundance (log10 values) of each OTU within the respective sample. OTUs are clustered according to their average relative abundance. (C) Heatmap showing the abundance of <i>Acetobacter</i> and <i>Lactobacillus</i> species in <i>Chd1</i>^<i>WT/WT</i> and <i>Chd1</i>^<i>-/-</i> samples identified by alignment of sequencing reads to all respective sequences in the SILVA database at an identity threshold of 99%. All OTUs with fewer than 10 counts, were excluded. Color bars denote the relative abundance (log10 values) of each species within the respective sample.</p

Impact of the Chromatin Remodeling Factor CHD1 on Gut Microbiome Composition of <i>Drosophila melanogaster</i>

<div><p>The composition of the intestinal microbiota of <i>Drosophila</i> has been studied in some detail in recent years. Environmental, developmental and host-specific genetic factors influence microbiome composition in the fly. Our previous work has indicated that intestinal bacterial load can be affected by chromatin-targeted regulatory mechanisms. Here we studied a potential role of the conserved chromatin assembly and remodeling factor CHD1 in the shaping of the gut microbiome in <i>Drosophila melanogaster</i>. Using high-throughput sequencing of 16S rRNA gene amplicons, we found that <i>Chd1</i> deletion mutant flies exhibit significantly reduced microbial diversity compared to rescued control strains. Specifically, although <i>Acetobacteraceae</i> dominated the microbiota of both <i>Chd1</i> wild-type and mutant guts, <i>Chd1</i> mutants were virtually monoassociated with this bacterial family, whereas in control flies other bacterial taxa constituted ~20% of the microbiome. We further show age-linked differences in microbial load and microbiota composition between <i>Chd1</i> mutant and control flies. Finally, diet supplementation experiments with <i>Lactobacillus plantarum</i> revealed that, in contrast to wild-type flies, <i>Chd1</i> mutant flies were unable to maintain higher <i>L</i>. <i>plantarum</i> titres over time. Collectively, these data provide evidence that loss of the chromatin remodeler CHD1 has a major impact on the gut microbiome of <i>Drosophila melanogaster</i>.</p></div

Runtime summary for Kabuki syndrome study.

<p>Listed are overall and key runtime statistics (in hours).</p