KOBAS pipeline

KOBAS specifications

Information


Unique identifier OMICS_02228
Name KOBAS
Alternative names KEGG Orthology Based Annotation System, KOBAS2
Interface Web user interface
Restrictions to use None
Computer skills Basic
Version 3.0
Stability Stable
Maintained Yes

Publications for KEGG Orthology Based Annotation System

KOBAS citations

 (31)
2018
PMCID: 5954142

[…] of development, we focused on differential genes that have a role in hormone biosynthesis pathway and development. the enrichment analysis of go and kegg pathways was performed with degs by using kobas 3.0 software [http://kobas.cbi.pku.edu.cn/home.do]34,35. pathway enrichment analysis finds the most significantly enriched pathways by applying a hypergeometric test to map all degs to give […]

2018
PMCID: 5944317

[…] information of mirna targets was obtained from neller et al. (2016). gene ontology (go) term distribution and enrichment analysis were conducted with blast2go software (conesa et al., 2005). kobas 2.0 (xie et al., 2011) was used to identify enriched kegg pathways. for enrichment analysis, the test set comprised targets with highly correlated mirnas (pcc > |0.8|), […]

2018
PMCID: 5884930

[…] (htseq v0.6.1), identification of differentially expressed genes (degs) (deseq v1.10.1), enrichment analysis of degs by go enrichment analysis (goseq release2.12) and kegg pathways analysis (kobas v2.0), were carried out based on a previous report (wang h. et al., 2016). the rna-seq data have been deposited in the genome sequence archive in big data center, beijing institute of genomics […]

2018
PMCID: 5761711

[…] down-regulated degs. moreover, a total of 158 (79.79%) up-regulated and 40 (20.21%) down-regulated demirnas were identified. the dernas were enriched in the kegg pathway by kobas 3.0 (http://kobas.cbi.pku.edu.cn/), in order to preliminarily investigate the tumorigenesis of gastric cancer. we found that the dernas were mainly enriched in “transcriptional misregulation in cancer, metabolic […]

2017
PMCID: 5793157

[…] and a fold change >2. the kegg pathway enrichment of degs was evaluated using a hypergeometric test with a significance threshold of 0.05 after the benjamini and hochberg fdr correction in kobas (2.0) [32]., to validate the results of transcriptome sequencing, the expression of 10 degs involved in plant hormone signal transduction and phenylpropanoid biosynthesis was investigated using […]

KOBAS institution(s)
Center for Bioinformatics, State Key Laboratory of Protein and Plant Gene Research, College of Life Sciences, Peking University, Beijing, China

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