pipeline risk（差异表达基因分析：差异倍数（fold change）, 差异的显著性（P-value））

本文目录

• 差异表达基因分析：差异倍数(fold change), 差异的显著性(P-value)
• 介绍静园的历史的英语作文

差异表达基因分析：差异倍数(fold change), 差异的显著性(P-value)

Differential gene expression analysis：差异表达基因分析 Differentially expressed gene (DEG)：差异表达基因 差异表达分析是目前比较常用的识别疾病相关miRNA以及基因的方法，目前也有很多差异表达分析的方法，但比较简单也比较常用的是Fold change方法。 它的优点是计算简单直观，缺点是没有考虑到差异表达的统计显著性；通常以2倍差异为阈值，判断基因是否差异表达。Fold change的计算公式如下： 即用疾病样本的表达均值除以正常样本的表达均值。 差异表达分析的目的： 识别两个条件下表达差异显著的基因，即一个基因在两个条件中的表达水平，在排除各种偏差后，其差异具有统计学意义。我们利用一种比较常见的T检验（T-test）方法来寻找差异表达的miRNA。T检验的主要原理为：对每一个miRNA计算一个T统计量来衡量疾病与正常情况下miRNA表达的差异，然后根据t分布计算显著性p值来衡量这种差异的显著性，T统计量计算公式如下： 差异倍数(fold change) fold change翻译过来就是倍数变化，假设A基因表达值为1，B表达值为3，那么B的表达就是A的3倍。一般我们都用count、TPM或FPKM来衡量基因表达水平，所以基因表达值肯定是非负数，那么fold change的取值就是(0, +∞). 为什么我们经常看到差异基因里负数代表下调、正数代表上调？因为我们用了log2 fold change。 当expr(A) 《 expr(B)时，B对A的fold change就大于1，log2 fold change就大于0（见下图），B相对A就是上调； 当expr(A) 》 expr(B)时，B对A的fold change就小于1，log2 fold change就小于0。 通常为了防止取log2时产生NA，我们会给表达值加1（或者一个极小的数），也就是log2(B+1) - log2(A+1). 【需要一点对数函数的基础知识】为什么不直接用表达之差，差值接有正负啊？ 假设A表达为1，B表达为8，C表达为64；直接用差值，B相对A就上调了7，C就相对B上调了56；用log2 fold change，B相对A就上调了3，C相对B也只上调了3.  通过测序观察我们发现，不同基因在细胞里的表达差异非常巨大，所以直接用差显然不合适， 用log2 fold change更能表示相对的变化趋势。 虽然大家都在用log2 fold change，但显然也是有缺点的： 一、到底是5到10的变化大，还是100到120的变化大？ 二、5到10可能是由于技术误差导致的。所以当基因总的表达值很低时，log2 fold change的可信度就低了，尤其是在接近0的时候。 A disadvantage and serious risk of using fold change in this setting is that it is biased and may misclassify differentially expressed genes with large differences (B − A) but small ratios (B/A), leading to poor identification of changes at high expression levels. Furthermore, when the denominator is close to zero, the ratio is not stable, and the fold change value can be disproportionately affected by measurement noise. 差异的显著性(P-value)  这就是统计学的范畴了，显著性就是根据假设检验算出来的。假设检验首先必须要有假设，我们假设A和B的表达没有差异（H0，零假设），然后基于此假设，通过t test（以RT-PCR为例）算出我们观测到的A和B出现的概率，就得到了P-value， 如果P-value《0.05，那么说明小概率事件出现了，我们应该拒绝零假设，即A和B的表达不一样，即有显著差异。 显著性只能说明我们的数据之间具有统计学上的显著性，要看上调下调必须回去看差异倍数。 对于得到的显著性p值，我们需要进行多重检验校正（FDR），比较常用的是BH方法（Benjamini and Hochberg, 1995）。 这里只说了最基本的原理，真正的DESeq2等工具里面的算法肯定要复杂得多。 这张图对q-value（校正了的p-value）取了负log，相当于越显著，负log就越大，所以在火山图里，越外层的岩浆就越显著，差异也就越大。 只需要看懂DEG结果的可以就此止步，想深入了解的可以继续。下面可以继续讨论的问题有： 1、RNA-seq基本分析流程/2、 2、DEG分析的常用算法/3、 3、常见DEG工具的方法介绍和相互比较前言 做生物生理生化生信数据分析时，最常听到的肯定是“差异(表达)基因分析”了，从最开始的RT-PCR，到基因芯片microarray，再到RNA-seq，最后到现在的single cell RNA-seq，统统都在围绕着差异表达基因做文章。 （开个脑洞：再下一步应该会测细胞内特定空间内特定基因的动态表达水平了） 表达量 ：我们假设基因转录表达形成的mRNA的数量反映了基因的活性，也会影响下游蛋白和代谢物的变化。我们关注的是 基因的表达 ，不是结构，也是不是isoform。 为什么差异基因分析这么流行？ 一是中心法则得到了确立，基因表达是核心的一个环节，决定了下游的蛋白组和代谢组； 二是建库测序的普及，获取基因的表达水平变得容易。 在生物体内，基因的表达时刻都在动态变化，不一定服从均匀分布，在不同时间、发育程度、组织和环境刺激下，基因的表达肯定会发生变化。 差异基因分析主要应用在： 发育过程中关键基因的表达变化 - 发育研究 突变材料里什么核心基因的表达发生了变化 - 调控研究 细胞在受到药物处理后哪些基因的表达发生了变化 - 药物研发 目前我们对基因和转录组的了解到什么程度了？ 基本的建库方法？建库直接决定了我们能测到什么序列，也决定了我们能做什么分析！ 基因表达的normalization方法有哪些？ 第一类错误、第二类错误是什么？ 多重检验的校正？FDR？10x流程解释 The mean UMI counts per cell of this gene in cluster i The log2 fold-change of this gene’s expression in cluster i relative to other clusters  The p-value denoting significance of this gene’s expression in cluster i relative to other clusters, adjusted to account for the number of hypotheses (i.e. genes) being tested.The differential expression analysis seeks to find, for each cluster, genes that are more highly expressed in that cluster relative to the rest of the sample. Here a differential expression test was performed between each cluster and the rest of the sample for each gene. The Log2 fold-change (L2FC) is an estimate of the log2 ratio of expression in a cluster to that in all other cells. A value of 1.0 indicates 2-fold greater expression in the cluster of interest. The p-value is a measure of the statistical significance of the expression difference and is based on a negative binomial test. The p-value reported here has been adjusted for multiple testing via the Benjamini-Hochberg procedure. In this table you can click on a column to sort by that value. Also, in this table genes were filtered by (Mean UMI counts 》 1.0) and the top N genes by L2FC for each cluster were retained. Genes with L2FC 《 0 or adjusted p-value 》= 0.10 were grayed out. The number of top genes shown per cluster, N, is set to limit the number of table entries shown to 10000; N=10000/K^2 where K is the number of clusters. N can range from 1 to 50. For the full table, please refer to the "differential_expression.csv" files produced by the pipeline.不同单细胞DEG鉴定工具的比较 Comparative analysis of differential gene expression analysis tools for single-cell RNA sequencing data For data with a high level of multimodality, methods that consider the behavior of each individual gene, such as DESeq2, EMDomics, Monocle2, DEsingle, and SigEMD, show better TPRs. 这些工具敏感性高，就是说不会漏掉很多真的DEG，但是会包含很多假的DEG。 If the level of multimodality is low, however, SCDE, MAST, and edgeR can provide higher precision. 这些工具精准性很高，意味着得到的DEG里假的很少，所以会漏掉很多真的DEG，不会引入假的DEG。time-course DEG analysis Comparative analysis of differential gene expression tools for RNA sequencing time course data  参考： Question: How to calculate "fold changes" in gene expression? Exact Negative Binomial Test with edgeR Differential gene expression analysis

介绍静园的历史的英语作文

英文介绍Park, located in Heping District Tianjin city, Anshan Road No. 70, (the original palaceIsland Japanese Concession District Road), founded in 1921. On the early name dry Park, as the Beiyang government minister Lu Zongyu mansion in japan. 1929 July to 1931 November, the last emperor Pu Yi lived in this, renamed "Jing Yuan", meaning "to keep quiet I magnanimous".Park, located in Heping District Tianjin city, Anshan Road No. 70, built in 1921, covers an area of about 3016 square meters, construction area of 1900 square meters, is a special level of protection in Tianjin city historic buildings, Tianjin municipal units of cultural relics protection. On the early name dry Park, as the Beiyang governmentminister Lu Zongyu in Japan in 1929 July - 1931 mansion, in November, the last emperor Puyi with Queen’s Wanrong, imperial concubine Wenxiu in the residential,renamed "Park", meaning "to keep quiet I magnanimous". The park has eclectic brick wood structure buildings a, thawing Spanish style and Japanese style in one, lush,quiet and pleasant, is a typical representative of Tianjin concession period courtyardprivate residence.Puyi moved out after several different owners, park, has experienced many changes,using successively as office space and residential, hospital, building erection of illegalconstruction 600 square metres, to consolidation has become a veritable decrepit. In July 20, 2007, finishing after repair of Jingyuan as national AAA level scenic spotsopen, has won the "China tourism brand charm scenic spot", Tianjin patriotism education base, the national popular science education base and the national youth civilization title.1925 by Feng Yuxiang out of Beijing Pu Yi, Zhang Yuan came to Tianjin, after 2 yearswith Queen’s Wanrong, imperial concubine Wenxiu came to live with the street dry garden. Pu Yi the dry Park was renamed Park, take "to keep quiet I noble spirit" in italy. PuYi in the park "wait and see, wait time", to continue his absurd emperor career,dormant standby, attempts to restore the Manchu empire. 9.18 after the incident, Puyiof the opportunity came, he after a quiet garden with Japanese spy chief Toihara Kenji commune, in 1931 November 10 night from Jingyuan quietly slipped out the back door, secretly left Tianjin, arrived in the northeast, and the assistance of the Japaneseemperor of Manchukuo, as Kant on the. Park after the departure of the last emperor,become a veritable garden of quiet.After the liberation of new China, Jing Yuan by the national possession and as acivilian use, hospital in succession private bus cover up to live more than 40 households, the original architectural style has ceased to exist, the main building shoedestruction. Because of disrepair, building drainage pipeline corrosion seriously, often blocked, resulting in an overflow of sewage, environmental mess, people suffer. Times change, historical change, 80 Park several easy advocate, to the beginning of this century, here has become home to 45 residents of residential compounds. "Old times before walking Wang Yan, flying into the homes of ordinary people". Generation of the imperial apartments, has become the common people residence. These residents ride luangai private, there are a lot of illegal construction, the original principal is also dilapidated buildings, the original style almost does not exist, but there is a big security risk, the competent department at the time it even included in the ranks of dangerous buildings. Generation of garden park, there was the danger of being dismantled.中文介绍静园，位于天津市和平区鞍山道70号，（原日本租界区宫岛路），始建于1921年。静园初名乾园，为北洋政府驻日公使陆宗舆宅邸。1929年7月—1931年11月，末代皇帝溥仪居住于此，更名“静园”，寓意“静以养吾浩然之气”。静园，位于天津市和平区鞍山道70号，建于1921年，占地面积约3016平米，建筑面积约1900平米，为天津市特殊保护级别的历史风貌建筑、天津市文物保护单位。静园初名乾园，为北洋政府驻日公使陆宗舆宅邸，1929年7月—1931年11月，末代皇帝溥仪携皇后婉容、淑妃文绣于此居住，更名“静园”，寓意“静以养吾浩然之气”。园内建有折中主义砖木结构楼房一座，融西班牙式和日式风格于一体，草木葱郁，静谧宜人，是天津租界时期庭院式私人宅邸的典型代表。溥仪搬出后，静园几番易主，历经变迁，先后作为办公用房和住宅使用，院内、楼内搭建违章建筑600平方米，到整理前已成为名副其实的大杂院。2007年7月20日，整理修复后的静园作为国家AAA级旅游景区对外开放，先后获得“中国旅游品牌魅力景区”、天津市爱国主义教育基地、全国科普教育基地和全国青年文明号等称号。1925年溥仪被冯玉祥撵出北京后，来到天津张园，2年后携皇后婉容、淑妃文绣来到同街乾园居住。溥仪随后把乾园改名为静园，取“静以养吾浩然之气”之意。溥仪在静园“静观变化、静待时机”，继续他荒唐的皇帝生涯，蛰伏待机，图谋复辟满清帝国。9.18事变后，溥仪的机会来了，他在静园与日本特务头子土肥原贤二密谈之后，于1931年11月10晚从静园后门悄悄溜出，秘密离开天津，到达东北，并在日本人的协助下，当上了伪满的康德皇帝。静园在末代帝王离开之后，成为了名副其实的安静之园。新中国解放后，静园被国家占有并作为民宅使用，院中陆续私搭乱盖，最多时住了40多户人家，原有的建筑风貌已不复存在，主体建筑履遭破坏。由于年久失修，建筑物内排水管道腐蚀严重，经常堵塞，造成污水外溢，环境脏乱不堪，老百姓苦不堪言。时代更替，历史变迁，80年间静园几番易主，到本世纪初，这里成了住有45户居民的大杂院。“旧时王谢堂前燕，飞入寻常百姓家”。一代帝王的寓所，竟成了普通百姓的居住地。这些居民们私搭乱盖，有很多违章建筑，原先的建筑主体也破败不堪，原有风貌几近不存，而且存在很大的安全隐患，当时的主管部门甚至把它列入了危房的行列。一代名园静园，竟有被拆除的危险。