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Fig. 2 | Microbiome

Fig. 2

From: A multi-source domain annotation pipeline for quantitative metagenomic and metatranscriptomic functional profiling

Fig. 2

Functional analysis of MT data collected on five ocean sites. a Comparative table of domain abundance classification. Rows represent the Metagenomic GO-Slim functional classes that are the most represented, in at least one of the ocean samples. The level of domain abundance (entries of the table; normalised domain abundance, \(N^{S}_{I}\) defined in the “Methods” section, is rescaled here in the interval [0,1]) for Antarctic (ANT), North Pacific (NPAC), Equatorial Pacific (EPAC), Arctic (ARC) and North Atlantic (NATL) samples that are described. Samples are arranged in five columns reporting, for each functional class, the level of abundance obtained with MetaCLADE and HMMer. The colour bar ranks high levels of abundance in dark red and low levels in blue. The ranking of Metagenomic GO-Slim functional classes (from top to bottom in the table) is fixed by the average abundance of a domain in the five samples detected by MetaCLADE. Note that only the most abundant subset of GO-Slim classes is reported. b MetaCLADE analysis of domains belonging to the GO-term “ion transport” (GO.0006811). Results are displayed by GO-terms association (left) and by domain name (right). Column heights correspond to the estimation \(N^{S}_{I}\) of domain abundance relative to each sample S and functional class I (see the “Domain abundance” section in the “Methods” section). For each environmental sample, the abundance of the first five most represented domains in the sample is plotted (note that each column has five colours.) c Hierarchical tree graph of GO-terms for “ion transport” obtained with MetaCLADE and described in b for the ANT sample. The count of domains classified with a given GO-term in ANT is represented by the colour of the associated box. The colour scale represents the number of domains identified for a GO-term. Red corresponds to >150 domain hits. Each box in the tree graph is coloured independently of its position in the tree graph because each domain is associated to a single box. There is no cumulative effect in the counting. d Hierarchical tree graph of GO-terms for “ion transport” obtained with HMMer. The GO-terms are associated to domains identified by HMMer in the ANT sample, compared to c. e Distribution of species originating CCMs used to annotate the five MT datasets. Due to the different number of reads in the datasets (and hence, the variable number of identified domains), we report the proportion of species, organised in clades, for each dataset

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