Screenshot of the METAREP Compare Page.

<p>The Compare page allows users to filter, compare and visualize annotation attributes across multiple datasets. As illustrated in the upper panel, the user can find and select datasets of interest (here pooled body habitats were selected). The middle panel illustrates filter and compare options (here datasets were filtered for the pyruvate dehydrogenase complex and the heatmap plot option was selected). The bottom panel shows the compare results and allows users to switch between annotation attributes and specify its level of granularity (here the taxonomy attribute and phylum level were selected).</p

Selection of KEGG pathways found to be differentially abundant in three oral habitats sorted by the ratio of the median abundances.

<p>Selection of KEGG pathways found to be differentially abundant in three oral habitats sorted by the ratio of the median abundances.</p

Heatmap plots of three enzymatic markers.

<p>Marker abundance is contrasted across phyla (columns) and body habitats (rows) using Morisita-Horn distances in combination with the average linkage clustering method. Colors encode the relative abundance of the selected feature-dataset combination (dark red 0% to white 100%) while the dendograms at the top and left show annotation feature and dataset differences, respectively.</p

Screenshots of METAREP statistical result panels.

<p>List of phyla and pathways that are differentially abundant between the buccal mucosa (n = 116) and supragingival plague (n = 89) habitats. Taxonomic differences reported by Metastats with confidence intervals () shown in (a), differences in KEGG pathway abundance detected by the Wilcoxon rank-sum test are shown in (b).</p

Hierarchical cluster plots of 48 samples taken from 12 females and 12 males at two different time points.

<p>Hierarchical clustering analysis of a random subset of human microbiome samples taken from five human body regions clustered by NCBI taxonomy at the family level (a) and by KEGG pathways (b). Clusters were generated by the average linkage clustering method using the Morisita-Horn index to generate a distance matrix (shown on the x-axis). Dataset labels encode the following information [donor ID]-[habitat]-[gender]-[time point]-[sample ID]-[annotation-type]. For example, the dataset label 159814214-an-m-2-SRS047225-mtr encodes a sample from a male donor (ID 159814214) taken from the anterior nares site at time point 2 with sample ID (SRS047225) annotated by the metabolic reconstruction (HUMAnN) pipeline (mtr). The dotted line represents the level at which the tree was cut for analysis. The resulting clusters are labeled as follows: AN (anterior nares), BM (buccal mucosa), SP (supragingival plaque), ST (stool), and PF (posterior fornix).</p

Number of pathways that are differentially abundant for each statistical test and oral habitat combination.

<p>Rows indicate the habitat in which pathways were significantly overrepresented. Columns indicate the habitat in which pathways were significantly underrepresented. For example, the Wilcoxon rank-sum test found 39 pathways to be enriched in buccal mucosa when compared with tongue dorsum.</p

Summary of available datasets by body habitat sorted by the number of WGS reads.

<p>Columns 2–5 refer to the HUMAnN datasets.</p

Software architecture overview.

<p>The METAREP software integrates several open source tools to import, store and analyze metagenomics annotations. Users can analyze stored data using a variety of web based tools. A subset of the web functionality is available via a programmatic access module which allows data retrieval directly from the MySQL database and Lucene index files.</p

A phylogenetic tree built from amino acid sequences using FastTree for the gene encoding the large subunit terminase.

<p>Selected reference sequences are colored red and green. Representative Indian Ocean VF and LF sequences are colored pink and purple respectively. GOS Phase I sequences are colored blue. Confidence values are displayed on the tree.</p

Functional characterization of Indian Ocean viral sequences from the viral and larger fractions of metagenomic data in the context of KEGG pathways.

<p>The inset pie charts represent the breakdown of the Metabolism super-pathway (top) and Energy metabolism pathway (bottom). The percentages of viral sequences attributed to the Energy metabolism pathway are indicated on the Metabolism pie charts.</p