Herbert John M J, Buffa Francesca M, Vorschmitt Henrik, Egginton Stuart, Bicknell Roy
Cancer Research UK Angiogenesis Group, Institute for Biomedical Research, Schools of Immunity and Infection and Cancer studies, College of Medicine and Dentistry, University of Birmingham, Birmingham, B15 2TT, UK.
BMC Genomics. 2009 Oct 23;10:490. doi: 10.1186/1471-2164-10-490.
Physiological processes occur in many species for which there is yet no sequenced genome and for which we would like to identify the genetic basis. For example, some species increase their vascular network to minimise the effects of reduced oxygen diffusion and increased blood viscosity associated with low temperatures. Since many angiogenic and endothelial genes have been discovered in man, functional homolog relationships between carp, zebrafish and human were used to predict the genetic basis of cold-induced angiogenesis in Cyprinus Carpio (carp). In this work, carp sequences were collected and built into contigs. Human-carp functional homolog relationships were derived via zebrafish using a new Conditional Stepped Reciprocal Best Hit (CSRBH) protocol. Data sources including publications, Gene Ontology and cDNA libraries were then used to predict the identity of known or potential angiogenic genes. Finally, re-analyses of cold carp microarray data identified carp genes up-regulated in response to low temperatures in heart and muscle.
The CSRBH approach outperformed all other methods and attained 8,726 carp to human functional homolog relationships for 16,650 contiguous sequences. This represented 3,762 non-redundant genes and 908 of them were predicted to have a role in angiogenesis. The total number of up-regulated differentially expressed genes was 698 and 171 of them were putatively angiogenic. Of these, 5 genes representing the functional homologs NCL, RHOA, MMP9, GRN and MAPK1 are angiogenesis-related genes expressed in response to low temperature.
We show that CSRBH functional homologs relationships and re-analyses of gene expression data can be combined in a non-model species to predict genes of biological interest before a genome sequence is fully available. Programs to run these analyses locally are available from http://www.cbrg.ox.ac.uk/~jherbert/.
许多物种都会发生生理过程，而这些物种尚未有测序基因组，我们希望确定其遗传基础。例如，一些物种会增加其血管网络，以尽量减少与低温相关的氧气扩散减少和血液粘度增加的影响。由于在人类中已经发现了许多血管生成和内皮基因，因此利用鲤鱼、斑马鱼和人类之间的功能同源关系来预测鲤（鲤鱼）冷诱导血管生成的遗传基础。在这项工作中，收集了鲤鱼序列并构建成重叠群。利用一种新的条件逐步相互最佳匹配（CSRBH）协议，通过斑马鱼得出人类与鲤鱼的功能同源关系。然后使用包括出版物、基因本体论和cDNA文库在内的数据源来预测已知或潜在血管生成基因的身份。最后，对冷鲤鱼微阵列数据的重新分析确定了在心脏和肌肉中对低温有上调反应的鲤鱼基因。
CSRBH方法优于所有其他方法，对于16,650个连续序列获得了8,726个鲤鱼与人类的功能同源关系。这代表了3,762个非冗余基因，其中908个被预测在血管生成中起作用。上调的差异表达基因总数为698个，其中171个被假定为血管生成相关基因。其中，代表功能同源物NCL、RHOA、MMP9、GRN和MAPK1的5个基因是对低温有反应而表达的血管生成相关基因。
我们表明，在基因组序列完全可用之前，可以将CSRBH功能同源关系和基因表达数据的重新分析结合起来，用于非模式物种中预测具有生物学意义的基因。可从http://www.cbrg.ox.ac.uk/~jherbert/获得在本地运行这些分析的程序。
