Predicting co-complexed protein pairs from heterogeneous data: Supplementary information

Jian Qiu and William Stafford Noble

PLoS Computational Biology. 4(4):e1000054, 2008.

MIPS labels

The following files are tab-delimited text, with identifiers in the first row and column.

Sequence kernels:

• Pfam kernel
• motif kernel
• spectrum kernel

Diffusion kernels:

• two-hybrid matrix, diffusion kernel
• genetic interaction matrix, diffusion kernel
• APMS matrix, diffusion kernel
• APMS without data from Gavin et al. and Krogan et al. matrix, diffusion kernel

Co-expression, co-regulation, co-localization, GO and interolog features for the RBF kernel:

• MIPS data set
• Gavin et al. data set
• Krogan et al. data set

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Predicted new members of MIPS complexes Each predicted new member has at least two predicted co-complexed relationships and 50% overlap with members of the MIPS complex.

Members of new complexes (see section 3.7 of the paper):

• complex 1
• complex 2
• complex 3
• complex 4

Each complex is a connected component on the network of cliques of at least size 3 with no protein in the manually curated MIPS complex catalogue. In each file, the first column lists the systematic names and the second column lists the standard names of the members in the connected component.

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