Galaxy | Tool Preview

metaQuantome: expand (version 2.0.2+galaxy0)
must be created by 'metaQuantome: download'
must be created by 'metaQuantome: create samples file'
Tabular file with a peptide sequence column and a functional assignment column with GO terms, EC number, or COG.
The column name within the function file that corresponds to the peptide sequences
The column name within the function file with the functional terms
The column name within the intensity file that corresponds to the peptide sequences

metaQuantome expand

The expand module is the first analysis step in the metaQuantome analysis workflow, and can be run to analyze function, taxonomy, or function and taxonomy together.

To prepare to run this module, you must create your samples file with "metaQuantome: create samples file" and download the necessary databases with "metaQuantome: database".

Some example analysis workflows are:

  1. Get the functional, taxonomic, or functional-taxonomic distribution: run expand, filter, and viz.
  2. Cluster analysis: run expand, filter, and viz. The viz module has heatmaps and PCA plots for cluster analysis.
  3. Differential expression: run expand, filter, stat, and viz.

The following information is required for all 3 analysis modes (function, taxonomy, and function-taxonomy).

  • experimental design information.
  • a tab-separated peptide intensity file.
  • the name of the peptide column in the intensity file.

Function mode

In function mode, the following information is required:

  • the ontology being used: Gene Ontology (GO), Clusters of Orthologous Groups (COG), or Enzyme Commission (EC) numbers.
  • a tab-separated functional annotation file, with a peptide column and a functional annotation column. An entry in the functional annotation column may contain multiple functional annotations separated by commas.
  • the name of the peptide column in the functional annotation file.
  • the name of the functional annotation column in the functional annotation file.

Taxonomy mode

In taxonomy mode, the following information is required:

  • a tab-separated taxonomy annotation file, with a peptide column and a taxonomy annotation column. The taxonomic annotations should be the lowest common ancestor (LCA) for each peptide, preferably given as NCBI taxonomy IDs.
  • the name of the peptide column in the taxonomic annotation file.
  • the name of the taxonomy annotation column in the taxonomy annotation file.

Function-Taxonomy mode

In the combined mode, all of the above must be provided. In addition, the "target rank" must be provided, which is the desired taxonomic rank at which to summarize the function/taxonomy results.

Output of the expand module

The structure of the output file depends on the analysis mode and the experimental design, but the columns generally look like this, with one row for each term:

term id info about term. (one or more columns) mean term intensity (by sample group) term intensity (by sample) number of unique peptides (by sample) number of sample children in each sample
term1 name, rank, etc. note that this is the log2 of the mean intensity this is the log2 of term intensity in each sample. Missing data is coded as NA. integer. 0 is coded as NA integer. 0 is coded as NA

The next step in the metaQuantome workflow is "filter", which filters out rows that don't meet certain conditions on the intensity, the number of unique peptides annotated with each term, and the number of sample children.

Questions, Comments, Problems, Kudos

Please file any issues at https://github.com/galaxyproteomics/tools-galaxyp/issues.