Prediction and bioinformatics analysis of human gene expression profiling regulated by amifostine.
- Author:
Bo YANG
1
;
Li-Li CAI
;
Xiao-Hua CHI
;
Xue-Chun LU
;
Feng ZHANG
;
Shuai TUO
;
Hong-Li ZHU
;
Li-Hong LIU
;
Jiang-Wei YAN
;
Chao-Wei TUO
Author Information
1. Department of Geriatric Hematology, Chinese PLA General Hospital, Beijing 100853, China.
- Publication Type:Journal Article
- MeSH:
Amifostine;
pharmacology;
Computational Biology;
Gene Expression;
drug effects;
Gene Expression Profiling;
methods;
Humans;
Microarray Analysis;
Molecular Sequence Annotation
- From:
Journal of Experimental Hematology
2011;19(3):711-716
- CountryChina
- Language:Chinese
-
Abstract:
Objective of this study was to perform bioinformatics analysis of the characteristics of gene expression profiling regulated by amifostine and predict its novel potential biological function to provide a direction for further exploring pharmacological actions of amifostine and study methods. Amifostine was used as a key word to search internet-based free gene expression database including GEO, affymetrix gene chip database, GenBank, SAGE, GeneCard, InterPro, ProtoNet, UniProt and BLOCKS and the sifted amifostine-regulated gene expression profiling data was subjected to validity testing, gene expression difference analysis and functional clustering and gene annotation. The results showed that only one data of gene expression profiling regulated by amifostine was sifted from GEO database (accession: GSE3212). Through validity testing and gene expression difference analysis, significant difference (p < 0.01) was only found in 2.14% of the whole genome (460/192000). Gene annotation analysis showed that 139 out of 460 genes were known genes, in which 77 genes were up-regulated and 62 genes were down-regulated. 13 out of 139 genes were newly expressed following amifostine treatment of K562 cells, however expression of 5 genes was completely inhibited. Functional clustering displayed that 139 genes were divided into 11 categories and their biological function was involved in hematopoietic and immunologic regulation, apoptosis and cell cycle. It is concluded that bioinformatics method can be applied to analysis of gene expression profiling regulated by amifostine. Amifostine has a regulatory effect on human gene expression profiling and this action is mainly presented in biological processes including hematopoiesis, immunologic regulation, apoptosis and cell cycle and so on. The effect of amifostine on human gene expression need to be further testified in experimental condition.
