GeneTrail—advanced gene set enrichment analysis
Citations
13,102 citations
Cites background from "GeneTrail—advanced gene set enrichm..."
...Moreover, a number of tools, such as Onto-Express (62), easyGO (66), GoMiner (10), eGOn (42), GoSurfer (25), GOFFA (50) and GeneTrail (57), are able to display the enrichment analysis results on the DAG or a tree structure so that users may easily explore the enrichment results in neighboring nodes....
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...However, some recent tools or new releases of early-generation tools, such as Onto-Express (62), DAVID (61), WebGestalt (40), Fatigo+ (56), FACT (30), g:Profiler (64), GAzer (63) and GeneTrail (57), etc., extended their backend bio-databases by integrating wide-range heterogeneous data content (e.g....
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...However, some recent tools or new releases of early-generation tools, such as Onto-Express (62), DAVID (61), WebGestalt (40), Fatigo+ (56), FACT (30), g:Profiler (64), GAzer (63) and GeneTrail (57), etc....
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6,201 citations
Cites methods from "GeneTrail—advanced gene set enrichm..."
...To benchmark the performance of the various enrichment analysis methods implemented within Enrichr, namely, the proportion test, the Z-score and the combined score, as well as other similar published methods, for example, the over representation analysis (ORA) method (11), as well as simple methods such as the Jaccard distance or the number of overlapping genes, we processed 489 experiments that genetically perturbed (knockdown, knockout or overexpression) transcript factors (TFs) from 293 studies available from GEO....
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3,293 citations
Cites background from "GeneTrail—advanced gene set enrichm..."
...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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3,157 citations
Cites methods from "GeneTrail—advanced gene set enrichm..."
...A few tools have been developed that use a threshold free approach including GSEA [12], FatiScan [13], GO-stat [14], GeneTrail [15] and iGA [16]....
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1,357 citations
Additional excerpts
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References
83,420 citations
"GeneTrail—advanced gene set enrichm..." refers methods in this paper
...Therefore, GeneTrail offers two adjustment methods, the conservative Bonferroni adjustment and the control of the false discovery rate (FDR) according to Benjamini and Hochberg (24)....
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35,225 citations
"GeneTrail—advanced gene set enrichm..." refers methods in this paper
...Additionally, GeneTrail uses a local copy of the GO database (1) that includes electronically inferred annotations (IEAs) and manually curated annotations....
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...Some of the developed tools focus on the analysis of only one type of functional categories for example various Gene Ontology (GO) (1) based tools, among them FatiGO (2), BiNGO (3), and GOstat (4)....
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34,830 citations
7,240 citations
4,229 citations
"GeneTrail—advanced gene set enrichm..." refers background in this paper
...The current version of BNþþ integrates for example the following biological data sources: RefSeq ( 12 ), KEGG (13), TRANSPATH (14), TRANSFAC (15), DIP (16), MINT (17), HPRD (18), IntAct (19)....
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