Replicate high-density rat genome oligonucleotide microarrays reveal hundreds of regulated genes in the dorsal root ganglion after peripheral nerve injury.
Replicate high-density rat genome oligonucleotide microarrays reveal hundreds of regulated genes in the dorsal root ganglion after peripheral nerve injury.
复制标题
DOI：
10.1186/1471-2202-3-16
复制
发表时间：
2002-10-25
期刊：
影响因子：
2.4
通讯作者：
Woolf CJ
中科院分区：
文献类型：
--
作者：
Costigan M;Befort K;Karchewski L;Griffin RS;D'Urso D;Allchorne A;Sitarski J;Mannion JW;Pratt RE;Woolf CJ
采用大鼠寡核苷酸微阵列检测坐骨神经横断后3天背根神经节（DRG）基因表达的变化。使用两组三重复微阵列进行了两次比较，naïve与naïve和naïve与肛门切开术。通过naïve和naïve的比较来评估微阵列变异性。尽管需要进行大量的假设检验，但这些结果支持使用P < 0.05显著性阈值来检测受调节基因。对于naïve与肛肠切开术的比较，单独的2倍切断导致估计错误率为16%；结合>1.5倍的表达变化和P < 0.05的显著性将估计误差降低到5%。2倍剪断鉴定出178个基因，而>1.5倍和P < 0.05标准联合鉴定出240个推定调控基因，我们已列出。其中许多都没有被描述为在DRG中通过肛门切开术进行调节。Northern blot、定量槽blot和原位杂交验证了24个转录本的表达。这些数据与阵列的一致性率为83%；大多数错配代表低表达水平的基因，反映了阵列敏感性的局限性。实际mRNA差异与微阵列间的相对变化呈显著相关（r2 = 0.8567）。个体基因调控的时间模式各不相同。我们确定了微阵列分析的参数，减少了错误，同时确定了许多假定的调控基因。这些基因的功能分类提示细胞结构成分的重组，免疫和炎症细胞表达的基因的激活以及参与神经传递的基因的下调。
Rat oligonucleotide microarrays were used to detect changes in gene expression in the dorsal root ganglion (DRG) 3 days following sciatic nerve transection (axotomy). Two comparisons were made using two sets of triplicate microarrays, naïve versus naïve and naïve versus axotomy. Microarray variability was assessed using the naïve versus naïve comparison. These results support use of a P < 0.05 significance threshold for detecting regulated genes, despite the large number of hypothesis tests required. For the naïve versus axotomy comparison, a 2-fold cut off alone led to an estimated error rate of 16%; combining a >1.5-fold expression change and P < 0.05 significance reduced the estimated error to 5%. The 2-fold cut off identified 178 genes while the combined >1.5-fold and P < 0.05 criteria generated 240 putatively regulated genes, which we have listed. Many of these have not been described as regulated in the DRG by axotomy. Northern blot, quantitative slot blots and in situ hybridization verified the expression of 24 transcripts. These data showed an 83% concordance rate with the arrays; most mismatches represent genes with low expression levels reflecting limits of array sensitivity. A significant correlation was found between actual mRNA differences and relative changes between microarrays (r2 = 0.8567). Temporal patterns of individual genes regulation varied. We identify parameters for microarray analysis which reduce error while identifying many putatively regulated genes. Functional classification of these genes suggest reorganization of cell structural components, activation of genes expressed by immune and inflammatory cells and down-regulation of genes involved in neurotransmission.
登录
查看更多内容
DOI：
10.1073/pnas.93.9.3978
发表时间：
1996-04-30
影响因子：
11.1
作者：
Alberi, S;Raggenbass, M;DuboisDauphin, M
通讯作者：
DuboisDauphin, M
DOI：
10.1006/bbrc.1999.1683
发表时间：
1999-11-19
影响因子：
3.1
作者：
Bono, F;Lamarche, I;Herbert, JM
通讯作者：
Herbert, JM
影响因子：
4.8
作者：
Chou, TT;Trojanowski, JQ;Lee, VMY
通讯作者：
Lee, VMY
DOI：
10.1097/00005072-199810000-00004
发表时间：
1998-10-01
影响因子：
3.2
作者：
Carroll, SL;Frohnert, PW
通讯作者：
Frohnert, PW
影响因子：
5.3
作者：
Bennett, DLH;Boucher, TJ;Shelton, DL
通讯作者：
Shelton, DL