Alon Samach1. 1. The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, Faculty of Agriculture, Food and Environmental Quality Sciences, The Hebrew University of Jerusalem, Rehovot, 76100, Israel. samach@agri.huji.ac.il
Abstract
BACKGROUND: Studying a process in a new species often relies on focusing our attention to a candidate gene, encoding a protein similar to one with a known function. Not all the choices seem to be prudent. SCOPE: This Viewpoint includes an overview of issues that are encountered during research of candidate genes. Defining a match for a gene of interest, deciding whether variation in ESTs or RNAseq data for a certain transcript, represent more than one gene. The problem of incorrect annotation of genes due to incorrect in-silico splicing, is also mentioned. The author's humble opinion on how to deal with these issues is provided. CONCLUSIONS: The vast amount of new sequence data provides us with great possibilities for giant leaps in our understanding. Still, we cannot afford to skip over the tedious steps required to confirm that we are indeed studying the correct gene, and try to be sure that the complex expression pattern we observe is not a composite of several genes.
BACKGROUND: Studying a process in a new species often relies on focusing our attention to a candidate gene, encoding a protein similar to one with a known function. Not all the choices seem to be prudent. SCOPE: This Viewpoint includes an overview of issues that are encountered during research of candidate genes. Defining a match for a gene of interest, deciding whether variation in ESTs or RNAseq data for a certain transcript, represent more than one gene. The problem of incorrect annotation of genes due to incorrect in-silico splicing, is also mentioned. The author's humble opinion on how to deal with these issues is provided. CONCLUSIONS: The vast amount of new sequence data provides us with great possibilities for giant leaps in our understanding. Still, we cannot afford to skip over the tedious steps required to confirm that we are indeed studying the correct gene, and try to be sure that the complex expression pattern we observe is not a composite of several genes.
Authors: Anusak Pinyopich; Gary S Ditta; Beth Savidge; Sarah J Liljegren; Elvira Baumann; Ellen Wisman; Martin F Yanofsky Journal: Nature Date: 2003-07-03 Impact factor: 49.962
Authors: Patrick A Reeves; Yuehui He; Robert J Schmitz; Richard M Amasino; Lee W Panella; Christopher M Richards Journal: Genetics Date: 2006-12-18 Impact factor: 4.562
Authors: S A Chervitz; L Aravind; G Sherlock; C A Ball; E V Koonin; S S Dwight; M A Harris; K Dolinski; S Mohr; T Smith; S Weng; J M Cherry; D Botstein Journal: Science Date: 1998-12-11 Impact factor: 47.728
Authors: Dmitry N Grigoryev; Shwu-Fan Ma; Rafael A Irizarry; Shui Qing Ye; John Quackenbush; Joe G N Garcia Journal: Genome Biol Date: 2004-04-27 Impact factor: 13.583
Authors: Natalia Muñoz-Fambuena; Carlos Mesejo; María C González-Mas; Eduardo Primo-Millo; Manuel Agustí; Domingo J Iglesias Journal: Ann Bot Date: 2013-02-06 Impact factor: 4.357
Authors: Mari-Cruz Castillo; Javier Forment; José Gadea; Jose Luis Carrasco; José Juarez; Luís Navarro; Gema Ancillo Journal: Ann Bot Date: 2013-09-19 Impact factor: 4.357