Hello,
I entered gene IDs corresponding to a list of up- and downregulated DEGs (gene signature) in the query tool available in CMap (www.clue.io/query), and obtained a list of compounds with different normalized connectivity scores (ncs) among other parameters as output. I selected only compounds with a negative ncs and with a minimum threshold value for other parameters, according to their tutorial, in order to be left only with compounds that tend to regulate the gene signature oppositely as presented in the input. The output list also contains a column with the targets for each compound, and I thought this target column would be "custom made" for each query in the sense that, for compounds with negative ncs, this column would only include genes that are part of the list of DEGs introduced by the user (instead of showing all known targets), thus indicating which genes in my initial list of DEGs are being oppositely regulated by each compound. However, this not the case since some compounds with negative ncs only have targets that are not part of the DEG input list initially entered by the user. So, how can compounds show in the output list with negative ncs for my query if none of their targets are part of my initial DEG list? Thanks!
