Network analysis: Is low confidence score valid (STRING DB)
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Saransh • 0
Last seen 3.1 years ago

Hello everyone, i am working on network analysis of Differentially Expressed Genes, but the problem i am facing is that, the gene set is very short (of around 16 genes only), so when i'm trying to build an interaction using these genes in STRING webtool, the nodes starts to dissociate from the interaction when i set the confidence score to 0.400 or above (as the genes are related to Homo sapiens). So, to build an interaction between these genes, i've to decrease the confidence score to 0.150. At this score only i'am getting an interaction. So, i want to ask whether this low confidence score is valid for this short gene set related to Homo sapiens or else what should i do in this case?

STRINGdb Network • 1.8k views
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Kevin Blighe ★ 4.0k
Last seen 4 weeks ago
Republic of Ireland

In my opinion, the score of 0.15 is too low, as it implies that almost 9 out of every 10 interactions are possibly false-positives. Please see the details, here:

In STRING, each protein-protein interaction is annotated with one or more 'scores'.

Importantly, these scores do not indicate the strength or the specificity of the interaction. Instead, they are indicators of confidence, i.e. how likely STRING judges an interaction to be true, given the available evidence. All scores rank from 0 to 1, with 1 being the highest possible confidence. A score of 0.5 would indicate that roughly every second interaction might be erroneous (i.e., a false positive).



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