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IMG/M: a data management and analysis system for metagenomes.

Markowitz VM, Ivanova NN, Szeto E, Palaniappan K, Chu K, Dalevi D, Chen IM, Grechkin Y, Dubchak I, Anderson I, Lykidis A, Mavromatis K, Hugenholtz P, Kyrpides NC - Nucleic Acids Res. (2007)

Bottom Line: IMG/M is a data management and analysis system for microbial community genomes (metagenomes) hosted at the Department of Energy's (DOE) Joint Genome Institute (JGI).IMG/M consists of metagenome data integrated with isolate microbial genomes from the Integrated Microbial Genomes (IMG) system.IMG/M provides IMG's comparative data analysis tools extended to handle metagenome data, together with metagenome-specific analysis tools.

View Article: PubMed Central - PubMed

Affiliation: Biological Data Management and Technology Center, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, USA.

ABSTRACT
IMG/M is a data management and analysis system for microbial community genomes (metagenomes) hosted at the Department of Energy's (DOE) Joint Genome Institute (JGI). IMG/M consists of metagenome data integrated with isolate microbial genomes from the Integrated Microbial Genomes (IMG) system. IMG/M provides IMG's comparative data analysis tools extended to handle metagenome data, together with metagenome-specific analysis tools. IMG/M is available at http://img.jgi.doe.gov/m.

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Abundance Profile Tools. The ‘Abundance Profile Viewer’ (1) provides an overview of the relative abundance of protein families (COGs and Pfams) and functional families (enzymes) across selected metagenomes, normalized for genome size or using z-score. Abundance of protein/functional families is displayed as a heat map (2), with each cell hyperlinked to the list of genes assigned to a particular family. A protein family can be saved in the ‘Function Cart’ by clicking its identifier such as COG0642 (3). For protein families in the ‘Function Cart’ a selective ‘Function Profile’ can be also computed (4). The ‘Abundance Comparison’ tool (5) takes into account the stochastic nature of metagenome datasets and tests whether the differences in abundance can be ascribed to chance variation or not. In addition to the gene count based abundance, the results provided by this tool include an assessment of statistical significance in terms of D-score (6) or P-value.
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Figure 2: Abundance Profile Tools. The ‘Abundance Profile Viewer’ (1) provides an overview of the relative abundance of protein families (COGs and Pfams) and functional families (enzymes) across selected metagenomes, normalized for genome size or using z-score. Abundance of protein/functional families is displayed as a heat map (2), with each cell hyperlinked to the list of genes assigned to a particular family. A protein family can be saved in the ‘Function Cart’ by clicking its identifier such as COG0642 (3). For protein families in the ‘Function Cart’ a selective ‘Function Profile’ can be also computed (4). The ‘Abundance Comparison’ tool (5) takes into account the stochastic nature of metagenome datasets and tests whether the differences in abundance can be ascribed to chance variation or not. In addition to the gene count based abundance, the results provided by this tool include an assessment of statistical significance in terms of D-score (6) or P-value.

Mentions: Several ‘Abundance Profile’ tools can be used for comparing the functional capabilities of metagenomes and genomes. The ‘Abundance Profile Viewer’ provides an overview of the relative abundance of protein families (COGs and Pfams) and functional families (enzymes) across selected metagenomes and isolate genomes, as illustrated by the example in pane 1 of Figure 2 which shows the abundance profiles of COGs across three whale-fall microbiomes. Abundance of protein/functional families is displayed as a heat map over all families of a specific type (COGs, Pfams, or enzymes), as shown in pane 2 of Figure 2, with red corresponding to the most abundant families. Each column on the map corresponds to a genome or metagenome, while each row corresponds to a family. Clicking on the cell will retrieve the list of genes assigned to this particular family in this genome or metagenome, while clicking on the identifier of the family displayed on right side of the column (e.g. COG0642) will add the corresponding family to the ‘Function Cart’, as shown in pane 3 of Figure 2. For protein families in the ‘Function Cart’ a selective ‘Function Profile’ can be computed, as shown in pane 4 of Figure 2.Figure 2.


IMG/M: a data management and analysis system for metagenomes.

Markowitz VM, Ivanova NN, Szeto E, Palaniappan K, Chu K, Dalevi D, Chen IM, Grechkin Y, Dubchak I, Anderson I, Lykidis A, Mavromatis K, Hugenholtz P, Kyrpides NC - Nucleic Acids Res. (2007)

Abundance Profile Tools. The ‘Abundance Profile Viewer’ (1) provides an overview of the relative abundance of protein families (COGs and Pfams) and functional families (enzymes) across selected metagenomes, normalized for genome size or using z-score. Abundance of protein/functional families is displayed as a heat map (2), with each cell hyperlinked to the list of genes assigned to a particular family. A protein family can be saved in the ‘Function Cart’ by clicking its identifier such as COG0642 (3). For protein families in the ‘Function Cart’ a selective ‘Function Profile’ can be also computed (4). The ‘Abundance Comparison’ tool (5) takes into account the stochastic nature of metagenome datasets and tests whether the differences in abundance can be ascribed to chance variation or not. In addition to the gene count based abundance, the results provided by this tool include an assessment of statistical significance in terms of D-score (6) or P-value.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2238950&req=5

Figure 2: Abundance Profile Tools. The ‘Abundance Profile Viewer’ (1) provides an overview of the relative abundance of protein families (COGs and Pfams) and functional families (enzymes) across selected metagenomes, normalized for genome size or using z-score. Abundance of protein/functional families is displayed as a heat map (2), with each cell hyperlinked to the list of genes assigned to a particular family. A protein family can be saved in the ‘Function Cart’ by clicking its identifier such as COG0642 (3). For protein families in the ‘Function Cart’ a selective ‘Function Profile’ can be also computed (4). The ‘Abundance Comparison’ tool (5) takes into account the stochastic nature of metagenome datasets and tests whether the differences in abundance can be ascribed to chance variation or not. In addition to the gene count based abundance, the results provided by this tool include an assessment of statistical significance in terms of D-score (6) or P-value.
Mentions: Several ‘Abundance Profile’ tools can be used for comparing the functional capabilities of metagenomes and genomes. The ‘Abundance Profile Viewer’ provides an overview of the relative abundance of protein families (COGs and Pfams) and functional families (enzymes) across selected metagenomes and isolate genomes, as illustrated by the example in pane 1 of Figure 2 which shows the abundance profiles of COGs across three whale-fall microbiomes. Abundance of protein/functional families is displayed as a heat map over all families of a specific type (COGs, Pfams, or enzymes), as shown in pane 2 of Figure 2, with red corresponding to the most abundant families. Each column on the map corresponds to a genome or metagenome, while each row corresponds to a family. Clicking on the cell will retrieve the list of genes assigned to this particular family in this genome or metagenome, while clicking on the identifier of the family displayed on right side of the column (e.g. COG0642) will add the corresponding family to the ‘Function Cart’, as shown in pane 3 of Figure 2. For protein families in the ‘Function Cart’ a selective ‘Function Profile’ can be computed, as shown in pane 4 of Figure 2.Figure 2.

Bottom Line: IMG/M is a data management and analysis system for microbial community genomes (metagenomes) hosted at the Department of Energy's (DOE) Joint Genome Institute (JGI).IMG/M consists of metagenome data integrated with isolate microbial genomes from the Integrated Microbial Genomes (IMG) system.IMG/M provides IMG's comparative data analysis tools extended to handle metagenome data, together with metagenome-specific analysis tools.

View Article: PubMed Central - PubMed

Affiliation: Biological Data Management and Technology Center, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, USA.

ABSTRACT
IMG/M is a data management and analysis system for microbial community genomes (metagenomes) hosted at the Department of Energy's (DOE) Joint Genome Institute (JGI). IMG/M consists of metagenome data integrated with isolate microbial genomes from the Integrated Microbial Genomes (IMG) system. IMG/M provides IMG's comparative data analysis tools extended to handle metagenome data, together with metagenome-specific analysis tools. IMG/M is available at http://img.jgi.doe.gov/m.

Show MeSH
Related in: MedlinePlus