逻辑思维里最近有一期【什么是全覆盖级的读书？】，那么什么是全覆盖呢？对整个局面有智力掌控感，谁一出手你就是知道怎么回事儿，这就叫全覆盖，没有做到全覆盖，你就不在圈子里。可是读书要做到全覆盖，可是太难了。课中说读书读到一定水平，你眼中的世界不再是无限的，而是非常有限的。我们读书不是为了记住一本书都讲些什么，而是为了建立一套自己对世界的认知感。
好，我懂了，是认知感。就是读书不能以读书为本，必须以自己为本，以修炼【认知感】为本。那么，我想快速了解我之前下载的过的文献，但是由于自己的sudu问题，放置了很久以至于删也不得，放文件夹都不知道起什么文件夹名字的地步的文献。快速给它们归归类。所以想要-快速读一下短的文献，要读够5篇。哪怕以偏概全。
第一篇
A 5-MicroRNA Signature for Lung Squamous Cell Carcinoma Diagnosis and hsa-miR-31 for Prognosis.
2011年的，很久远的了
【思路】
- miRNA-677个
- 用了PCA和SVM来建立这个miRNA的分类期-分SCC和正常组织
- 找到了5个miRNA
- 用Kaplan–Meier analysis, univariate Cox analysis, and multivariate Cox analysi来验证
- 其中 hsa-miR-31的高表达对差预后影响最大
- 数据上传到gse15008
【结果】
22个差异表达中通过PCA-SVM筛选到剩下5个
判断准确性-The analysis of the original training group using this classifier had a predictive accuracy of 94.1%. The classifier was subsequently validated with an independent test cohort comprising another 26 SCC patients and displayed an accuracy of 96.2% with this group
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image-20200612182933385
- 高表达 hsa-miR-31在中国人群中差预后
image-20200612183038031
说明hsa-miR-31是独立的预后影响因子
- 说-hsa-miR-31 targets DICER1 but not PPP2R2A and LATS2
immunoblots of DICER1, PPP2R2A, and LATS2 proteins in SK-MES-1 cells transiently transfected with hsa- miR-31 and control microRNA, respectively.可以看到转然后hsa-miR-31只有DICER1的表达量降低。
第二篇
Integration of copy number and transcriptomics provides risk stratification in prostate cancer: A discovery and validation cohort study
2015年
【背景】
Understanding the heterogeneous genotypes and phenotypes of prostate cancer is fundamental to improving the way we treat this disease. As yet, there are no validated descriptions of prostate cancer subgroups derived from integrated genomics linked with clinical outcome.
【方法】
In a study of 482 tumour, benign and germline samples from 259 men with primary prostate cancer, we used integrative analysis of copy number alterations (CNA) and array transcriptomics to identify genomic loci that affect expression levels of mRNA in an expression quantitative trait loci (eQTL) approach, to stratify patients into subgroups that we then associated with future clinical behaviour, and compared with either CNA or transcriptomics alone.
自己的理解，通过CNA和array transcriptomics来找打影响mRNA表达量的位点，结合临床信息，将病人分为亚组。
【结果】
- identified five separate patient subgroups
- These subgroups were able to consistently predict biochemical relapse
- show the relative contributions of gene expression and copy number data on phenotype
- confirm alterations in six genes previously associated with prostate cancer (MAP3K7, MELK, RCBTB2, ELAC2, TPD52, ZBTB4)
- confirm a number of previously pub- lished molecular changes associated with high risk disease, including MYC amplification, and NKX3-1, RB1 and PTEN deletions, as well as over-expression of PCA3 and AMACR, and loss of MSMB in tumour tissue
【图结果】
三线表-会做吧
The percentage of samples containing copy number aberrations (CNA) at each locus is shown by gain/loss (red/blue)，其中前面列出的那几个基因在那个PCA3的那些基因里面。
下面这个图是5个subgroup，然后纵轴是发生gain or loss的比例，并且那些标注的基因就是op ten strongest DEGs in each cluster。我肉眼看到那些标注基因是落在一些gain or loss的区域上，这个理解应该也是符合文章主题吧。但也有个别的不是，比如PCA3。
接下来是发现组和验证组分别做热图展示
接下来比较生存期咯
第三篇
LncRNA profile study reveals a three-lncRNA signature associated with the survival of patients with oesophageal squamous cell carcinoma.
2013年
【思路是比较清晰】
但是有个疑问就是， 【 coefficient of variance >0.10 】是什么呢？然后还有就是后面的这些6389个基因说是聚类把tumor和nontumor区分开，仅仅有6个misclassified，好像这个聚类没有关系，并不能说明这些基因的好坏，我记得老师讲过的。
In total, 6389 lncRNAs with a coefficient of variance >0.10 were selected from the 8900 lncRNAs for clustering analysis. Hierarchical clustering of these 6389 lncRNAs based on centred Pearson correlation clearly separated OSCC tissues from normal tissues (figure 2).
第四篇
Mda-9/Syntenin Is Expressed in Uveal Melanoma and Correlates with Metastatic Progression.
2012年
【背景】
Identification of patients at high risk of metastases may provide indication for a frequent follow-up for early detection of metastases and treatment. The analysis of the gene expression profiles of primary human uveal melanomas showed high expression of SDCBP gene (encoding for syndecan-binding protein-1 or mda-9/syntenin), which appeared higher in patients with recurrence, whereas expression of syndecans was lower and unrelated to progression.
【结果】
没说如何找到SDCBP，但是由于此次数据集的follow-up的时间比较短，最长的也就67个月，所以追加了两个数据集做验证。第一个数据集：在高风险组SDCBP高表达；第二个数据集：转移组SDCBP也是高表达。
Kaplan-Meier analysis of Mda-9/syntenin protein expression and disease-free survival in patients with primary tumors. Patients with low mda-9/syntenin expression (dark line) showed longer survival than patients with high expression (gray line) (P,0.014).
剩下的结果是免疫组化的验证看侵袭情况的。
第五篇
Coupled electrophysiological recording and single cell transcriptome analyses revealed molecular mechanisms underlying neuronal maturation.
2016年
【背景】
Here we report success in per- forming both electrophysiological and whole-genome transcriptome analyses on single human neurons in culture. 翻译就是：电生理学和全基因组转录组分析单一的在细胞培养的人类神经元。
Using Weighted Gene Coexpression Network Analyses (WGCNA), we identified gene clusters highly correlated with neuronal maturation judged by electro- physiological characteristics.翻译就是：利用加权基因共表达网络分析(WGCNA)，我们确定了通过电生理特征判断与神经成熟高度相关的基因簇。
【图片结果】
文章涉及了神经元细胞的培养，细节没有看，记录几个看起来相对熟悉的图。
(D) PCA of single-cell transcriptomes including neuron and peripheral blood samples suggested that neurons were distinct from peripheral blood cells.
(E) Pan-neuronal genes were exclusively expressed in neurons but not blood samples.
(F) Gene clustering of all 20 single cells and 21 blood samples (a1–a21) revealed a neuronal specific gene module (blue module).这个WGCNA分出来基因模块。
(G) GO analyses of the blue module (4255 genes). Length of bars indicates the significance (−log10 transferred P-value, Fisher’s exact test). Genes shown in right are well-known genes with corresponding functionsblue模块
(H) Hub-gene net- work of the blue module.
以后再读！