Abstract
Proteins and non-coding RNAs are functional products of the genome that are central for crucial cellular processes. With recent technological advances, researchers can sequence genomes in the thousands and probe numerous genomic activities of many species and conditions. Such studies have identified thousands of potential proteins, RNAs, and associated activities. However, there are conflicting interpretations of the results and therefore which regions of the genome are "functional." Here we investigate the relative strengths of associations between coding and non-coding gene functionality and genomic features, by comparing reliably annotated functional genes to nongenic regions of the genome. We find that the strongest and most consistent associations between functional genes and genomic features are transcriptional activity and evolutionary conservation. We also evaluated sequence-based statistics, genomic repeats, and epigenetic and population variation data. Other features strongly associated with function include histone marks, chromatin accessibility, genomic copy number, and sequence alignment statistics such as coding potential and covariation. We also identify potential issues with SNP annotations in short non-coding RNAs, as some highly conserved ncRNAs have significantly higher than expected SNP densities. Our results demonstrate the importance of evolutionary conservation and transcription activity for indicating protein-coding and non-coding gene function. Both should be taken into consideration when differentiating between functional sequences and biological or experimental noise.