KOBAS
1. What is KOBAS 3.0?
KOBAS (KEGG Orthology Based Annotation System) is a web server for gene/protein functional annotation (Annotation module) and functional set enrichment (Enrichment module). Given a set of genes or protein, it can determine whether a pathway, disease, and Gene Ontology(GO) term shows statistically significant. The last version of KOBAS, KOBAS 2.0, has abundant annotation information of gene sets from multiple databases covering pathways (KEGG PATHWAY, Reactome, Biocyc, Panther), diseases (KEGG DISEASE, OMIM, NHGRI GWAS Catalog), and GO terms, and more than 4,000 species are supported. Since KOBAS 2.0 is widely used by worldwide researchers, we update it to KOBAS 3.0, which supports more data formats as input and more accurate functional enrichment algorithms.
KOBAS 3.0 is composed by two function, Annotation and Enrichment, as follows:
1.1 Annotation
For Annotation module, it accepts gene/protein list as input, including IDs or sequences. And it generates annotations for each gene based on multiple databases about pathways, diseases, and Gene Ontology. That is, for each gene, you can find which pathways, diseases, and Gene Ontology are related to this gene.
1.2 Enrichment
Enrichment module gives you the answer of which pathways, diseases, and GO terms is statistically significant associated with the genes/proteins you just input.
For Enrichment module, there are two modules according to their differences in input format:
1.2.1 Gene list Enrichment
This module is called “Identify” in KOBAS 2.0. It accepts same input formats as Annotation module, and the results of Annotation module as input is also allowed (see details at 3.1). It is based on the first generation gene set enrichment method, a gene-level statistic called Overrepresentation Analysis(ORA), a simple and frequently used test based on the hypergeometric distribution. Many tools have applied this methods, such as DAVID. However, we support other distributions like binominal test, chi-square test, frequency list and 3 FDR correction methods, like Benjamini and Hochberg (1995), Benjamini and Yekutieli (2001), and QVALUE.
1.2.2 Exp-data Enrichment
This module is a new feature in KOBAS 3.0. Allowing the gene expression as input gives a big change for functional gene sets enrichment because it makes us be able to use set based second or net-based gene set enrichment method, which use the information of molecular measures where the ORA ignores. By considering the coordinated changes in gene expression, these methods account for dependence between genes in a pathway, which ORA does not.
This module has integrated 9 methods including set-based methods: Globaltest, GSEA, GSA PADOG, PLAGE, GAGE, SAFE and net-based methods: GANPA, CEPA.
Furthermore, to detect the enriched gene sets supported by multiple methods, Exp-data Enrichment module gives gene set enrichment score and probability of being enriched sets based on the results of 9 gene set enrichment(GSE) methods.
KOBAS的更多相关文章
- 使用GEO数据库来筛选差异表达基因,KOBAS进行KEGG注释分析
前言 本文主要演示GEO数据库的一些工具,使用的数据是2015年在Nature Communications上发表的文章Regulation of autophagy and the ubiquiti ...
- KEGG and Gene Ontology Mapping in Bioinformatic Method
使用KOBAS进行KEGG pathway和Gene Ontology分析 Article from Blog of Alfred-Feng http://blog.sina.com.cn/u/170 ...
- (转)基因芯片数据GO和KEGG功能分析
随着人类基因组计划(Human Genome Project)即全部核苷酸测序的即将完成,人类基因组研究的重心逐渐进入后基因组时代(Postgenome Era),向基因的功能及基因的多样性倾斜.通过 ...
随机推荐
- Spring MVC 重定向
@RequestMapping("/testRedirect") public String testRedirect(){ System.out.println("te ...
- 使用 C++11 编写类似 QT 的信号槽——上篇
了解 QT 的应该知道,QT 有一个信号槽 Singla-Slot 这样的东西.信号槽是 QT 的核心机制,用来替代函数指针,将不相关的对象绑定在一起,实现对象间的通信. 考虑为 Simple2D 添 ...
- sts,eclipse里面配置tomcat
第一步:点击window-->preferences-->server-->Runtime Environments点击add. 第二步:选择本机上面有的tomcat版本点击next ...
- RxJava 与观察者模式
RxJava到底是什么?让我们直接跳过官方那种晦涩的追求精确的定义,其实初学RxJava只要把握两点:观察者模式和异步,就基本可以熟练使用RxJava了. 异步在这里并不需要做太多的解释,因为在概念和 ...
- kafka相关资料
先来说一下Kafka与RabbitMQ的对比: RabbitMQ,遵循AMQP协议,由内在高并发的erlanng语言开发,用在实时的对可靠性要求比较高的消息传递上. kafka是Linkedin于20 ...
- Linux逻辑卷的拉伸和缩小
相对于普通磁盘优势是逻辑卷可以在线动态的拉伸(不用先unmount操作),只要vg中有足够的空间即可 1:首先查看vg是否有足够的空间 [root@gechong mapper]# vgdisplay ...
- HTML CSS + DIV实现整体布局 part2
9.盒模型的层次关系 我们通过一个经典的盒模型3D立体结构图来理解,如图: 从上往下看,层次关系如下: 第1层:盒子的边框(border), 第2层:元素的内容(content).内边 ...
- debug-stripped.ap_' specified for property 'resourceFile' does not exist.(转载)
1.错误描述 更新Android Studio到2.0版本后,出现了编译失败的问题,我clean project然后重新编译还是出现抑郁的问题,问题具体描述如下所示: Error:A problem ...
- 将2020年交期的PR回写出来了
OUT_pr表中的交期为2020年和2019年,不应该 回写的PR却回写出来了 优化如下:
- LocalDateTime json格式化
参考https://www.cnblogs.com/xiaozhang9/p/jackson.html?utm_source=itdadao&utm_medium=referral <d ...