My understanding is that wig format is mainly used to display (positive) signal density in experiments suchs as ChIP-seq, RNA-seq, etc. However, I encounter now and then wig files from ChIP-seq experiments where some values are equal to "-1". Is there a particular meaning attached to "-1" in the context of ChIP-seq wig files?
The .wig format can display anything. For example, COHCAP creates .wig files with delta beta values that range from -1 to 1.
So, you'll have to check the details for the algorithm producing the .wig files. If intensity values are centered around a baseline threshold, negative values would not be significant. However, it's not possible to say more without knowing more about the algorithm that produced the files.
For ChIP-seq datasets, often times negative WIG values mean that there is input enrichment in that location but I echo the other responses in that it is important to understand where the WIG came from so you will know how to properly interpret the values it gives you.
You need to look at the supporting information for that, a value could be anything from fold change to some arbitrary number indicating an event with a particular and pecluliar meaning
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One such case is the wig file in GSM640756. It is indicated in the GEO dataset entry that "The WIG files were similarly created by extending mapped reads 300bp and calculating the overlapping density in 25 bp bins." There does not seem to be any more information that could explain the "-1" values in the manuscript either. So, I guess, since there is no standard meaning for negative values (thanks for the answers!), the only way is to contact the authors.