生存分析在线工具2020年4月吐血整理!

PubPeer

老的生存分析在线工具不断更新的同时,新的工具不断涌现,真是让人应接不暇。今天在这将现有的这些工具做一个综合整理。关于在线分析软件相关文献的发表期刊和年份我分别用红色和黑色加粗字体标记了,在选择相应工作的时候可以作为参考。加了

的是网页使用比较顺畅的。

01

Kaplan Meier-plotter

网址:http://kmplot.com/analysis/index.php?p=background

简介

The Kaplan Meier plotter is capable to assess the effect of 54k genes on survival in 21 cancer types. The largest datasets include breast (n=6,234), ovarian (n=2,190), lung (n=3,452), and gastric (n=1,440) cancer. The miRNA subsystems include 11k samples from 20 different cancer types. The system includes gene chip and RNA-seq data – sources for the databases include GEO, EGA, and TCGA. Primary purpose of the tool is a meta-analysis based discovery and validation of survival biomarkers.

使用者点评

这个网页提供的内置的乳腺癌、卵巢癌、肺癌、肝癌、胃癌数据库,不能选择TCGA特定的数据库。而且分析的多是Microarray而不是主流的RNAseq数据,所以看一眼就行了,不是一个主流的网站。(感觉是做测序的瞧不起做芯片的)

相关论文

1. Gyorffy B, Surowiak P, Budczies J, Lanczky A. Online survival analysis software to assess the prognostic value of biomarkers using transcriptomic data in non-small-cell lung cancer, PLoS One (IF=2.776), 2013 Dec 18;8(12):e82241. doi: 10.1371/journal.pone.0082241.阅读此文

2. Nagy A, Lánczky A, Menyhárt O, Gyrffy B. Validation of miRNA prognostic power in hepatocellular carcinoma using expression data of independent datasets,Scientific Reports (IF=4.011), 2018;8:9227 阅读此文

02

PROGgene

网址:http://genomics.jefferson.edu/proggene/

简介

PROGgene – Pan Cancer Prognostics Database。与其它软件不同的是这个工具提供了基因表达水平比值的预后分析。不过,应该和Normalized by gene(例如GEPIA2)的功能一样的效果。

第二版新功能简介如下:

NEW FEATURES IN VERSION 2

Perform Survival Analysis in a Variety of new ways

Users can now perform analysis on single genes, or select to perform analysis on mean expression of a group of user defined genesUsers can now perform analysis on Gene-Gene ratioAlso, users can perform analysis on entire gene signaturesChose from a repository of more than 10000 curated/published gene signatures.

New/Additional Datasets

We have added new datasets for tissue types in version 2. We have also introduced datasets for 3 tissue types for first time

Efficient use of covariates

Users can now divide cohorts selected for analysis by covariates available for the cohort. Also, users can now adjust survival model for available covariates

Better graphs with statistics

Click on the hyperlinked smaller graph on results page to get high resolution publication quality images. Also available are summary statistics for the survival model in table format

详见:http://genomics.jefferson.edu/proggene/intro.php

可惜的是,今天试用的时候,最后一步竟然不行,大家看看运气吧!

相关论文

VERSION 1oswami CP and Nakshatri H. PROGgene: gene expression based survival analysis web application for multiple cancers. J Clin Bioinforma (非SCI或ESCI). 2013 Oct 28;3(1):22 阅读此文

VERSION 2oswami CP and Nakshatri H. PROGgeneV2: enhancements on the existing database. BMC Cancer (IF=2.933). 2014 14:970. 阅读此文

03

SurvExpress

网址:http://bioinformatica.mty.itesm.mx:8080/Biomatec/SurvivaX.jsp

简介

最后一步无法操作

相关论文

Aguirre-Gamboa, R., Gomez-Rueda, H., Martínez-Ledesma, E., Martínez-Torteya, A., Chacolla-Huaringa, R., Rodriguez-Barrientos, A., … & Trevino, V. (2013). SurvExpress: an online biomarker validation tool and database for cancer gene expression data using survival analysis. PloS One (IF=2.776), 8 (9). 阅读此文

04

KM-express

网址:http://ec2-52-201-246-161.compute-1.amazonaws.com/kmexpress/index.php

简介

哎~又是一个好难打开的网站

相关论文

Chen, X., Miao, Z., Divate, M., Zhao, Z., & Cheung, E. (2018). KM-express: an integrated online patient survival and gene expression analysis tool for the identification and functional characterization of prognostic markers in breast and prostate cancers. Database-the Journal of Biological Databases and Curation (IF=3.683), 2018. 阅读此文

05

PrognoScan

网址:http://dna00.bio.kyutech.ac.jp/PrognoScan/index.html

简介

好素的首页▲

相关论文

Mizuno, H., Kitada, K., Nakai, K., & Sarai, A. (2009). PrognoScan: a new database for meta-analysis of the prognostic value of genes. BMC Medical Genomics (IF=2.568), 2 (1), 18. 阅读此文

06

lnCAR: lncRNA Explorer

网址:https://lncar.renlab.org/

简介

主要功能就是做lncRNA的差异表达和生存分析

相关论文

Zheng, Y., Xu, Q., Liu, M., Hu, H., Xie, Y., Zuo, Z., & Ren, J. (2019). lnCAR: a comprehensive resource for lncRNAs from Cancer Arrays. Cancer Research (IF=8.378), 79 (8), 2076-2083. 阅读此文

07

UALCAN

网址:http://ualcan.path.uab.edu/analysis.html

简介

使用者点评

可以调节的参数较少,而且设置起来特别别扭,而且图表都很丑。

相关论文

Chandrashekar, D. S., Bashel, B., Balasubramanya, S. A. H., Creighton, C. J., Ponce-Rodriguez, I., Chakravarthi, B. V., & Varambally, S. (2017). UALCAN: a portal for facilitating tumor subgroup gene expression and survival analyses. Neoplasia (IF=3.837), 19 (8), 649-658. 阅读此文

08

OncoLnc

网址:http://www.oncolnc.org/

简介

名字虽然是带lnc,但是不仅仅有lncRNA,还有mRNA和miRNA。

相关论文

Anaya, J. (2016). OncoLnc: linking TCGA survival data to mRNAs, miRNAs, and lncRNAs. PeerJ Computer Science (新入选SCI,无IF), 2 , e67. 阅读此文

09

OncomiR

网址:http://www.oncomir.org/

简介

使用者点评

生成的生存曲线清晰度差,无PDF格式文件。

相关论文

Wong, N. W., Chen, Y., Chen, S., & Wang, X. (2018). OncomiR: an online resource for exploring pan-cancer microRNA dysregulation. Bioinformatics (IF=4.531), 34 (4), 713-715. 阅读此文

10

MethSurv

网址:https://biit.cs.ut.ee/methsurv/

简介

TCGA数据库中收录的主要是450K芯片的数据,也有一些早期27K芯片的数据。本文所述的MethSurv就是基于TCGA数据集中的450K数据构建的可视化分析工具。MethSurv适用于没有特定生物信息学技能(不熟悉编程分析)的研究人员和临床医生,主要用于探索与癌症患者生存相关的甲基化生物标记物。

相关论文

Modhukur, V., Iljasenko, T., Metsalu, T., Lokk, K., Laisk-Podar, T., & Vilo, J. (2018). MethSurv: a web tool to perform multivariable survival analysis using DNA methylation data. Epigenomics (IF=4.404), 10 (3), 277-288. 阅读此文

11

BloodSpot

网址:http://servers.binf.ku.dk/bloodspot/

简介

加载半天就出现上面这个鬼样子▲

提供健康和恶性造血中基因和基因特征的基因表达谱,包括来自人类和小鼠的数据。除了显示集成表达图的默认图外,还有两个额外的可视化级别; 一个交互式树,显示样本之间的层次关系,以及Kaplan-Meier生存图。数据库被细分为几个可供浏览的数据集。

相关论文

Bagger, F. O., Sasivarevic, D., Sohi, S. H., Laursen, L. G., Pundhir, S., Snderby, C. K., … & Porse, B. T. (2016). BloodSpot: a database of gene expression profiles and transcriptional programs for healthy and malignant haematopoiesis. Nucleic acids research (IF=11.147), 44 (D1), D917-D924. 阅读此文

12

GEPIA 2

网址:http://gepia2.cancer-pku.cn/#survival

简介

在线TCGA基因表达和生存分析的工具(GEPIA2),2019年发表在NAR上,目前已更新到2.0版本。

使用者点评

北大做的一个在线生信系统,可以分析存活曲线、共表达、癌肿分析等,非常好用,而且在墙内,所以速度很优秀。

相关论文

Tang, Z., Kang, B., Li, C., Chen, T., & Zhang, Z. (2019). GEPIA2: an enhanced web server for large-scale expression profiling and interactive analysis. Nucleic acids research (IF=11.147), 47 (W1), W556-W560. 阅读此文

Tang, Z., Li, C., Kang, B., Gao, G., Li, C., & Zhang, Z. (2017). GEPIA: a web server for cancer and normal gene expression profiling and interactive analyses. Nucleic acids research (IF=11.147), 45 (W1), W98-W102. 阅读此文

13

GenomicScape

网址:http://www.genomicscape.com/microarray/survival.php

简介

数据不是非常丰富,包括结直肠癌、白血病、肝癌、淋巴癌、多发性骨髓瘤和卵巢癌的芯片数据。另外,图丑得不要不要的,这线条粗得,啧啧啧…如下图,感受一下。大家看看能不能调吧!

相关论文

Kassambara, A., Rème, T., Jourdan, M., Fest, T., Hose, D., Tarte, K., & Klein, B. (2015). GenomicScape: an easy-to-use web tool for gene expression data analysis. Application to investigate the molecular events in the differentiation of B cells into plasma cells. PLoS Computational Biology (IF=4.428), 11 (1).

14

ExSurv

网址:https://exsurv.soic.iupui.edu/

简介

ExSurv is a web resource for studying the survival contributions of exons across human cancers using RNA-seq data. ExSurv is the first web server which provides exon level survival significance by using the RNA-seq expression datasets and the clinical metadata for four cancer types from The Cancer Genome Atlas (TCGA) project. We pre-calculated the prognostic significance of more than 600,000 annotated exons in Ensembl using survival package in R. We stored the TCGA clinical data, exon survival p-values and the expression of the significant exons for visualizing the survival curves in a MySQL database. We developed an integrated backend using PHP and R and used JavaScript in the frontend. The PHP/R backend is reponsible for querying the MySQL database upon user input, calling R to visualize the corresponding database results (using survival package) and returning these results to the frontend. In the frontend, the results are shown to the users in an organized way as a table where each row corresponds to an exon in the queried gene symbol or Ensembl gene ID. It is possible to export the survival plots in SVG (scalable vector graphics) format and the raw data used to generate the plot in TSV (tab-separated values) format.

肿瘤类型目前只有乳腺癌、胶质瘤、肾癌和肝癌。

相关论文

Hashemikhabir, S., Budak, G., & Janga, S. C. (2016). ExSurv: A web resource for prognostic analyses of exons across human cancers using clinical transcriptomes. Cancer informatics (ESCI), 15 , CIN-S39367. 阅读此文

15

LOGpc

网址:http://bioinfo.henu.edu.cn/DatabaseList.jsp

简介

LOGpc ( Long-term Outcome and Gene Expression Profiling Database of pan-cancers ) encompasses 209 expression datasets, provides 13 types of survival terms for 31310 patients of 27 distinct malignancies.

相关论文

这个工具是2019、2020年才开始出现的,该课题组发表的相关论文太多了,懒得写了。几乎每种癌症都发一篇文章,这个操作够骚的。详见:http://bioinfo.henu.edu.cn/results.html。主要发表的期刊如下:

Front Oncol (IF=4.137)

Front Genet (IF=3.517)

Cancer Med (IF=3.357)

Mol Carcinog (IF=3.411)

Cancer Manag Res (IF=2.243)

Future Oncol (IF=2.279)

其它乱七八糟可能用得上的工具

16. CBioportal

,是一个全能的TCGA生信分析平台,可以选择的数据库数量是所有网站中最多的,但不是所有的数据源都有survival信息,例如肺腺癌。另外,好像很多数据是基因拷贝数和突变,而不是表达量。还有,没有健康对照组,相当尴尬。

17. Watson,提供的数据库类别多,和CBioportal收录的互有补充。有人觉得界面不大人性化,画出来的图很丑。目前我用的移动宽带打不开…

18. UCSC Xena,非常全能的数据库,存活曲线只是其中一个小功能,更多的是统计和分析。But…网站想打开也是够呛。

19. GDC portal,TCGA自家的工具,能不能打开好像也是看网络心情。可能需要用VPN搞起!

20.SurvMicro,和SurvExpress是一家的,2019年10月份链接(即发表的论文中的链接)失效了,不过备用链接打开了,但最后一步也无法操作。课题组说没钱了…

Aguirre-Gamboa, R., & Trevino, V. (2014). SurvMicro: assessment of miRNA-based prognostic signatures for cancer clinical outcomes by multivariate survival analysis. Bioinformatics (IF=4.531), 30 (11), 1630-1632. 阅读此文

21. CANSURV,不想说了,浏览器又在转圈圈,开不动…不过,发现个可下载的软件CanSurv version 1.4(2018年5月发行版本),不知道是不是一家的,也没时间研究了。链接在这:

https://surveillance.cancer.gov/cansurv/download,大家自己瞅瞅。

Yu et al. (2005). CANSURV: a Windows program for population-based cancer survival analysis. Computer methods and programs in biomedicine , 80 (3), 195-203.

22. OSA (Online Survival Analysis),这个不是打不开,而是网站直接就有错误…希望早点修复吧!不过好像不是我所想的那个样子。

Montes-Torres et al. (2016). Advanced online survival analysis tool for predictive modelling in clinical data science. PloS One (IF=2.776), 11 (8).

23. SurvCurv,没人的数据,其它的还不是非常熟悉,感兴趣的自行摸索。

Ziehm et al. (2015). SurvCurv database and online survival analysis platform update. Bioinformatics (IF=4.531), 31 (23), 3878-3880. 阅读此文。

24.TCPA v3.0,此数据库是基于蛋白质组学结果的,不仅仅是生存分析,还有更多的功能。网站能打开,但是非常慢,你们自己想办法看看吧!

Chen et al. (2019). TCPA v3. 0: an integrative platform to explore the pan-cancer analysis of functional proteomic data. Molecular & Cellular Proteomics (IF=4.828), 18 (8 suppl 1), S15-S25. 阅读此文。

25.LCE

,专注肺癌基因表达和临床关系的数据库。

Cai et al. (2019). LCE: an open web portal to explore gene expression and clinical associations in lung cancer. Oncogene (IF=6.634), 38 (14), 2551-2564. 阅读此文

26.DriverDBv3

,能打开,就是速度有点慢。

Liu, S. H., Shen, P. C., Chen, C. Y., Hsu, A. N., Cho, Y. C., Lai, Y. L., … & Chung, I. F. (2020). DriverDBv3: a multi-omics database for cancer driver gene research. Nucleic acids research (IF=11.147), 48 (D1), D863-D870. 阅读此文

27. LncACTdb 2.0,在做生存分析方面,操作极其简单粗暴!

Wang, P., Li, X., Gao, Y., Guo, Q., Wang, Y., Fang, Y., … & Liu, W. (2019). LncACTdb 2.0: an updated database of experimentally supported ceRNA interactions curated from low-and high-throughput experiments. Nucleic acids research (IF=11.147), 47 (D1), D121-D127. 阅读此文

28.Oncomine,需要用高效单位邮箱注册,不是很方便使用。

Measure

Measure

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