After checking the NCBI help page, I am still unclear about the difference between protein and replication interactions for HIV.
http://www.ncbi.nlm.nih.gov/genome/viruses/retroviruses/hiv-1/interactions/
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1$\begingroup$ I'm not entirely sure what you're asking. What is your specific question? That help page seems clear enough. $\endgroup$ – James Jul 7 '15 at 8:32
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$\begingroup$ What is the difference between options protein and replication $\endgroup$ – girl101 Jul 7 '15 at 8:33
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1$\begingroup$ I've suggested a pretty major edit. Feel free to role back, but I think the question is much clearer now. $\endgroup$ – James Jul 7 '15 at 8:47
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$\begingroup$ These edits provided by users are good, perhaps the OP could add what their interpretation of the two terms are so it is easier to identify where the misunderstanding is. $\endgroup$ – rg255 Jul 7 '15 at 9:15
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$\begingroup$ what is OP????? $\endgroup$ – girl101 Jul 7 '15 at 9:17
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Interactions denote protein-protein interactions, which means physical association between proteins. By nature, these networks/graphs are undirected.
Replication interactions (actually a not very good term) denote gene regulatory interactions that affect HIV replication. These sets also include the regulatory effects of HIV genes on host genes (and hence the terminology is unsuitable). These networks are directed as well as signed (positive or negative interactions i.e. activation or inhibition respectively).
You can see for yourself, from the dropdown boxes and the interaction lists in this page.
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$\begingroup$ So its basically just PPI not leading to virus replication versus PPI that lead to virus replication?? $\endgroup$ – girl101 Jul 7 '15 at 9:16
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$\begingroup$ @Rishika in the PPI networks the final outcome is not considered. The "replication" interactions are more about proteins regulating transcription (which happen basically via protein-DNA interactions). $\endgroup$ – WYSIWYG Jul 7 '15 at 9:19
