Difference between revisions of "FlyBase:GSEA"

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=Gene Set Enrichment Tools=
 
=Gene Set Enrichment Tools=
  
 +
Some examples of GSEA tools with links and information. A list of more GSEA tools can be found [[FlyBase:Drosophila_Online_Resources#Gene_Set_Enrichment_Analysis|<b>here</b>]].
  
*<b>Selected Gene Set Enrichment Tool Information</b>
+
It is recommended that users conduct their GSEA with more than one tool as all have different features, use statistically significant results and compare the overlap between enriched sets to further interpretation. With any GSEA, there will be genes within the analysis set that are not represented in the gene set libraries, e.g. genes that have very little characterisation. These may be of interest for further study, even though they are not in an enriched set.
  
Some examples of GSEA tools with links and information. It is recommended that users conduct their GSEA with >tool as all have different features, use statistically significant results and compare the overlap between enriched sets to further interpretation. With any GSEA, there will be genes within the analysis set that are not represented in the gene set libraries, e.g. genes that have very little characterisation. These may be of interest for further study, even though they are not in an enriched set
 
  
{| class="wikitable" border="1"
+
 
 +
====<b>Selected Gene Set Enrichment Tool Information</b>====
 +
{| class="wikitable"
 
|-
 
|-
! Tool
+
! '' Tool''!!''Backronym''!!''Publication''!!''Enrichment sets''!!''Organism(s)''!!''ID conversion''!!''Multiple set enrichment available''!!''Parallel gene list analysis''!!''Custom background input''!!''Stats''!!''Visualisation''!!''Other features''!!''API''!!''Update Notes''!!''Help/tutorials''
! Backronym
 
! Publication
 
! Enrichment sets
 
! Organism(s)
 
! ID conversion
 
! Multiple set enrichment available
 
! Parallel gene list analysis
 
! Custom background input
 
! Stats
 
! Visualisation
 
! Other features
 
! API
 
! Update Notes
 
! Help/tutorials
 
 
|-
 
|-
! [https://david.ncifcrf.gov/ DAVID]
+
| [https://david.ncifcrf.gov/ <b>DAVID</b>] ||Database for Annotation, Visualization and Integrated Discovery ||[https://pubmed.ncbi.nlm.nih.gov/35325185/ PMID:35325185] ||Many (e.g. GO, interaction, domains, UniProt KeyWord, drug, human expression, disease, pathways) ||Large coverage ||Yes ||Yes ||No ||Yes ||p-value, Benjamini ||Bar chart and limited gene/term bin heat map; will also group bar charts in sets ||Manipulation of gene lists. ||[https://david.ncifcrf.gov/content.jsp?file=DAVID_API.html Yes] ||Updated ~twice yearly [https://david.ncifcrf.gov/content.jsp?file=update.html Updates] ||[https://david.ncifcrf.gov/helps/tutorial.pdf Tutorial]
! Database for Annotation, Visualization and Integrated Discovery
+
|- bgcolor="lightgrey"
! [https://pubmed.ncbi.nlm.nih.gov/35325185/ PMID:35325185]
 
! Many (e.g. GO, interaction, domains, UniProt KeyWord, drug, human expression, disease, pathways)
 
! Large coverage
 
! Yes
 
! Yes
 
! No
 
! Yes
 
! p-value, Benjamini
 
! Bar chart and limited gene/term bin heat map; will also group bar charts in sets
 
! Manipulation of gene lists.
 
! [https://david.ncifcrf.gov/content.jsp?file=DAVID_API.html Yes]
 
! Updated ~twice yearly [https://david.ncifcrf.gov/content.jsp?file=update.html Updates]
 
! [https://david.ncifcrf.gov/helps/tutorial.pdf Tutorial]
 
 
|-
 
|-
! [https://maayanlab.cloud/Enrichr/ Enrichr]
+
| [https://maayanlab.cloud/Enrichr/ <b>Enrichr</b>] ||- ||[https://pubmed.ncbi.nlm.nih.gov/33780170/ PMID:33780170] ||Many (e.g. GO, disease, interaction, domains, phenotype, pathways), especially for [https://maayanlab.cloud/Enrichr/#libraries human] ||[https://maayanlab.cloud/Enrichr/ Enrichr Human & mouse], sites for [https://maayanlab.cloud/modEnrichr/ Mod-specific sets]: [https://maayanlab.cloud/FlyEnrichr/ FlyEnrichr (D.mel)], [https://maayanlab.cloud/YeastEnrichr/ YeastEnrichr (S.cerevisiae)], [https://maayanlab.cloud/WormEnrichr/ WormEnrichr (C. elegans)], [https://maayanlab.cloud/FishEnrichr/ FishEnrichr (D. rerio)] ||No ||Yes ||Yes ||No ||p-value, z-score ||Bar chart, table ||Analysis sharing feature. Other viewing features such as networks and gene-set similarity grid available for some set genes. ||[https://maayanlab.cloud/FlyEnrichr/help#api Yes] ||See [https://maayanlab.cloud/Enrichr/#new New] and [https://maayanlab.cloud/Enrichr/#libraries Libraries] ||[https://maayanlab.cloud/Enrichr/help#basics Help center]
! -
 
! [https://pubmed.ncbi.nlm.nih.gov/33780170/ PMID:33780170]
 
! Many (e.g. GO, disease, interaction, domains, phenotype, pathways), especially for [https://maayanlab.cloud/Enrichr/#libraries human]
 
! [https://maayanlab.cloud/Enrichr/ Enrichr Human & mouse], sites for [https://maayanlab.cloud/modEnrichr/ Mod-specific sets]: [https://maayanlab.cloud/FlyEnrichr/ FlyEnrichr (D.mel)], [https://maayanlab.cloud/YeastEnrichr/ YeastEnrichr (S.cerevisiae)], [https://maayanlab.cloud/WormEnrichr/ WormEnrichr (C. elegans)], [https://maayanlab.cloud/FishEnrichr/ FishEnrichr (D. rerio)]
 
! No
 
! Yes
 
! Yes
 
! No
 
! p-value, z-score
 
! Bar chart, table
 
! Analysis sharing feature. Other viewing features such as networks and gene-set similarity grid available for some set genes.
 
! [https://maayanlab.cloud/FlyEnrichr/help#api Yes]
 
! See [https://maayanlab.cloud/Enrichr/#new New] and [https://maayanlab.cloud/Enrichr/#libraries Libraries]
 
! [https://maayanlab.cloud/Enrichr/help#basics Help center]
 
 
|-
 
|-
! [https://go.princeton.edu/cgi-bin/GOTermFinder GO term finder]
+
| [https://go.princeton.edu/cgi-bin/GOTermFinder <b>GO term finder</b>] ||- ||[https://pubmed.ncbi.nlm.nih.gov/15297299/ PMID:15297299] ||GO ||Many (see [https://go.princeton.edu/cgi-bin/GOTermFinder dropdown menu])  ||Yes ||No ||No ||Yes ||p-value, Bonferroni, FDR ||GO graph with heat map ||Can select to use regulates links in the GO. Select evidence codes to exclude (HTP not listed). Upload a custom gene association file. [https://metacpan.org/dist/GO-TermFinder Open Source]. ||No ||Updated with [https://geneontology.org/stats.html GO release] (monthly) || -
! -
 
! [https://pubmed.ncbi.nlm.nih.gov/15297299/ PMID:15297299]
 
! GO
 
! Many [https://go.princeton.edu/cgi-bin/GOTermFinder see dropdown menu]  
 
! Yes
 
! No
 
! No
 
! Yes
 
! p-value, Bonferroni, FDR
 
! GO graph with heat map
 
! Can select to use regulates links in the GO. Select evidence codes to exclude (HTP not listed). Upload a custom gene association file. [https://metacpan.org/dist/GO-TermFinder Open Source].  
 
! No
 
! Updated with [https://geneontology.org/stats.html GO release] (monthly)
 
!
 
 
|-
 
|-
! [https://geneontology.org/ GO]/[https://pantherdb.org/ PANTHER]
+
| [https://geneontology.org/ <b>GO</b>]/[https://pantherdb.org/ <b>PANTHER</b>] ||Gene Ontology; Protein ANalysis THrough Evolutionary Relationships ||[https://pubmed.ncbi.nlm.nih.gov/34717010/ PMID:34717010] ||GO, GO Slim sets, PANTHER protein class, Reactome Pathways ||Large coverage ||No ||No ||Yes ||Yes ||p-value, FDR, Enrichment, Bonferroni, Fisher's Exact or Binomial test ||Hierarchical viewer of enrichment table; some graphical representation: pie, bar chart ||Can select set and statical method ||No ||Updated with [https://geneontology.org/stats.html GO release] (monthly) and [https://pantherdb.org/news/news20230917.jsp PANTHER release] || -
! Gene Ontology; Protein ANalysis THrough Evolutionary Relationships
 
! [https://pubmed.ncbi.nlm.nih.gov/34717010/ PMID:34717010]
 
! GO, GO Slim sets, PANTHER protein class, Reactome Pathways
 
! Large coverage
 
! No
 
! No
 
! Yes
 
! Yes
 
! p-value, FDR, Enrichment, Bonferroni, Fisher's Exact or Binomial test
 
! Hierarchical viewer of enrichment table; some graphical representation: pie, bar chart
 
! Can select set and statical method
 
! No
 
! Updated with [https://geneontology.org/stats.html GO release] (monthly) and [https://pantherdb.org/news/news20230917.jsp PANTHER release]
 
!
 
 
|-
 
|-
! [https://biit.cs.ut.ee/gprofiler/gost g:Profiler/g:GOSt]
+
| [https://biit.cs.ut.ee/gprofiler/gost <b>g:Profiler/g:GOSt</b>] ||- ||[https://pubmed.ncbi.nlm.nih.gov/31066453/ PMID:31066453] ||GO, KEGG, REACTOME, WikiPathways, TRANSFAC, mirTarBase, Human Protein Atlas, CORUM, HPO ||[https://biit.cs.ut.ee/gprofiler/page/docs#organism Large coverage] ||[https://biit.cs.ut.ee/gprofiler/convert Yes] ||Yes ||Yes ||Yes ||p-value, tailor-made algorithm g:SCS, Bonferroni, Benjamini-Hochberg. ||Interactive Manhattan plot, heat map ||Can select set and statical method, select to exclude electronic GO annotations and different gene sets to enrich for. [https://biit.cs.ut.ee/gprofiler/orth Ortholog mapping] [https://biit.cs.ut.ee/gprofiler/page/r R package] ||[https://biit.cs.ut.ee/gprofiler/page/apis Yes] ||Regular updates [https://biit.cs.ut.ee/gprofiler/page/news News]. Also has [https://biit.cs.ut.ee/gprofiler/page/archives archived versions] || [https://biit.cs.ut.ee/gprofiler/page/docs Documentation]
! -
 
! [https://pubmed.ncbi.nlm.nih.gov/31066453/ PMID:31066453]
 
! GO, KEGG, REACTOME, WikiPathways, TRANSFAC, mirTarBase, Human Protein Atlas, CORUM, HPO
 
! [https://biit.cs.ut.ee/gprofiler/page/docs#organism Large coverage]  
 
! [https://biit.cs.ut.ee/gprofiler/convert Yes]
 
! Yes
 
! Yes
 
! Yes
 
! p-value, tailor-made algorithm g:SCS, Bonferroni, Benjamini-Hochberg.
 
! Interactive Manhattan plot, heat map
 
! Can select set and statical method, select to exclude electronic GO annotations and different gene sets to enrich for. [https://biit.cs.ut.ee/gprofiler/orth Ortholog mapping] [https://biit.cs.ut.ee/gprofiler/page/r R package]  
 
! [https://biit.cs.ut.ee/gprofiler/page/apis Yes]
 
! Regular updates [https://biit.cs.ut.ee/gprofiler/page/news News]. Also has [https://biit.cs.ut.ee/gprofiler/page/archives archived versions]
 
[https://biit.cs.ut.ee/gprofiler/page/docs Documentation]
 
 
|-
 
|-
! [https://cbl-gorilla.cs.technion.ac.il/ GOrilla]
+
| [https://cbl-gorilla.cs.technion.ac.il/ <b>GOrilla</b>] ||Gene Ontology enRIchment anaLysis and visuaLizAtion tool ||[https://pubmed.ncbi.nlm.nih.gov/19192299/ PMID:19192299] ||GO ||D. melanogaster, Arabidopsis, S.cerevisiae, C.elegans, zebrafish, human, mouse, rat ||No ||No ||No ||Yes ||p-value, FDR q-value (Benjamini and Hochberg), enrichment ||Heat map GO Graph view ||Certain stats can be customised. Can run MF, BP, CC the same time but output is separated ||No ||? ||[https://cbl-gorilla.cs.technion.ac.il/help.html Usage Instructions]
! Gene Ontology enRIchment anaLysis and visuaLizAtion tool
 
! [https://pubmed.ncbi.nlm.nih.gov/19192299/ PMID:19192299]
 
! GO
 
! D. melanogaster, Arabidopsis, S.cerevisiae, C.elegans, zebrafish, human, mouse, rat
 
! No
 
! No
 
! No
 
! Yes
 
! p-value, FDR q-value (Benjamini and Hochberg), enrichment
 
! Heat map GO Graph view
 
! Certain stats can be customised. Can run MF, BP, CC the same time but output is separated
 
! No
 
! ?
 
! [https://cbl-gorilla.cs.technion.ac.il/help.html Usage Instructions]
 
 
|-
 
|-
! [https://www.flyrnai.org/tools/pangea/ PANGEA]
+
| [https://www.flyrnai.org/tools/pangea/ <b>PANGEA</b>] ||PAthway, Network and Gene-set Enrichment Analysis ||[https://pubmed.ncbi.nlm.nih.gov/37125646/ PMID:37125646] ||GO, gene groups, pathways, disease, protein complexes, phenotype, expression ||D. melanogaster, C.elegans. zebrafish, human, mouse, rat ||[https://www.flyrnai.org/tools/pangea/web/gene_map/7227 Yes] ||Yes ||Yes ||Yes ||p-value, Bonferroni, Benjamini-Hochberg,  Benjamini-Yekutieli ||Heatmap, bar chart, network, dot plot ||Customisable tables, selectable sets and interactive, customisable visualisation tools. ||No ||Updated every two months ||[https://www.flyrnai.org/tools/pangea/web/about About]; [https://www.flyrnai.org/tools/pangea/web/about Video tutorial]
! PAthway, Network and Gene-set Enrichment Analysis
 
! [https://pubmed.ncbi.nlm.nih.gov/37125646/ PMID:37125646]
 
! GO, gene groups, pathways, disease, protein complexes, phenotype, expression
 
! D. melanogaster, C.elegans. zebrafish, human, mouse, rat
 
! [https://www.flyrnai.org/tools/pangea/web/gene_map/7227 Yes]
 
! Yes
 
! Yes
 
! Yes
 
! p-value, Bonferroni, Benjamini-Hochberg,  Benjamini-Yekutieli
 
! Heatmap, bar chart, network, dot plot
 
! Customisable tables, selectable sets and interactive, customisable visualisation tools.
 
! No
 
! Updated every two months
 
! [https://www.flyrnai.org/tools/pangea/web/about About]; [https://www.flyrnai.org/tools/pangea/web/about Video tutorial]
 
 
|-
 
|-
! [https://www.webgestalt.org/ WebGestalt]
+
| [https://www.webgestalt.org/ <b>WebGestalt</b>] ||- ||[https://pubmed.ncbi.nlm.nih.gov/31114916/ PMID:31114916] ||GO, pathways, PANTHER, MSigDB, PTMs, phenotype, chromosomal location, co-expression ||Many (see [https://www.webgestalt.org/ dropdown list]) ||No ||No ||No ||No ||p-value, FDR ||Table, bar chart, volcano plot and GO graph. Can select different methods of analysis: over-representation analysis, GSEA, Network-Topology based. ||GSEA for microarray data input, over-representation analysis for single GSEA or Network-topology based analysis (PPI network). Stand alone network viewer. ||[https://www.webgestalt.org/WG2019_manual.html Yes] ||2019 ||[https://www.webgestalt.org/WebGestalt_2019_Manual.pdf Manual]
! -
 
! [https://pubmed.ncbi.nlm.nih.gov/31114916/ PMID:31114916]
 
! GO, pathways, PANTHER, MSigDB, PTMs, phenotype, chromosomal location, co-expression
 
! Many (see [https://www.webgestalt.org/ dropdown list])
 
! No
 
! No
 
! No
 
! No
 
! P value, FDR
 
! Table, bar chart, volcano plot and GO graph. Can select different methods of analysis: over-representation analysis, GSEA, Network-Topology based.
 
! GSEA for microarray data input, over-representation analysis for single GSEA or Network-topology based analysis (PPI network). Stand alone network viewer.
 
! [https://www.webgestalt.org/WG2019_manual.html Yes]
 
! 2019
 
! [https://www.webgestalt.org/WebGestalt_2019_Manual.pdf Manual]
 
 
|}
 
|}
 
[[Category:DONE]]
 
[[Category:DONE]]

Latest revision as of 09:48, 22 September 2023

Gene Set Enrichment Tools

Some examples of GSEA tools with links and information. A list of more GSEA tools can be found here.

It is recommended that users conduct their GSEA with more than one tool as all have different features, use statistically significant results and compare the overlap between enriched sets to further interpretation. With any GSEA, there will be genes within the analysis set that are not represented in the gene set libraries, e.g. genes that have very little characterisation. These may be of interest for further study, even though they are not in an enriched set.


Selected Gene Set Enrichment Tool Information

Tool Backronym Publication Enrichment sets Organism(s) ID conversion Multiple set enrichment available Parallel gene list analysis Custom background input Stats Visualisation Other features API Update Notes Help/tutorials
DAVID Database for Annotation, Visualization and Integrated Discovery PMID:35325185 Many (e.g. GO, interaction, domains, UniProt KeyWord, drug, human expression, disease, pathways) Large coverage Yes Yes No Yes p-value, Benjamini Bar chart and limited gene/term bin heat map; will also group bar charts in sets Manipulation of gene lists. Yes Updated ~twice yearly Updates Tutorial
Enrichr - PMID:33780170 Many (e.g. GO, disease, interaction, domains, phenotype, pathways), especially for human Enrichr Human & mouse, sites for Mod-specific sets: FlyEnrichr (D.mel), YeastEnrichr (S.cerevisiae), WormEnrichr (C. elegans), FishEnrichr (D. rerio) No Yes Yes No p-value, z-score Bar chart, table Analysis sharing feature. Other viewing features such as networks and gene-set similarity grid available for some set genes. Yes See New and Libraries Help center
GO term finder - PMID:15297299 GO Many (see dropdown menu) Yes No No Yes p-value, Bonferroni, FDR GO graph with heat map Can select to use regulates links in the GO. Select evidence codes to exclude (HTP not listed). Upload a custom gene association file. Open Source. No Updated with GO release (monthly) -
GO/PANTHER Gene Ontology; Protein ANalysis THrough Evolutionary Relationships PMID:34717010 GO, GO Slim sets, PANTHER protein class, Reactome Pathways Large coverage No No Yes Yes p-value, FDR, Enrichment, Bonferroni, Fisher's Exact or Binomial test Hierarchical viewer of enrichment table; some graphical representation: pie, bar chart Can select set and statical method No Updated with GO release (monthly) and PANTHER release -
g:Profiler/g:GOSt - PMID:31066453 GO, KEGG, REACTOME, WikiPathways, TRANSFAC, mirTarBase, Human Protein Atlas, CORUM, HPO Large coverage Yes Yes Yes Yes p-value, tailor-made algorithm g:SCS, Bonferroni, Benjamini-Hochberg. Interactive Manhattan plot, heat map Can select set and statical method, select to exclude electronic GO annotations and different gene sets to enrich for. Ortholog mapping R package Yes Regular updates News. Also has archived versions Documentation
GOrilla Gene Ontology enRIchment anaLysis and visuaLizAtion tool PMID:19192299 GO D. melanogaster, Arabidopsis, S.cerevisiae, C.elegans, zebrafish, human, mouse, rat No No No Yes p-value, FDR q-value (Benjamini and Hochberg), enrichment Heat map GO Graph view Certain stats can be customised. Can run MF, BP, CC the same time but output is separated No ? Usage Instructions
PANGEA PAthway, Network and Gene-set Enrichment Analysis PMID:37125646 GO, gene groups, pathways, disease, protein complexes, phenotype, expression D. melanogaster, C.elegans. zebrafish, human, mouse, rat Yes Yes Yes Yes p-value, Bonferroni, Benjamini-Hochberg, Benjamini-Yekutieli Heatmap, bar chart, network, dot plot Customisable tables, selectable sets and interactive, customisable visualisation tools. No Updated every two months About; Video tutorial
WebGestalt - PMID:31114916 GO, pathways, PANTHER, MSigDB, PTMs, phenotype, chromosomal location, co-expression Many (see dropdown list) No No No No p-value, FDR Table, bar chart, volcano plot and GO graph. Can select different methods of analysis: over-representation analysis, GSEA, Network-Topology based. GSEA for microarray data input, over-representation analysis for single GSEA or Network-topology based analysis (PPI network). Stand alone network viewer. Yes 2019 Manual