AnnotationSet and related classes should respect organism's gene names

[fabio-t]

Related to #117, but more general and thus deserving of its own issue.

AnnotationSet fix_gene_names by default converts gene names to upper case. This is unnecessary when proper organism resolution is needed.

However, we do use jaspar_vertebrates, where a bunch of different organism-specific transcription factors are put together. So this requires a bigger discussion, and quite possibly we should leave to the user the decision of whether to "upper" all genes or keep the original name.