As an in vitro model for type II human lung cancer, A549 cells resist cytotoxicity via phosphorylation of proteins as demonstrated by many studies. However, to date, no large-scale phosphoproteome investigation has been conducted on A549. Here, we performed a systematical analysis of the phosphoproteome of A549 by using mass spectrometry (MS)-based strategies. This investigation led to the identification of 337 phosphorylation sites on 181 phosphoproteins. Among them, 67 phosphoproteins and 230 phosphorylation sites identified appeared to be novel with no previous characterization in lung cancer.
R currently supports two internal OOP systems (S3 and S4), and several others as add-on packages, such as R.oo, and OOP.
S3 is easy to use but not reliable enough for large software projects. The S3 system emphasize on generic functions and polymorphism. It’s a function centric system which is different from class centric system like JAVA.
不知道空窗期这个词是怎么来的，按照合理的推论应该是来自于西方，泊来之词。
空窗期顾名思义就是没人来爬自己的窗户，引申出来就是没人来找自己约会。这个符合西方的建筑特点，西方的建筑是立体的，体现出来就是窗户多。而爬窗约会也多次出现于西方的文学和影视作品中。《红与黑》中就有于连拿着个梯子，爬窗去偷情的描写。
而我们中国人的建筑是平面型的，体现在墙多，所以说，中国人的单身阶段应该称之为空墙期，意谓没人来翻墙。
苏轼曾做过一首词，名谓《蝶恋花》。词中有云：
花褪残红青杏小。
燕子飞时，绿水人家绕。
枝上柳绵吹又少。
天涯何处无芳草。
墙里秋千墙外道。
墙外行人，墙里佳人笑。
笑渐不闻声渐悄。
多情却被无情恼。
机房放着台机架机，闲着也是耗电，平时偶尔用putty登上去，没有图形界面还是有些不方便。
搜了一下，发现好几个软件可做这样的事，Xming是开源的，所以选择使用Xming+putty来远程连linux的桌面。
试用了一下，果然不错。
需要修改/etc/ssh/sshd_config，添加：
X11Forwrding yes
需要配置一下PuTTY，Connection-SSh-X11中选中Enable X11forwarding
其中X display location里填入localhost:0。
运行Xming，再用putty连到服务器上，运行程序，就OK了。就好像windows下的本地程序一般。整合性很好。
Abstract
SUMMARY: The semantic comparisons of Gene Ontology (GO) annotations provide quantitative ways to compute similarities between genes and gene groups, and have became important basis for many bioinformatics analysis approaches. GOSemSim is an R package for semantic similarity computation among GO terms, sets of GO terms, gene products and gene clusters. Four information content (IC)- and a graph-based methods are implemented in the GOSemSim package, multiple species including human, rat, mouse, fly and yeast are also supported. The functions provided by the GOSemSim offer flexibility for applications, and can be easily integrated into high-throughput analysis pipelines. AVAILABILITY: GOSemSim is released under the GNU General Public License within Bioconductor project, and freely available at http://bioconductor.org/packages/2.6/bioc/html/GOSemSim.html.
[bootstrap](http://en.wikipedia.org/wiki/Bootstrapping_(statistics))是对观测数据集进行有放回（replacement）的随机抽样，以评估总体的各项统计指标。可以用于假设检验、参数估计。好处是并不要求大样本，也不要求正态数据，并且对于不同的统计指标使用的是同样的计算方法。结果也更为可靠，坏处是计算量大。
统计推断(statistical inference)是基于样本统计值的抽样分布来计算的，抽样分布需要从总体中许多的样本来计算，在只有一个样本的情况下，bootstrap对这一随机样本进行有放回的重复抽样，每一个重抽样本与原始随机样本一样大，每次计算相应的抽样的统计值，重复了N次之后，就可以计算统计值的bootstrap分布。
下面做一个小小的试验：
a <- c(seq(1:10), rnorm(50))
#创建一个样本，60个数据，非正态分布的，如下图
泰勒公式学过微积分都应该知道，可以翻wiki复习一下，https://zh.wikipedia.org/wiki/泰勒公式.
用R简单实现一下：
efv <- function(f, value, variable="x", a=0, eps=0.001) {
#estimate function value using Taylor theorem
assign(eval(variable), a)
fv.old <- eval(f)
k <- 1
repeat {
df <- D(f, variable)
if (df == 0)
break
fv.new <- fv.old + eval(df)*(value-a)^k/factorial(k)
if (fv.new - fv.old < eps)
break
fv.old <- fv.new
f <- df
k <- k+1
}
return (fv.new)
}
