PMC:4331675 / 14672-18208
Annnotations
{"target":"https://pubannotation.org/docs/sourcedb/PMC/sourceid/4331675","sourcedb":"PMC","sourceid":"4331675","source_url":"https://www.ncbi.nlm.nih.gov/pmc/4331675","text":"Results and discussion\nAs examples to demonstrate the use of this package, integrated PPI data from the PINA, iRefIndex and STRING databases for six model species are available for downloading from our website. Users should cite the databases accordingly when using these files. When integrating interactions from different databases, the function combinePPI will also count the number of valid proteins and protein interactions from each database. In view of the fact that the STRING database includes not only known PPIs but also predicted associations, only high confidence interactions from STRING are retained in these samples. The threshold of the STRING score is set to 700 by default, which can be changed manually with the function formatSTRINGPPI.\nTaking Homo sapiens as an example, 14,646, 14,906, and 14,050 valid proteins are identified in the PINA, iRefIndex and STRING databases. Generated by the combinePPI function of this cisPath package, Tables 2 and 3 present the proteins and protein interactions in a given database which overlap with the other two databases. The last column of each table shows the number of distinct proteins or protein interactions found in each database. Although the PINA database contains the least number of distinct proteins, and has only 1008 proteins not found in the other two databases, it contains 36,867 interactions that are distinct, and most of these are supported by scientific literature. The iRefIndex database contains a large number of distinct proteins, as well as a large number of distinct interactions, which are all well supported by scientific literature. The STRING database contains up to 191,324 distinct interactions, but most of these interactions are predicted by data mining. Sample R scripts used to download and format PPI data can be found on our website. Only a small portion of available PPI data is selected for examples in the source package. The file with complete PPI information can be downloaded from our web site.\nTable 2 Number of overlapping and distinct proteins listed for Homo sapiens in different databases. Each cell indicates the number of overlapping proteins from the two databases designated in the row and column; numbers on the diagonal indicate the total number of proteins from the database designated in the row and column. The last column indicates the number of distinct proteins from the given database.\nTable 3 Number of overlapping and distinct protein interactions listed for Homo sapiens in different databases. Each cell indicates the number of overlapping protein interactions from the two databases designated in the row and column, excluding PPIs with STRING scores of less than 700; numbers on the diagonal indicate the total number of proteins interactions from the database designated in the row and column. The last column indicates the number of distinct protein interactions from the given database. Compared to other existing tools such as Cytoscape [22] and the online web servers PINA and STRING, this cisPath package is especially useful for R and cloud users. For R users, this package can be installed and updated by using only two commands, and no other plugins are required. Users can view, edit, and save the output network views with most modern web browsers. Cloud users can simply connect to the RStudio server with a browser and construct and publish personalized PPI databases and networks. It allows the user to play the role of PPI database administrator, rather than simply act as a common user.","divisions":[{"label":"Title","span":{"begin":0,"end":22}},{"label":"Table caption","span":{"begin":2000,"end":2411}},{"label":"Table caption","span":{"begin":2411,"end":2923}}],"tracks":[{"project":"2_test","denotations":[{"id":"25708840-23132118-14883606","span":{"begin":2976,"end":2978},"obj":"23132118"}],"attributes":[{"subj":"25708840-23132118-14883606","pred":"source","obj":"2_test"}]}],"config":{"attribute types":[{"pred":"source","value type":"selection","values":[{"id":"2_test","color":"#d4ec93","default":true}]}]}}