In this repository we deposited the Supplementary data/script used in study "Genome-wide inference of Camponotus floridanus protein-protein interaction network using homologous mapping and interacting domain profile pairs".
Supplementary material can be found here in a single Excel Sheet containing all dastasheets.
Prelimnary orthology based C. floridanus network. Sheet can be imported in Cytoscape (www.cytoscape.org/) for further network analysis.
Domain supported interactions in C. floridanus network.
Subcellular localization and domain supported interactions in C. floridanus network.
Isoform filtered, subcellular localization and domain supported final interactions in C. floridanus network. Sheet can be imported in Cytoscape for further network analysis. Structural annotation of genes coding these proteins can be downloaded from the web-repository
Calculation of Z-statistics for centrality parameters in ant interactome against three independent datasets. Pair wise comparison chart of different parameters: clustering coefficient, degree distribution and mean shortest path for ant interactome against three randomly generate independent network is shown. The values were calculated through statistical Z-test.
Functional over-repsentation molecular function analysis of C. floridanus proteins present in the interactome.
Degree and orthology of C. floridanus proteins present in the interactome.
Supplementary Figure 1 (attach)
Supplementary Figure 2 (attach)
Script needed two files to run
(I) List of protein/gene identifiers. See the sample file here.
(II) List of interations which should be avoided. See the sample file here.
$ perl random_network_generator.pl file1.txt file2.txt > 100_random_networks
Note that 100_random_networks will be a single file. To split the file
$ perl split_networks.pl 100_random_networks
Script needed one file to run
(I) Table with one column of confidence subset classifications and one column with confidence scores. See the sample file here
Script needed one file to run
(I) A table with semantic similarity scores for each protein pair in PPI and randomly generated non-PPI networks. See the sample file here
Script needed two files to run
(I) A table of proteins in each network with confidence scores. See the sample file here
(II) A table with p-values calculated in the first part of the script for manual p-value addition to the figure. See the sample file here
Script needed four files to run
(I) A table with proteins classified according to being bottleneck or not, and their localization status (single vs. multiple). See the sample file here
(II) A table with proteins classified according to being hub or not, and their localization status (single vs. multiple). See the sample file here
(III) A table with p-values calculated in the first part of the script for manual p-value addition to the figure. See the sample file here
(IV) Exact numbers and percentages of single and multiple-localization in hubs, non-hubs, bottlenecks, non-bottlenecks. See the sample file here
If you have any questions or requirement of any other data from our manuscript, please feel free to contact me (shishir.gupta@uni-wuerzburg.de) or Prof. Dr. Thomas Dandekar (dandekar@biozentrum.uni-wuerzburg.de).