Fight when you can, against the journal editor or reviewers. Don't always assume they are right and you are wrong, even when it's about English expression. ps. Why should I care? Here is the background info. A reviewer said "topography is not a driving mechanism," and asked the authors to use "topographic-induced xxx." Ok, I may also prefer "topographically-induced xxx," BUT it is NOT wrong to use "topographically-driven xxx." Don't argue with me, just google and see 15+ million citations are out there.
在 描述基因、基因mRNAs或由其编码的蛋白质水平的变化时，经常会因错误使用命名规则而引发混淆。如果作者一会儿提及基因表达水平，一会儿转至蛋白质水 平，再过一会又回到基因，这只会乱上加乱，尤其是当基因和蛋白质同名时。因此，作者应确切地告知读者你提及的到底是基因还是蛋白质。不同物种有不同的命名 规则，但一般来说，基因名称应写成斜体，蛋白质则采用正体。大小写常用于区分不同物种：一般地，对于小鼠、大鼠和鸡，基因名称首字大写，其余小写；对于 人、灵长类和某些家禽/家畜，基因名称均使用大写字母。在描述mRNA时一般使用基因名称(如，“levels of p53 mRNA”)，也可用“for”来加以连接(如，“levels of the mRNA for p53”)。“表达”(expression)一词通常用于描述基因表达，如果用于描述蛋白质和mRNA水平，就会引发混乱；因此，在提及蛋白质时，建议 不用“表达”一词，而是直接改用“level”(或“levels”)。应高度注意所提及物种的适用命名规则；在文章中只要提及蛋白质、基因或mRNA的 名称，应确保其是明白无误的。 • “Expression of the Igf1 gene was increased in our transgenic mice” (这里在提及基因时使用了斜体并加上“gene”一词，读者能够一目了然) • “The levels of IGF1 mRNA were elevated in our patient group” (这是人类基因的正确命名规则) • “The serum IGF1 levels were elevated in the transgenic mice” (这里很显然提及的是蛋白质，使用大写字母是适宜的，尽管物种是小鼠，因为这是小鼠蛋白质的正确命名规则) Protein and gene nomenclature One very common cause of confusion is use of the incorrect nomenclature to describe changes in the levels of genes, their mRNAs or the proteins that they encode. Constant changing from describing gene expression levels to protein levels and back again can also add to the confusion, especially because the names are often the same. Therefore, it needs to be completely clear to the reader exactly what level you are talking about. Nomenclature differs among species, but generally gene names should be described in italics and protein names in normal font. Case (upper vs lower) is often used to distinguish between species: generally, for mouse, rat and chicken, gene names are spelt with an upper case first letter and the rest in lower case; for humans, primates and some domestic species, gene names are spelt with all capital letters. Descriptions of mRNAs generally use the gene name (for example, “levels of p53 mRNA”) or you can refer to the mRNA “for” a given protein (for example “levels of the mRNA for p53”). The word “expression” is usually used to describe gene expression and can induce confusion when used to describe protein and mRNA levels; in most cases referring to proteins the word “expression” can simply be replaced with the word “level” (or “levels”). Be aware of the correct nomenclature for your species of subject and ensure that everywhere you refer to a protein, gene or mRNA by name in the text it is completely clear which of those you are referring to. • “Expression of the Igf1 gene was increased in our transgenic mice” (use of italics and the word “gene” ensure that no confusion is possible here). • “The levels of IGF1 mRNA were elevated in our patient group” (correct nomenclature for human genes). • “The serum IGF1 levels were elevated in the transgenic mice” (here, it is clear that the protein is being referred to; capitals are appropriate in this case, even though the species is mouse, because it is the correct nomenclature for the mouse protein). Dr Daniel McGowan 分子神经学博士 理文编辑学术总监
I was updating my Blog on my experience on MU572 from HNL to PVG. I realized that I used "Excuse me" in a way that most of us never learned in class (in China). My blog is at http://blog.sciencenet.cn/home.php?mod=spaceuid=306792do=blogid=562351 So, I decided to google the phrase. Here is the result from http://en.wiktionary.org/wiki/excuse_me excuse me ( US ) Said as a request to repeat information. (Mandarin: 請再説一遍 ) Said as a request for an individual's attention. (Mandarin: 請問 ) Said as a request to pass. ( Mandarin: trad. 借過 , simpl. 借 过 ) Sorry , as an apology. (Mandarin: 對不起 ) Said as a request for an apology. (There is no translation, but I hope you know what it means from the way I used it to express myself on MU572. I don't think it's the language, but my tone, that expressed myself so well that the person immediately said: 對不起 , 對不起 , which is Chinese for sorry--in case you don't know any Chinese. )
第一次看到这个名词:insulator element(金山词霸把它译成绝缘体) A role for insulator elements in the regulation of gene expression response to hypoxia Nucl. Acids Res. (2012) 40(5): 1916-1927 first published online November 8, 2011 doi:10.1093/nar/gkr842 摘要:Hypoxia inducible factor (HIF) up-regulates the transcription of a few hundred genes required for the adaptation to hypoxia. This restricted set of targets is in sharp contrast with the widespread distribution of the HIF binding motif throughout the genome.(提出问题:HIF binding motif多,target少;顺式作用元件多,调节的目标蛋白少) Here, we investigated the transcriptional response of GYS1 and RUVBL2 genes to hypoxia to understand the mechanisms that restrict HIF activity toward specific genes(以两个具体的基因为研究模型). GYS1 and RUVBL2 genes are encoded by opposite DNA strands and separated by a short intergenic region (~1 kb) that contains a functional hypoxia response element equidistant to both genes. However, hypoxia induced the expression of GYS1 gene only(特殊情况出现) . Analysis of the transcriptional response of chimeric constructs derived from the intergenic region revealed an inhibitory sequence whose deletion allowed RUVBL2 induction by HIF(发现inhibitory sequence,这个就是绝缘子). Enhancer blocking assays, performed in cell culture and transgenic zebrafish, confirmed the existence of an insulator element within this inhibitory region that could explain the differential regulation of GYS1 and RUVBL2 by hypoxia(进一步实验). Hence, in this model, the selective response to HIF is achieved with the aid of insulator elements(为什么调节靶蛋白少了?因为顺式作用元件后面接了个绝缘子,呵呵有点意思) . This is the first report suggesting a role for insulators in the regulation of differential gene expression in response to environmental signals. 启示: 根据这个例子基因间序列也可能是有功能的,所以图位克隆的时候如果预测基因区无多态性,可以暂缓考虑跳楼.这个绝缘子估计目前用任何软件都预测不出来.
简介：J DIABETES COMPLICAT杂志属于医学行业，“内分泌学与代谢”子行业的偏低级别杂志。 投稿难度评价：影响因子不高，影响力也比较小，审稿时间也偏长，但容易投中。 审稿速度：较慢，6周-12周 级别/热度：黑 Medsci评语：冷门杂志，关注人极少。 journal of diabetes and its complications 期刊发表中国人的SCI文章列表，共计 7 篇文章 Guo QH; Lu JM; Pan CY; Lu ZH; Zou XM; Mu YM The kidney expression of matrix metalloproteinase-9 in the diabetic nephropathy of Kkay mice 2008 摘要 | google Wong J; Molyneaux L; Zhao DM; Constantino M; Gray RS; Twigg SM; Xu ZR; Yue DK Different accelerators to early-onset Type 2 diabetes: a comparison of Anglo-Celtic and Chinese patients 2008 摘要 | google Ren XY; Li YN; Qi JS; Niu T Peroxynitrite-induced protein nitration contributes to liver mitochondrial damage in diabetic rats 2008 摘要 | google Heng XP; Chen KJ; Hong ZF; He WD; Chu KD; Chen WL; Chen XZ; Zheng HX; Chen L; Yang LQ; Guo F; Lin ML Glucose endothelial cytotoxicity and protection by Dan Gua-Fang, a Chinese herb prescription in huVEC in hyperglycemia medium 2009 摘要 | google Xie XS; Wang YJ; Zuo C; Fan JM; Li XJ A case report of an effective treatment for diabetic foot ulcers with integration of traditional Chinese medicine and Western medicine 2009 摘要 | google Tam VHK; Lam EPK; Chu BCY; Tse KK; Fung LM Incidence and progression of diabetic retinopathy in Hong Kong Chinese with type 2 diabetes mellitus 2009 摘要 | google Lin Y; Ye SD; Chen Y; Li XC; Yang GW; Fan AH; Wang YX The effect of simvastatin on the serum monocyte chemoattractant protein-1 and intracellular adhesion molecule-1 levels in diabetic rats 2009 摘要 | google
“方法” 部分应包含足够的信息以供其他研究者准确重复你描述的试验；如果其中有关键信息遗漏，别人就无法完全重复你的实验条件；这会引起结果不一致，有可能造成误会，甚至还会被人指责造假。所以“方法”部分要力求全面。 “ 方法”部分应该使用过去时态，例如：“sections were stained with…” and “data were analyzed using…”。但是在提及图表时应使用现在时，例如：“The patients’ clinical characteristics are listed in Table 1”。 此外，当你在叙述某个事物的定义或当前对它公认的看法时也要用现在时，例如：“the cells were subjected to hypoxia, which induces HIF-1 expression…”。这句话中，虽然实验部分是用的过去时，但由于缺氧(hypoxia) 导致HIF-1是一个普遍现象而不是限定于本文的结果，因此后面半句应该用现在时。 要列出所有试剂的供应商以及设备的厂家；有的期刊还要求列出其地址，即国家、州(如为美国)和市。叙述设备、试剂盒、试剂的时候应该用常用术语来具体描述，不要只用厂商的专门术语或只写型号。比如，不要写成：“Absorbance in each well was measured at a wavelength of 492 nm using a Beckman Coulter AD 340C”，因为大多数人都对Beckman Coulter AD 340C没有任何概念；应该写成：“Absorbance in each well was measured at a wavelength of 492 nm using a multi-well plate reader (AD 340C, Beckman Coulter)”，或者“Absorbance in each well was measured at a wavelength of 492 nm using an AD 340C multi-well plate reader (Beckman Coulter Inc, Fullerton, CA, USA)”。 “方法”部分只能包括最终得出结果的实验方法。如果某个试验失败了或者没能提供你需要的结果，而且你已经决定论文中不提这些结果，那么也没有必要去谈其试验方法。用适当的子标题把各种不同目的的材料和方法分类。如果期刊设有“补充方法 ”（Supplementary Methods）部分，则可用这部分来详述细节，并让纸面刊出的“方法”部分保持简短。新方法应该详细叙述以便他人重复；标准和常用技术只须引用文献即可，但如果你的方法和文献有差异之处应予说明。尤其要保证所有单位都正确，实验条件(如时间、温度)都清楚。最后，如果开展了统计学分析来评价研究结果的意义，则应在“方法”的最后一段叙述你的统计学方法，包括所选择的显著性阈值。 实例 “…homogenates were spun at 10,000 × g and 4 °C for 12 min” 这句话包含了时间、温度两个重要细节。而： “…homogenates were spun at 10,000 × g” 和更简化的 “homogenates were centrifuged” 两个句子中就遗漏这些细节。这些细节有可能对得到你的结果很重要，所以应该给出。 同理，不要只写：“Then, 10 μl of a propidium iodide solution was added to the cells”，因为这对读者毫无意义，除非他们知道该溶液的浓度。应该写成：“Propidium iodide was added to the wells to a final concentration of 0.5 μg/ml”。 下图节选自《The Journal of Clinical Investigation》所发表的一篇论文(doi:10.1172/JCI37155;经同意转载)的方法部分。它显示了“方法”部分的各种要素以及他们如何组合的。 核查清单 1. 用清楚的子标题列出用于不同目的的方法和材料。 2. 研究方法用过去时。 3. 新方法给出充足的细节以便他人重复。 4. 已有方法可用参考文献。 5. 写明厂家/供应商，必要时应提供地址。 6. 说明所采用的统计学方法。 英文原文 Methods: what you did The methods section of your manuscript should contain sufficient information for a capable researcher to accurately repeat the experiments you describe; if essential information is left out, the exact conditions might not be replicated, leading to different results, potential misunderstandings, or worse, accusations of falsification. Thus, the methods section needs to be comprehensive. The methods section should be written in the past tense; for example, “sections were stained with…” and “data were analyzed using…”. An exception to this is references to tables or figures in the manuscript, for example “The patients’ clinical characteristics are listed in Table 1”. Another exception is when providing a definition or describing the current consensus on something: for example, “the cells were subjected to hypoxia, which induces HIF-1 expression…”. Here, although what was done is described in the past tense, the fact that hypoxia induces HIF-1 is described in the present tense because it is a general phenomenon not limited to the present paper. The suppliers of all reagents and the manufacturers of all equipment used should be listed; some journals also request that the locations, that is, city, state (if in the USA) and country, of these companies are provided. When describing equipment, kits, or reagents, you should use familiar terms to define the particular item you are describing, rather than just a manufacturer-specific term or model number. For example rather than writing “Absorbance in each well was measured at a wavelength of 492 nm using a Beckman Coulter AD 340C”, which would be meaningless to the majority of readers, you should write “Absorbance in each well was measured at a wavelength of 492 nm using a multi-well plate reader (AD 340C, Beckman Coulter)” or perhaps “Absorbance in each well was measured at a wavelength of 492 nm using an AD 340C multi-well plate reader (Beckman Coulter Inc, Fullerton, CA, USA)”. Methods should only be included if the results of the described experiments are provided; if an experiment you performed didn’t work, or didn’t provide the results you needed, and you have opted to leave the results out of your paper, then there is no need to describe the associated methods. Use appropriate subheadings to separate materials and methods with different purposes. If available, use a Supplementary Methods section to provide detailed information so that the printed methods section can be kept brief. Novel techniques need to be described in detail so that they can easily be replicated, but established and commonly used techniques can be referenced as long as any variations between the method used in the present study and that described in the cited study are clearly described. Above all, be precise and ensure that all units are correct and all conditions (for example, times and temperatures) are clear. Finally, if any statistical analysis was performed to assess the significance of your data, describe the statistical methods used, including the threshold(s) selected for significance, at the end of the methods section. Examples The sentence “…homogenates were spun at 10,000 × g and 4 °C for 12 min” includes the important details of time and temperature that would have been missing if the author simply wrote “…homogenates were spun at 10,000 × g”, or even more simply “homogenates were centrifuged”. These details could have been essential to obtaining the result you did, and so should be explained. Similarly, rather than saying “Then, 10 μl of a propidium iodide solution was added to the cells”, which is meaningless unless the reader knows the concentration of the propidium iodide solution, you should write “Propidium iodide was added to the wells to a final concentration of 0.5 μg/ml”. The figure below, showing a couple of excerpts from the methods section of paper published in The Journal of Clinical Investigation (doi:10.1172/JCI37155; reproduced with permission), indicates the important components of a methods section and how these fit together. Checklist 1. Clear subheadings for methods/materials with different purposes, with materials described first 2. Methods described in past tense 3. Novel methods described in full detail, sufficient for a capable researcher to reproduce 4. Established methods referenced to previous literature 5. Suppliers/manufacturers provided, including locations if requested 6. Statistical methods described Dr Daniel McGowan 分子神经学博士 理文编辑学术总监
Laboratory Head Professor Emma Whitelaw Summary Epigenetics is the study of mechanisms which modify DNA structure in subtle ways, and thus change gene expression, without influencing the DNA base sequence. Characteristics like physical appearance and personality traits are commonly considered to be the result of interactions between genetic and environmental factors alone. However, genetically identical individuals, raised in similar environments, for example identical twins, show variation in some phenotypes. These variations may be the result of epigenetic differences between these individuals. At this stage, the research is best carried out using mouse models but, in the near future, Professor Whitelaw hopes to be able to study humans directly. A successful grant application has resulted in the establishment of the Australian Centre for Cancer Epigenetics at the Institute. The centre has expanded the DNA sequencing and imaging capacities available at QIMR, not only in cancer research, but also for scientists working in other areas. The laboratory has been developing a mouse model of fetal alcohol syndrome and anticipate that this will inform the community of the effects of maternal consumption of alcohol during pregnancy. http://www.qimr.edu.au/page/Lab/Epigenetics/Epigenetics_student_projects/
i.e. 是拉丁文 id est 的缩写，它的意思就是“那就是说，换句话说”，等同于“that is，in other words” ，目的是用来 进一步 解释前面所说的观点。 e.g. 是拉丁文 exempli gratia 的缩写，它的意思是“举个例子，比如”，等同与“for example”,目的就是用几个例子来说明前面的观点。 etc.就比较好理解了，它是 etcetera 的缩写，意思是“等等”，相当于“and so on” e.g. 和 etc. 不能出现在同一句话中，因为 e.g. 是表示泛泛的举几个例子，并没有囊括所有的实例，其中就已经包含“等等”，如果再加一个 etc. 就画蛇添足了，例如下面这句话就是错的： Writing instructors focus on a number of complex skills that require extensive practice (e.g., organization, clear expression, logical thinking, etc.)
上海交通大学瑞金医院神经科，中科院健康科学研究所神经变性疾病研究组的研究人员发表了题为“DJ-1 modulates the expression of Cu/Zn-superoxide dismutase-1 through the Erk1/2–Elk1 pathway in neuroprotection”的文章，揭示了DJ-1在神经保护中抗氧化应激作用的新机制。 这一研究成果发表在Annals of Neurology杂志上。 http://onlinelibrary.wiley.com/journal/10.1002/(ISSN)1531-8249 Annals of Neurology Country : United States Subject Area : Neuroscience Subject Category : Neuroscience (miscellaneous) Publisher : John Wiley Sons Inc. . Publication type : Journals. ISSN : 03645134, 15318249 Coverage: 1977-2010 H Index : 182 Scope: Annals of Neurology publishes articles of broad interest with potential for high impact in understanding the mechanisms and treatment of Annals of Neurology publishes articles of broad interest with potential for high impact in understanding the mechanisms and treatment of diseases of the human nervous system. All areas of clinical and basic neuroscience, including new technologies, cellular and molecular neurobiology, population sciences, and studies of behavior, addiction, and psychiatric diseases are of interest to the journal. ( source ) 陈生弟，男，1955年出生，教授、主任医师、医学博士、博士生导师，附属瑞金医院党委副书记、神经科主任、神经病学教研室主任，研究所所长。1978年毕业于原上海第二医科大学，1986年获得原上海第二医科大学神经病学硕士学位，1991年获得原上海第二医科大学神经病学博士学位。 陈教授在以帕金森病和老年性痴呆为代表性的神经变性疾病的基础及临床研究领域取得了丰硕的成果和业绩，为我国神经病学科的快速发展和在国内外学术地位的迅速提升做出了重要贡献，8次应邀在国外学术会议上作大会报告及担任会议主席，在国际上尤其是在帕金森病及运动障碍性疾病研究领域已具有相当的知名度。先后主持、参加完成了包括国家“973”、“863”计划在内的科研基金40项，获得国家及省部级科技进步奖项19项。 陈教授发表学术论文300余篇，其中SCI收录近40篇；主编（译）7部以及参编近30部专著；当选“百千万人才工程”国家级人选,获得包括国家有突出贡献中青年专家、全国中青年医学科技之星、首批上海市医学领军人才、第六、八届市科技精英提名奖、市十佳优秀启明星、十佳医师、首届和第二届高校优秀青年教师、卫生系统青年最高奖“银蛇奖”二等奖，上海交通大学医学院高尚师德奖等在内的许多项荣誉称号。
Many people tell me: "Thank you for your help (with English editing). I hope I can help other people some day." This makes me very happy. I am sure there is a Chinese expression for such a kind thought. In English, it is called "pay it forward." (Clearly, I don't expect these people to edit my English writing, though they may point out the mistakes and typos I have in my Blog.) If we can all help others without expecting payback and people pay it forward, what a wonderful world we can all live in! Note: The expression " pay it forward " is used to describe the concept of asking that a good turn be repaid by having it done to others instead.
What is the "opposite" of “I love you”? You can start with “I hate you.” If you don’t want to sound like a 5-year-old child, you can try: I dislike that guy. I can’t stand that idiot. I can’t bear looking at him.
I dont mean to be rude; I am just borrowing a phrase I heard often in the past. Ms. LI Xia is correct about the way What a shame is used normally. Of course, one might say What a shame in a VERY COLD tone, and think privately: Hell, you deserve it! Or one may say: Shame on you with a big smile on her face, just to tease you Note: It's the economy, stupid was a phrase in American politics widely used during Bill Clinton 's successful 1992 presidential campaign against George H. W. Bush .
参考文献： Microarray data analysis and mining approaches Francesca Cordero , Marco Botta and Raffaele A. Calogero Corresponding author: Raffaele A. Calogero, Department of Clinical and Biological Sciences, University of Torino, Italy. Briefings in Functional Genomics and Proteomics 2008 6(4):265-281; doi:10.1093/bfgp/elm034 Although two-sample differential expression analysis is probably the most common experiment, multi-series time-course microarray experiments are useful approaches for exploring biological processes. In these types of experiments, the researcher is frequently interested in studying gene expression changes over time and in evaluating trend differences between the various experimental groups . The large amount of data, multiplicity of experimental conditions and the dynamic nature of the experiments pose great challenges to data analysis. A comprehensive review of research in time series expression data analysis was published by Bar-Joseph in 2004 . Recently, maSigPro Conesa has published two methods for time-course microarray data analysis . One is maSigPro , and is part of Bioconductor packages. ...This will ultimately be used to find what are the profile differences between experimental groups. ANOVA-SCA The other is ANOVA-SCA and combines ANOVA-modeling and a dimension reduction technique to extract targeted signals from data bypassing structural noise. ANOVA-SCA basically applies PCA to the estimated parameters in each source of variation of an ANOVA model. ANOVASCA seems an effective approach for separating the data variability present in a complex time course experiment to extract the signal of interest from noisy data . fully Bayesian approach Angelini and coworkers have recently described a fully Bayesian approach to detect differentially expressed genes in time-course experiments. Their approach allows to explicitly use biological prior information and deals with various technical difficulties that arise in microarray timecourse experiments such as a small number of observations, non-uniform sampling intervals, missing or multiple data and temporal dependence between observations for each gene. Authors compared their method with that implemented in R-package time course and in the EDGE software claiming that their algorithm provides results which are much closer to a biologists choice and delivers a lower percentage of false positive and negative answers than other algorithms . Fischer and coworkers have compared methods for identifying differentially expressed genes on time-series microarray data simulated from artificial gene networks. They suggest the use of ANOVA variants of Cui and Churchill on the bases of simulated data and Efron and Tibshiranis empirical Bayes Wilcoxon rank sum test in the case experimental background cannot be effectively corrected. CHPM Shi has instead proposed an approach, based on a probabilistic continuous hidden process model ( CHPM ), to identify the various biological processes involved in a specific biological experiment. This method integrates time series expression data with GO biological processes , modelling the observed gene expression levels as being generated by a combination of multiple GO biological processes whose activity levels vary over time. OTHER TOOLs： STEM Short Time-series Expression Miner (STEM) (~8 time points or fewer). STEM allows researchers to identify significant temporal expression profiles and the genes associated with these profiles and to compare the behavior of these genes across multiple conditions. STEM is fully integrated with the Gene Ontology (GO) database supporting GO category gene enrichment analyses for sets of genes having the same temporal expression pattern. STEM also supports the ability to easily determine and visualize the behavior of genes belonging to a given GO category or user defined gene set, identifying which temporal expression profiles were enriched for these genes. DREM Dynamic Regulatory Events Miner (DREM) takes as input time series gene expression data and input that associates transcription factors with the genes they regulate . This regulatory information could come from Chromatin Immunoprecipitation (ChIP)-chip experiments or transcription factor binding site motif information. The transcription-factor gene regulation input does not need to be associated with specific time points. DREM after executing a computational method described in outputs an annotated dynamic regulatory map based on the data that can be interactively explored. The dynamic regulatory map highlights bifurcation events in the time series, that is places in the time series where sets of genes which previously had roughly similar expression level diverge. Often these bifurcation events can be explained by transcription factors selectively regulation a certain subset of genes. DREM annotates these events with transcription factors potentially responsible for them. DREM is related to another time series expression analysis software the Short Time-series Expression Miner ( STEM ) . While STEM focuses on identifying independent significant patterns in short time series data , DREM provides a global map of the gene regulation of the time series . The DREM method also incorporates in transcription factor-gene regulation information. DREM also is not limited to analyzing short time series data as STEM is. Some of the input file formats and options are the same in DREM as in STEM, in particular options related to gene filtering and the Gene Ontology analysis. For these aspects of DREM which are the same as in STEM, the relevant portions of the STEM manual have been incorporated into this manual. BiGGEsTS An integrated environment for the biclustering ( Madeira and Oliveira, 2004 ) analysis of time series gene expression data . Biclusters may be analyzed with Gene Ontology annotations to find out which contain statistically relevant biological information or even filtered or sorted according to several numerical and statistical criteria. 应用举例： STEM Comprehensive transcriptional profiling of NaCl-stressed Arabidopsis roots reveals novel classes of responsive genes Yuanqing Jiang and Michael K Deyholos* Address: Department of Biological Sciences, University of Alberta, Edmonton, Canada BMC Plant Biology 2006, 6:25 doi:10.1186/1471-2229-6-25 用STEM做了聚类，然后以GOTerm为层次标注各term中包含哪些cluster，有几个。 Combined analysis reveals a core set of cycling genes Yong Lu 1 , Shaun Mahony 2 , Panayiotis V Benos 2 , Roni Rosenfeld 3 , Itamar Simon 4 , Linda L Breeden 5 and Ziv Bar-Joseph 1 ,3 1 Department of Computer Science, Carnegie Mellon University, Forbes Avenue, Pittsburgh, Pennsylvania 15213, USA 2 Department of Computational Biology, University of Pittsburgh Medical School, Lothrop Street, Pittsburgh, Pennsylvania 15213, USA 3 Machine Learning Department, Carnegie Mellon University, Forbes Avenue, Pittsburgh, Pennsylvania 15213, USA 4 Department of Molecular Biology, Hebrew University Medical School, Jerusalem, Israel 91120 5 Basic Sciences Division, Fred Hutchinson Cancer Center, Fairview Avenue N, Seattle, Washington 98109, USA Genome Biology 2007, 8 : R146 doi:10.1186/gb-2007-8-7-r146 用STEM做了GO的显著性检验，P值，似乎大材小用 实战 STEM，总结如下： 1.用已经筛出来的差异基因做为输入，另外，用gene symbol来去除冗余（多个探针组对应同一蛋白，可以用UniRef）；GO注释文件也以Gene symbol为ID（GO注释本来就是 注释 蛋白的，而非基因本身），但不可带有基因列表以外的Gene symbol。 2.可选STEM Cluster Method和K-means，设定Cluster数，进行GO Term富集分析。
multi-word expression，自2003年第一届aclMWEsworkshop来，几乎每年都有这样的一个workshop.关注焦点有identification,interpretation,disambiguation and applications。07年主要讨论抽取方法，08年则侧重评测，语料库的建设。 但中文的多次表达定义应如何？thinking...
标签: expression
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