Application of the gene expression knock-down data set in the LINCS project

• Main Authors: Chia-Yu Lu, 盧佳妤
• Other Authors: Ueng-Cheng Yang
• Format: Others
• Language: zh-TW
• Published: 2016
• Online Access: http://ndltd.ncl.edu.tw/handle/f9h2wn

碩士 === 國立陽明大學 === 生物醫學資訊研究所 === 104 === The LINCS (Library of Integrated Network-based Cellular Signature) release the amount of gene knock-down expression data. Using the shRNA clones designed by TRC (The NAi consortium), contains 3,936genes with 13,781shRNA clone, observing the gene expression of knock-down experiments in 15 cell lines after treating 96 hours. The expression of 22,268 gene probe sets are infer form L1000 platform estimates 978 important genes, called “landmark genes”. There are 3,936 genes with 6,187 probe sets in the LINCS knock-down data. According to the results of T-test, in the amount of gene perturbation, there are only 3,082probe sets (50%) can be observed the gene expression reduced in some cell lines. Using the weighted method of this research , integrating the expression of gene probe sets to find the efficiency of shRNA clone. Comparing with the results of the GPP (Genetic Perturbation Platform) and the RNAi Core, we find that the shRNA clone have the different effect in different cell lines. For example, TERT is direct activate by MYC, using the success experiments of shRNA clones can observe when knock-down the expression of MYC, the expression of TERT will be raised, validating the regulation between two genes in previous studies. Observing the gene with 3 probe sets, CDK1. The efficiency of different shRNA clones is not consistency with the intrinsic score of TRC in a cell line; but similar with the A549 cell line. The RNAi core in Taiwan collects the shRNA efficiency feedback of users, but the records of cell lines are unclear, so we cannot check the consistency of the knock-down efficiency. Using the LINCS knock-down data can assist us to find the better shRNA clones by given a cell line, but the covering of TRC shRNA clones in LINCS just about 2% currently, the practical utility of choosing shRNA clones need more LINCS data.