TY  - JOUR
A1  - Gerstein, Mark B.
A1  - Bruce, Can
A1  - Rozowsky, Joel S.
A1  - Zheng, Deyou
A1  - Du, Jiang
A1  - Korbel, Jan O.
A1  - Emanuelsson, Olof
A1  - Zhang, Zhengdong D.
A1  - Weissman, Sherman
A1  - Snyder, Michael
T1  - What is a gene, post-ENCODE? History and updated definition
Y1  - 2007/06/01 
JF  - Genome Research 
JO  - Genome Research 
SP  - 669 
EP  - 681 
DO  - 10.1101/gr.6339607 
VL  - 17 
IS  - 6 
UR  - http://genome.cshlp.org/content/17/6/669.abstract 
N2  - While sequencing of the human genome surprised us with how many protein-coding genes there are, it did not fundamentally change our perspective on what a gene is. In contrast, the complex patterns of dispersed regulation and pervasive transcription uncovered by the ENCODE project, together with non-genic conservation and the abundance of noncoding RNA genes, have challenged the notion of the gene. To illustrate this, we review the evolution of operational definitions of a gene over the past century—from the abstract elements of heredity of Mendel and Morgan to the present-day ORFs enumerated in the sequence databanks. We then summarize the current ENCODE findings and provide a computational metaphor for the complexity. Finally, we propose a tentative update to the definition of a gene: A gene is a union of genomic sequences encoding a coherent set of potentially overlapping functional products. Our definition sidesteps the complexities of regulation and transcription by removing the former altogether from the definition and arguing that final, functional gene products (rather than intermediate transcripts) should be used to group together entities associated with a single gene. It also manifests how integral the concept of biological function is in defining genes. 
ER  -