基于GEO数据库进行人类皮肤芯片核苷酸切除修复基因XPA表达的差异性
Parallel Mining of Gene Expression Differences of Nucleotide Excision Repair Gene XPA in Human Skin Microarrays based on GEO Database
-
摘要: 目的 从系统水平平行分析碱基切除修复相关途径中的重要基因XPA在众多人类皮肤疾病中的差异表达情况.方法 通过生物信息学的方法, 利用ScanGEO工具对GEO数据库中59个皮肤或皮肤疾病样品相关的基因芯片数据从核苷酸切除修复途径进行平行比对, 对XPA表达具有统计学意义的样本进行筛选和差异分析.结果 在皮肤恶性黑色素瘤、表皮损伤模型、DNA损伤和紫外线辐射、包皮成纤维细胞对弓形体RH 1型 (ROP5) 突变体感染的反应、白细胞介素-20亚族细胞因子对表皮角化细胞的影响、Egr-1对皮肤成纤维细胞体外过度表达的影响:时间过程、炎性树突状细胞的体外模型7个芯片样本中XPA的表达存在差异 (P<0.05) , 一般呈现下调表达.结论 基于GEO数据库和ScanGEO工具能够高效进行高通量共享数据的筛选和分析.Abstract: Objective To make a parallel mining the data of expression differences of a crucial gene XPA involved in nucleotide excision repair pathway of human skin microarrays by bioinformatics from the system level.Methods Using the ScanGEO, the data of microarrays which included the significant differences expression level of XPA were screened and analyzed from 59 human skin samples in the GEO database. Results There were 7 samples with the down-regulated expression of XPA: cutaneous malignant melanoma, epidermal injury model, DNA damage and UV radiation, foreskin fibroblast response to Toxoplasma gondii RH type 1 (ROP5) mutant infection, interleukin-20 subfamily cytokines effect on epidermal keratinocytes, Egr-1 overexpression effect on skin fibroblasts in vitro: time course, in vitro model for inflammatory dendritic cells.Present expression down. Conclusion Based on the GEO database and ScanGEO, high-throughput shared data can be screened and analyzed efficiently.
-
Key words:
- GEO database /
- Nucleotide excision repair /
- XPA /
- Gene expression differences
-
[1] [1] EDGAR R, DOMRACHEV M, LASH A E.Gene expression omnibus:NCBI gene expression and hybridization array data repository[J].Nucleic Acids Res, 2002, 30 (1) :207-210. [2] [2]LI Z, PENG Z, GU S, et al.Global analysis of mi RNA-m RNA interaction network in breast cancer with brain metastasis[J].Anticancer Res, 2017, 37 (8) :4455-4468. [3] [3]KOEPPEN K, STANTON B A, HAMPTON T H.ScanGEO:parallel mining of high-throughput gene expression data[J].Bioinformatics, 2017, 33 (21) :3500-3501. [4] [4]SUGITANI N, SHELL S M, SOSS S E, et al.Redefining the DNA-binding domain of human XPA[J].J Am Chem Soc, 2014, 136 (31) :10830-10833. [5] [5]ZHOU E Y, WANG H, LIN Z, et al.Clinical and molecular epidemiological study of xeroderma pigmentosum in China:A case series of 19 patients[J].J Dermatol, 2017, 44 (1) :71-75. [6] [6]LIN Y, CHAHALHS, WU W, et al.Association study of genetic variation in DNA repair pathway genes and risk of basal cell carcinoma[J].Int J Cancer, 2017, 141 (5) :952-957. [7] [7]CHAN G L, LITTLE J B.Resistance of plateau-phase human normal and xeroderma pigmentosum fibroblasts to the cytotoxic effect of ultraviolet light[J].Mutat Res, 1979, 63 (2) :401-412. [8] [8]MIYAMOTO I, MIURA N, NIWA H, et al.Mutational analysis of the structure and function of the xeroderma pigmentosum group A complementing protein.Identification of essential domains for nuclear localization and DNA excision repair[J].J Biol Chem, 1992, 267 (17) :12182-12187. [9] [9]ALEKSEEV S, COIN F.Orchestral maneuvers at the damaged sites in nucleotide excision repair[J].Cell Mol Life Sci, 2015, 72 (11) :2177-2186. [10] [10]PARK C H, MU D, REARDON J T, et al.The general transcription-repair factor TFIIH is recruited to the excision repair complex by the XPA protein independent of the TFIIE transcription factor[J].J Biol Chem, 1995, 270 (9) :4896-4902. [11] [11]SUGITANI N, SIVLEY R M, PERRY K E, et al.XPA:A key scaffold for human nucleotide excision repair[J].DNA Repair (Amst) , 2016, 44:123-135. [12] [12]LEE S H, KIM D K, DRISSI R.Human xeroderma pigmentosum group A protein interacts with human replication protein A and inhibits DNA replication[J].J Biol Chem, 1995, 270 (37) :21800-21805. [13] [13]LI L, PETERSON C A, LU X, et al.Mutations in XPA that prevent association with ERCC1 are defective in nucleotide excision repair[J].Mol Cell Biol, 1995, 15 (4) :1993-1998. [14] [14]WANG B, XU Q, YANG H W, et al.The association of six polymorphisms of five genes involved in three steps of nucleotide excision repair pathways with hepatocellular cancer risk[J].Oncotarget, 2016, 7 (15) :20357-20367. [15] [15]HUANG Y, WANG X, NIU X, et al.EZH2 suppresses the nucleotide excision repair in nasopharyngeal carcinoma by silencing XPA gene[J].Mol Carcinog, 2017, 56 (2) :447-463. [16] [16]NAOUALIC, JONES M, NABOULI I, et al.Epidemiological trends and clinicopathological features of cutaneous melanoma in sporadic and xeroderma pigmentosum Tunisian patients[J].Int J Dermatol, 2017, 56 (1) :40-48. [17] [17]ZHANG X, YE Z H, LIANG H W, et al.Down-regulation of mi R-146a-5p and its potential targets in hepatocellular carcinoma validated by a TCGA and GEO based study[J].FEBS Open Bio, 2017, 7 (4) :504-521.
点击查看大图
计量
- 文章访问数: 1942
- HTML全文浏览量: 691
- PDF下载量: 136
- 被引次数: 0