Babelomics:: advanced functional profiling of transcriptomics, proteomics and genomics experiments

被引：61

作者：

Al-Shahrour, Fatima ^{[1
]}

Carbonell, Jose ^{[1
]}

Minguez, Pablo ^{[1
,2
]}

Goetz, Stefan ^{[1
,2
]}

Conesa, Ana ^{[1
]}

Tarrraga, Joaquin ^{[1
,3
]}

Medina, Ignacio ^{[1
,2
]}

Alloza, Eva ^{[1
]}

Montaner, David ^{[1
,3
]}

Dopazo, Joaquin ^{[1
,2
,3
]}

机构：

[1] CIPF, Dept Bioinformat, E-46013 Valencia, Spain

[2] CIBER Enfermedades Raras CIBERER, E-46013 Valencia, Spain

[3] CIPF, INB, Funct Genom Node, E-46013 Valencia, Spain

来源：

NUCLEIC ACIDS RESEARCH | 2008年 / 36卷

关键词：

D O I：

10.1093/nar/gkn318

中图分类号：

Q5 [生物化学]; Q7 [分子生物学];

学科分类号：

071010 ; 081704 ;

摘要：

We present a new version of Babelomics, a complete suite of web tools for the functional profiling of genome scale experiments, with new and improved methods as well as more types of functional definitions. Babelomics includes different flavours of conventional functional enrichment methods as well as more advanced gene set analysis methods that makes it a unique tool among the similar resources available. In addition to the well-known functional definitions (GO, KEGG), Babelomics includes new ones such as Biocarta pathways or text mining-derived functional terms. Regulatory modules implemented include transcriptional control (Transfac, CisRed) and other levels of regulation such as miRNA-mediated interference. Moreover, Babelomics allows for sub-selection of terms in order to test more focused hypothesis. Also gene annotation correspondence tables can be imported, which allows testing with user-defined functional modules. Finally, a tool for the de novo functional annotation of sequences has been included in the system. This allows using yet unannotated organisms in the program. Babelomics has been extensively re-engineered and now it includes the use of web services and Web 2.0 technology features, a new user interface with persistent sessions and a new extended database of gene identifiers. Babelomics is available at http://www.babelomics.org.

引用

页码：W341 / W346

页数：6

共 58 条

[1] BABELOMICS: a suite of web tools for functional annotation and analysis of groups of genes in high-throughput experiments [J].