Identifying differentially activated pathways by augmenting activities of transcription factor target genes
There are many approaches to discovering significant pathways in expression profiling.Our objective is to develop a robust approach to capturing differentially expressed pathways in disease expression profiling using pathways that have a transcription factor(TF). After collecting TF target gene, the TF target gene activity information in pathway and the pathway activity information are calculated using a t test. The p values from two analyses are integrated by the Chi-square inverse method. We evaluated our method using two cancer microarray data sets and comparing our results with those from two other pathway analysis methods. Our approach finds differentially expressed pathways that are directly associated with essential thrombocythemia, as well as general pathways that reflect cancer type-nonspecific traits and cancer type-specific pathways in breast cancer data.To test the robustness of our approach, we analyzed two lung data sets. Our approach also provides consistent and biologically reliable results. This study shows that it is better to find significant pathways in expression profiling where the TF target information is integrated within the pathway activity information. Our proposed approach is robust, and can also find cancer type-specific differentially expressed pathways.
Hyunchul Jung Eunjung Lee Jongwon Kim Doheon Lee
Department of Bio and Brain Engineering, KAIST, 373-1 Guseong-dong, Yuseong-gu, Daejeon, 305-701, So Department of Laboratory Medicine and Genetics, Sungkyunkwan University, School of Medicine,Sarnsung
国际会议
The Second International Symposium(OSB08)(第二届国际优化及系统生物学学术会议)
云南丽江
英文
365-374
2008-10-31（万方平台首次上网日期，不代表论文的发表时间）