In this chapter, we focused on the analysis of genomes, transcriptomes, and proteomes and considered important applications and findings from these endeavors. At the same time, we found many opportunities to consider the methods and reasoning by which much of this information was acquired. From the explanations given in the chapter, what answers would you propose to the following fundamental questions?
(a) How do we know which contigs are part of the same chromosome?
(b) How do we know if a genomic DNA sequence contains a protein-coding gene?
(c) What evidence supports the concept that humans share substantial sequence similarities and gene functional similarities with model organisms?
(d) How can proteomics identify differences between the number of protein-coding genes predicted for a genome and the number of proteins expressed by a genome?
(e) How has the concept of a reference genome evolved to encompass a broader understanding of genomic variation in humans?
(f) How have microarrays demonstrated that, although all cells of an organism have the same genome, some genes are expressed in almost all cells, whereas other genes show celland tissue-specific expression?