Figure - PMC

Skip to main content

An official website of the United States government

Here's how you know

Here's how you know

Official websites use .gov
A .gov website belongs to an official government organization in the United States.

Secure .gov websites use HTTPS
A lock ( ) or https:// means you've safely connected to the .gov website. Share sensitive information only on official, secure websites.

View full-text article in PMC

. 2010 Aug 10;38(22):7877–7884. doi: 10.1093/nar/gkq699

Search in PMC
Search in PubMed
View in NLM Catalog
Add to search

© The Author(s) 2010. Published by Oxford University Press.

This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.5), which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

PMC Copyright notice

Figure 1. — Illustration of the orthology detection problem. To demonstrate this problem, we compare the regulons of the transcription factors pcaR and dtxR of Corynebacterium glutamicum (CG) and Corynebacterium efficiens (CE). The red nodes represent the respective regulators, the others their target genes. Directed edges correspond to transcriptional regulatory interactions. Undirected edges symbolize putative orthologies due to sequence-based similarity. While for pcaR all 12 target genes are conserved in both organisms, for dtxR multiple problems occur: dtxR regulates 64 genes in CG but only 27 in CE. From these target genes, only nine are clearly evolutionarily conserved, i.e. one-to-one relationship, such as glyR and ce0466. The others are either inhomologous (green nodes) or show multiple, ambiguous sequence-based similarities, i.e. one-to-many or many-to-many relationship; cg0159, cg0160 (CG), and ce0125 (CE) may serve as an example here.