邏輯思維里最近有一期【什么是全覆蓋級(jí)的讀書肆汹？】抡柿，那么什么是全覆蓋呢？對(duì)整個(gè)局面有智力掌控感叁鉴，誰一出手你就是知道怎么回事兒途样，這就叫全覆蓋江醇，沒有做到全覆蓋，你就不在圈子里何暇√找梗可是讀書要做到全覆蓋，可是太難了裆站。課中說讀書讀到一定水平条辟，你眼中的世界不再是無限的，而是非常有限的宏胯。我們讀書不是為了記住一本書都講些什么羽嫡，而是為了建立一套自己對(duì)世界的認(rèn)知感。

好肩袍，我懂了杭棵，是認(rèn)知感。就是讀書不能以讀書為本氛赐，必須以自己為本魂爪，以修煉【認(rèn)知感】為本。那么艰管，我想快速了解我之前下載的過的文獻(xiàn)滓侍，但是由于自己的sudu問題，放置了很久以至于刪也不得牲芋，放文件夾都不知道起什么文件夾名字的地步的文獻(xiàn)粗井。快速給它們歸歸類街图。所以想要-快速讀一下短的文獻(xiàn)浇衬，要讀夠5篇。哪怕以偏概全餐济。

第一篇

A 5-MicroRNA Signature for Lung Squamous Cell Carcinoma Diagnosis and hsa-miR-31 for Prognosis.

2011年的耘擂，很久遠(yuǎn)的了

【思路】

• miRNA-677個(gè)
• 用了PCA和SVM來建立這個(gè)miRNA的分類期-分SCC和正常組織
• 找到了5個(gè)miRNA
• 用Kaplan–Meier analysis, univariate Cox analysis, and multivariate Cox analysi來驗(yàn)證
• 其中 hsa-miR-31的高表達(dá)對(duì)差預(yù)后影響最大
• 數(shù)據(jù)上傳到gse15008

【結(jié)果】

• 22個(gè)差異表達(dá)中通過PCA-SVM篩選到剩下5個(gè)

• 判斷準(zhǔn)確性-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

• image-20200612182933385

• 高表達(dá) hsa-miR-31在中國(guó)人群中差預(yù)后
  image-20200612183038031

• 說明hsa-miR-31是獨(dú)立的預(yù)后影響因子

image-20200612183227335

• 說-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.可以看到轉(zhuǎn)然后hsa-miR-31只有DICER1的表達(dá)量降低。

image-20200612183504533

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.

自己的理解絮姆，通過CNA和array transcriptomics來找打影響mRNA表達(dá)量的位點(diǎn)醉冤，結(jié)合臨床信息秩霍，將病人分為亞組。

【結(jié)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

【圖結(jié)果】

三線表-會(huì)做吧

image-20200612184830397

The percentage of samples containing copy number aberrations (CNA) at each locus is shown by gain/loss (red/blue)蚁阳，其中前面列出的那幾個(gè)基因在那個(gè)PCA3的那些基因里面铃绒。

image-20200612185036509

下面這個(gè)圖是5個(gè)subgroup，然后縱軸是發(fā)生gain or loss的比例螺捐，并且那些標(biāo)注的基因就是op ten strongest DEGs in each cluster颠悬。我肉眼看到那些標(biāo)注基因是落在一些gain or loss的區(qū)域上，這個(gè)理解應(yīng)該也是符合文章主題吧定血。但也有個(gè)別的不是赔癌，比如PCA3。

image-20200612185739376

接下來是發(fā)現(xiàn)組和驗(yàn)證組分別做熱圖展示

image-20200612185948959

接下來比較生存期咯

image-20200612190039105

第三篇

LncRNA profile study reveals a three-lncRNA signature associated with the survival of patients with oesophageal squamous cell carcinoma.

2013年

【思路是比較清晰】

但是有個(gè)疑問就是澜沟， 【 coefficient of variance >0.10 】是什么呢灾票？然后還有就是后面的這些6389個(gè)基因說是聚類把tumor和nontumor區(qū)分開，僅僅有6個(gè)misclassified茫虽，好像這個(gè)聚類沒有關(guān)系刊苍，并不能說明這些基因的好壞，我記得老師講過的濒析。

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).

image-20200612191248526

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.

【結(jié)果】

沒說如何找到SDCBP班缰，但是由于此次數(shù)據(jù)集的follow-up的時(shí)間比較短，最長(zhǎng)的也就67個(gè)月悼枢，所以追加了兩個(gè)數(shù)據(jù)集做驗(yàn)證埠忘。第一個(gè)數(shù)據(jù)集：在高風(fēng)險(xiǎn)組SDCBP高表達(dá)；第二個(gè)數(shù)據(jù)集：轉(zhuǎn)移組SDCBP也是高表達(dá)馒索。

image-20200612223421429

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).

image-20200612224426911

剩下的結(jié)果是免疫組化的驗(yàn)證看侵襲情況的莹妒。

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. 翻譯就是：電生理學(xué)和全基因組轉(zhuǎn)錄組分析單一的在細(xì)胞培養(yǎng)的人類神經(jīng)元。

Using Weighted Gene Coexpression Network Analyses (WGCNA), we identified gene clusters highly correlated with neuronal maturation judged by electro- physiological characteristics.翻譯就是：利用加權(quán)基因共表達(dá)網(wǎng)絡(luò)分析(WGCNA)绰上，我們確定了通過電生理特征判斷與神經(jīng)成熟高度相關(guān)的基因簇旨怠。

【圖片結(jié)果】

文章涉及了神經(jīng)元細(xì)胞的培養(yǎng)，細(xì)節(jié)沒有看蜈块，記錄幾個(gè)看起來相對(duì)熟悉的圖鉴腻。

(D) PCA of single-cell transcriptomes including neuron and peripheral blood samples suggested that neurons were distinct from peripheral blood cells.

image-20200612231237492

(E) Pan-neuronal genes were exclusively expressed in neurons but not blood samples.

image-20200612231353282

(F) Gene clustering of all 20 single cells and 21 blood samples (a1–a21) revealed a neuronal specific gene module (blue module).這個(gè)WGCNA分出來基因模塊。

image-20200612231402334

(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模塊

image-20200612231529456

(H) Hub-gene net- work of the blue module.

image-20200612231536498

以后再讀百揭！