SanXoT software package

The SanXoT software package is a bioinformatic resource made in the Cardiovascular Proteomics Lab at CNIC to build workflows for quantitative high-throughput proteomics, systems biology and the statistical analysis, integration and comparison of experiments.

In includes the following programs:

For performing statistics:

• SanXoT, the central program, performing the integration of any lower level set of data, to any higher level set of data.
• SanXoTSieve, tool for detecting outliers in a SanXoT integration.
• Klibrate, calculator of the constant k for the inital calibration of data.

Systems biology specific:

• Sanson, detector of cateogories containing similar sets of proteins, showing changing proteins within each category.
• SanXoTGauss, generator of gaussian graphs associated to each category.
• Coordinometer, to calculate the degree of a coordination with given qc and ca stat files.
• Arbor, creator of Gene Ontology-like tree graphs, showing changing proteins in each category.
• Camacho, generator of relation files from text tables, especially from DAVID.
• SanXoTSqueezer, a detector of relevant categories in a systems biology analysis, filtering by FDR and number of proteins.
• Anselmo, a program to identify which integration holds the median of the variance from a set of randomised SanXoT integrations.

To integrate experiments:

• Cardenio, to generate the global relations and data files for several replicates (biological or technical) to be merged.

• For post-translational modifications:

• Trilogy, to tag peptides in relations files where non-modified peptides are used as reference in PTM analysis.

For other functions:

• MaesePedro, a tool for pseudoinverting FASTA protein databases.
• CataPep, a tool to make zero the XCorrs of all PSMs in an MSF file, excluding those provided in a white list.
• Aljamia, for parsing data between text files with tab separated tables.