miPALM (Module Inference by Parametric Local Modularity)

miPALM is a novel algorithm for detecting protein complexes from large protein protein interaction networks with improved accuracy than previous methods.

The algorithm uses a novel graph theoretic measure, parametric local modularity, to identify highly connected sub-networks as candidate protein complexes.

The software is implemented in Matlab and is freely available for academic use.

• Download Windows version

• Download Linux version

Please cite: Jongkwang Kim and Kai Tan. Discover Protein Complexes in Protein-Protein Interaction Networks Using Parametric Local Modularity BMC Bioinformatics 2010. 11:521.

Usage

miPALM -a 0.364 -d 2.4 [-i input.net] [-o output.txt]

where -a and -d are standard parameters of miPALM and other command line parameters are optional:

• -i (default standard dialog box) is a Pajek file containing unique node IDs and interactions among them.

• -o (default standard file output) is the file to contain the detected complexes by miPALM. Default output file will be named as "input_a0.364_d2.4.txt" in "results" sub-folder.

Example

Given the input file called "my_input.net":

*Vertices 4

1 "P46677"

2 "P21372"

3 "P20433"

4 "Q00916"

*Edges

1 2

1 3

2 3

2 4

3 4

Please note that the example above has no edge-weight on the 3rd column and no vertex-position.

• miPALM might be run as

miPALM -a 0.374 -d 2.33

• To specify a user input file name (using the default output-file name)

miPALM -a 0.374 -d 2.33 -i my_input.net

• To specify a user!/s output file name (using the default dialog box for input-file)

miPALM -a 0.374 -d 2.33 -o my_output.net

• To input "Yeast_PPI_DIP_FULL.net" in the sub-folder "data" and to generate output file "my_output.txt" in the sub-folder "results"

miPALM -a 0.374 -d 2.33 -i data\Yeast_PPI_DIP_FULL.net -o results\my_output.txt

The generated "my_output.txt" looks like this:

Rank Score Proteins Complex

--------------------------------------------------------------

1 5.75 9 P09119 P54784 P32833 P54791 P54790 P38826 P50874 P32579 P38185

2 5.33 10 P41543 P39007 P33767 P48439 Q99380 Q92316 P46964 P53062 P47818 Q04629

3 5.25 9 P45976 Q06102 P29468 Q12102 Q01329 P38912 P39927 P53538 Q03713

4 5.09 12 P32074 P22804 P11076 P20606 P22214 P25385 P22213 P41834 P40509 P05738 P43621 P28791

5 5.00 9 P34253 Q04868 Q06706 P38874 Q02908 P42935 Q02884 Q06177 P46974

6 5.00 5 P36116 P39904 Q99260 P47061 Q12071

7 5.00 7 P40480 P36124 P14832 P25357 P53685 P53096 P22943

8 4.89 10 Q07468 P53129 P37898 P12868 Q03308 P27801 P39702 P38959 P20795 P38273

9 4.83 13 P09547 P32479 P32480 P22082 P18480 P43554 P32591 P38064 Q06090 P53628 Q05123 Q12406 Q06349

10 4.75 9 P32349 P22276 P35718 P32910 P04051 P20436 Q04307 P17890 P47076

In addition to *.txt file above, miPALM also generates another text file to contain protein node-numbers of a complex in each line. For more details, see "README.txt" file in the uncompressed folder.

For your subsequent analysis and visualization, miPALM automatically exports *.txt file to *.sif and *.net file for each predicted complex which can be imported into Cytoscape and Pajek, respectively.

Figure 1. The top-scored sub-network in Yeast DIP-PPI network detected by miPALM and visualized by Cytoscape.

Email to tank1@email.chop.edu for bug-reporting.