During the last decade, we witnessed the huge impact of the comparative genomics for understanding genomes (from the genome organization to their annotation). However, those genomic approaches quickly reach their limits when one looks at investigating the functional properties of genes in the wide genome context. Such limitation may be overcome thanks to recent high-throughput experimental progresses like those obtained via metabolic and co-expression studies, that produce so-called omics data. Therefore, integrating those data and state-of-the-art computational genomic comparison is a natural evolution. This paper achieves such an integration and proposes a heuristic algorithm IISCS that incorporates omics knowledge into the IILCS heuristic, already known as accurate to compare genomes. When applied on bacteria, one emphasize large functional units composed of several operons.