I am conducting a differential gene expression analysis to determine the difference in the change in gene expression in each sex due to a treatment in human samples. For this type of study would you recommend UCSC or ensembl? I am concerned by the significant difference in GO terms and kegg pathway results that I get from alignment and differential expression analysis using GRCh37 ensembl genome vs hg19 genome for human samples. There was a significant difference between the two all the way through the workflow, which was to be expected since the two reference genomes and annotations are different. I was wondering which one is most reliable? My results are so different between the two that I'm finding it hard to make sense of it all. Any help would be greatly appreciated. 
Could you please be more specific with your workflow, tools used and input files. Maybe you can share some of the input files and intermediate results with us? Overal, huge difference in GO terms for same genes in different annotations is strange. 

You obviously looked at [https://www.biostars.org/p/113100/][1] , right?


  [1]: https://www.biostars.org/p/113100/