KOBAS 2.0: a web server for annotation and identification of enriched pathways and diseases
Citations
2,959 citations
Cites methods from "KOBAS 2.0: a web server for annotat..."
...There are a several functional enrichment analysis tools such as Enrichr (1), WebGestalt (2), Metascape (3), KOBAS (4) and AgriGO (5) suitable for positioning the novel findings against the body of previous knowledge....
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...There are a several functional enrichment analysis tools such as Enrichr (1), WebGestalt (2), Metascape (3), KOBAS (4) and AgriGO (5) suitable for positioning the novel findings against the body of previous knowledge....
[...]
679 citations
495 citations
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References
83,420 citations
"KOBAS 2.0: a web server for annotat..." refers methods in this paper
...0, we add two more popular FDR correction methods: Benjamini-Hochberg (40) and Benjamini-Yekutieli (41)....
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...We used ‘annotate’ to map sequences of upregulated probe sets in CA as well as the entire probe sets to KEGG human genes with default cutoffs and then used ‘identify’ to perform hypergeometric test and Benjamini-Hochberg FDR correction to find significantly enriched pathways and diseases by using the two results of ‘annotate’ as input and background, respectively....
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...In KOBAS 2.0, we add two more popular FDR correction methods: Benjamini-Hochberg (40) and Benjamini-Yekutieli (41)....
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35,225 citations
31,015 citations
"KOBAS 2.0: a web server for annotat..." refers background or methods in this paper
...DAVID can perform only ID mapping to rhesus genes in its two pathway databases (KEGG PATHWAY and Panther) and as a result, identified no statistically significantly enriched pathways or diseases (with default options and corrected P 0.05)....
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...We then used both DAVID (15,16) and KOBAS 2....
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...Except for DAVID, all these tools integrate limited pathway and disease databases (for a comparison, see Supplementary Table S1)....
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...A growing number of tools have been developed for pathway and disease identification, including, but not limited to, MAPPFinder (13), EASE (14), DAVID (15,16), ArrayXPath (17), WebGestalt (18), FuncCluster (19), PageMan (20), GENECODIS (21,22), GeneTrail (23), g:Profiler (24), FunNet (25) and PaLS (26)....
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...We then used both DAVID (15,16) and KOBAS 2.0 to annotate these probe sets and identify enriched pathways and diseases by using the entire probe sets on the chip as background....
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24,024 citations
13,102 citations
"KOBAS 2.0: a web server for annotat..." refers background or methods in this paper
...DAVID can perform only ID mapping to rhesus genes in its two pathway databases (KEGG PATHWAY and Panther) and as a result, identified no statistically significantly enriched pathways or diseases (with default options and corrected P 0.05)....
[...]
...We then used both DAVID (15,16) and KOBAS 2....
[...]
...Except for DAVID, all these tools integrate limited pathway and disease databases (for a comparison, see Supplementary Table S1)....
[...]
...A growing number of tools have been developed for pathway and disease identification, including, but not limited to, MAPPFinder (13), EASE (14), DAVID (15,16), ArrayXPath (17), WebGestalt (18), FuncCluster (19), PageMan (20), GENECODIS (21,22), GeneTrail (23), g:Profiler (24), FunNet (25) and PaLS (26)....
[...]
...We then used both DAVID (15,16) and KOBAS 2.0 to annotate these probe sets and identify enriched pathways and diseases by using the entire probe sets on the chip as background....
[...]