转录组定性分析.ppt

A?fusion gene?is a hybrid gene formed from two previously separate genes. It can occur as the result of a?translocation?(A),?interstitial deletion?(B), or?chromosomal inversion?(B). A schematic showing the ways a fusion gene can occur at a chromosomal level. Often, fusion genes are?oncogenes; examples include?BCR-ABL,[1]?TEL-AML1 (ALL?with t(12?; 21)), AML1-ETO (M2 AML?with t(8?; 21)) andTMPRSS2-ERG?with an interstitial deletion on chromosome 21, often occurring in prostate cancer.[2]?Most fusion genes are found from hematological cancers, sarcomas and prostate cancer.[3][4] * DNA层面的结构变异，导致基因位置、结构发生变化，从而形成融合基因。 染色体之间、染色体内（分为相同链和不同链） 作用机制： 出了soapfusion之外，还有defuse，fuionhunter，soapfuse，FusionSeq，tophat-fusion，chimerascan等 之前的方法是没有用到pair-end reads进行过滤的 并且效率比较低 * A：51PE 400-600bp insert size B：36-100PE 200-500bp insert size /2013/14/2/R12/abstract * Linked SNPs?(also called indicative SNPs) do not reside within genes and do not affect protein function. Nevertheless, they do correspond to a particular drug response or to the risk for getting a certain disease. Causative SNPs?affect the way a protein functions, correlating with a disease or influencing a persons response to medication. Causative SNPs come in two forms: Coding SNPs, located within the coding region of a gene, change the amino acid sequence of the genes protein product. Non-coding SNPs, located within the genes regulatory sequences, change the level of gene expression and, therefore, how much RNA and protein is produced. * 贝叶斯理论，先验概率 Basic 过滤，后面RNA-edit里面也会提到 * weblogo 例子：镰刀形细胞贫血 * RNA的编辑有三种机制： 一是碱基替换编辑，编辑复合体识别二级结构钟某些特殊的区域，或者直接识别一段特殊的序列。 二是碱基插入编辑， 三是向导RNA为模板的插入编辑。即RNA编辑所需要的信息或者来自向导RNA，或者来自被编辑的RNA自身。其编辑过程为：gRNA-I首先以其5’端与前提RNA互补配对，从3’向5’方向插入UMP。gRNA-II继续完成编辑的全过程。 次黄嘌呤，通过两个氢键配对碱基C * The editing involves cytidine deaminase that deaminates a cytidine base into a uridine base. An example of C-to-U editing is with the apolipoprotein B gene in humans. Apo B100 is expressed in the liver and apo B48 is expres