I am analysing a published rnaseq read counts table that is upper quartile normalised. I have correlated a transcript of interest (transcript A) against all other transcripts and obtained a 2 column table with transcript/gene names in the first column and Pearson correlation (ranging from -1 to 1) in the second column. I want to annotate the gene list so that I can get the gene function in a 3rd column. I've passed the list of genes into enrichr but the list of gene functions that it returns is not the same length as the list of genes that I passed in. Any ideas on how else I can do this?
There may be an issue with ID matching, or it may be that it simply could not enrich those 3000 'missing' genes. No need to input the correlation values, as it won't use them and may throw a syntax error.
Another thing to check is thresholds used for enrichment:
- minimum genes per enrichment term