Random Information Report: Gene set enrichment analysis
Name: Matthew Huang
Address: Unit 2611 Box 5936, DPO AE 85523
Email:
[email protected]Phone: +1-885-668-9215x3291
Company: Lee and Sons
Job: Cytogeneticist
{{Short description|Bioinformatics method}}
{{cs1 config|name-list-style=vanc|display-authors=6}}
[[File:Gsea meta.png|thumb|right|500 px|Schematic overview of the modular structure underlying procedures for gene set e
'''Gene set enrichment analysis (GSEA)''' (also called '''functional enrichment analysis''' or '''pathway enrichment analysis''')
Researchers performing [[high-throughput screening|high-throughput experiments]] that yield sets of genes (for example, g
== Background ==
After the completion of the [[Human Genome Project]], the problem of how to interpret and analyze it remained. In order to
== Methods ==
Gene set enrichment analysis uses ''[[A priori and a posteriori|a priori]]'' gene sets that have been grouped together by their
In the method that is typically referred to as standard GSEA, there are three steps involved in the analytical process.<ref na
# Calculate the ''enrichment score'' (ES) that represents the amount to which the genes in the set are over-represented at e
# Estimate the statistical significance of the ES. This calculation is done by a phenotypic-based permutation test in order to
#*Calculating significance this way tests for the dependence of the gene set on the diagnostic/phenotypic labels<ref name=
# Adjust for multiple hypothesis testing for when a large number of gene sets are being analyzed at one time. The enrichme
This can be described as:
<math display="block">
\begin{alignat}{1}
& P_{hit}(S, i)= \sum_{g_j \in S, j \leq i}\dfrac{|r_j|^p}{N_R}; \\[0.6ex]
& P_{miss}(S, i) = \sum_{g_j \not \in S, j \leq i}\dfrac{1}{N - N_H}; \\[0.6ex]
& N_R = \sum_{g_j \in S}|r_j|^p; \\[0.6ex]
& ES=P(S, i)=P_{hit}(S, i)-P_{miss}(S,i)=max(|P_{hit}(S, i)-P_{miss}(S, i)|) \\[0.6ex]
\end{alignat}
</math>
Where <math>r</math> is the rank of the gene, <math>p</math> is the power usually set to 1 (if it were 0, it would be equ
=== Limitations and proposed alternatives ===
==== SEA ====
When GSEA was first proposed in 2003 some immediate concerns were raised regarding its methodology. These criticism
==== SGSE ====
One other limitation to Gene Set Enrichment Analysis is that the results are very dependent on the algorithm that clusters t
1. Calculating the association between principal components and gene sets.<ref name="Frost_2015" />
2. Using the weighted Z-method to calculate the association between the gene sets and the spectral structure of the data
== Tools ==
GSEA uses complicated statistics, so it requires a computer program to run the calculations. GSEA ha
=== MOET===
Multi-Ontology Enrichment Tool (MOET) is a web-based ontology analysis tool that provides functiona
=== NASQAR ===
NASQAR (Nucleic Acid SeQuence Analysis Resource) is an open source, web-based platform for high
=== PlantRegMap===
The [[gene ontology]] (GO) annotation for 165 plant species and GO enrichment analysis is available.<
=== MSigDB ===
The Molecular Signatures Database hosts an extensive collection of annotated gene sets that can be u
=== Broad Institute ===
The [[Broad Institute]] website is in cooperation with MSigDB and has a downloadable GSEA software
=== WebGestalt ===
WebGestalt <ref>{{cite web|title=WebGestalt (WEB-based GEne SeT AnaLysis Toolkit)|url=http://www
=== Enrichr ===
Enrichr<ref>{{cite journal | vauthors = Chen EY, Tan CM, Kou Y, Duan Q, Wang Z, Meirelles GV, Clark
=== GeneSCF ===
GeneSCF is a real-time based functional enrichment tool with support for multiple organisms<ref name
=== DAVID ===
[[DAVID]] is the database for annotation, visualization and integrated discovery, a [[bioinformatics]] too
=== Metascape ===
[[Metascape]] is a biologist-oriented gene-list analysis portal.<ref>{{cite journal | vauthors = Zhou Y, Zh
===AmiGO 2===
The [[Gene Ontology]] (GO) consortium has also developed their own online GO term enrichment tool,
allowing species-specific enrichment analysis versus the complete database, coarser-grained GO slim
===GREAT===
Genomic region enrichment of annotations tool (GREAT) is a software which takes advantage of ''regu
=== FunRich ===
The Functional Enrichment Analysis (FunRich) tool<ref>{{cite web|title=FunRich :: Download|url=http:/
=== FuncAssociate ===
The FuncAssociate tool enables Gene Ontology and custom enrichment analyses.<ref name="Berriz_
=== InterMine ===
Instances of [[InterMine]] automatically provide enrichment analysis <ref>{{Cite web | url=https://interm
=== ToppGene suite ===
ToppGene is a one-stop portal for gene list enrichment analysis and candidate gene prioritization base
=== QuSAGE ===
Quantitative Set Analysis for Gene Expression (QuSAGE)] is a computational method for gene set enr
<ref>{{cite web | vauthors = Bolen C, Yaari G, Thakar J, Meng H, Turner J, Blankenship D, Kleinstein S
=== Blast2GO ===
Blast2GO is a bioinformatics platform for functional annotation and analysis of genomic datasets.<ref>
=== g:Profiler ===
g:Profiler is a toolset for finding biological categories enriched in gene lists, conversions between gene
== Applications ==
=== Genome-wide association studies ===
[[Single-nucleotide polymorphism]]s, or SNPs, are single base mutations that may be associated with d
=== Spontaneous preterm birth ===
Gene set enrichment methods led to the discovery of new suspect genes and biological pathways rela
=== Cancer cell profiling ===
Gene set enrichment analysis can be used to understand the changes that cells undergo during [[carci
=== Schizophrenia ===
GSEA can be used to help understand the molecular mechanisms of complex disorders. Schizophreni
=== Depression ===
GSEA can help provide molecular evidence for the association of biological pathways with diseases. P
== See also ==
*[[Gene Ontology Term Enrichment]]
== References ==
{{Reflist}}
== Further reading ==
{{refbegin}}
* {{cite journal | vauthors = Subramanian A, Tamayo P, Mootha VK, Mukherjee S, Ebert BL, Gillette MA
* {{cite journal | vauthors = Reimand J, Isserlin R, Voisin V, Kucera M, Tannus-Lopes C, Rostamianfar
* {{cite journal | vauthors = Chicco D, Agapito G | title = Nine quick tips for pathway enrichment analysi
{{refend}}
== External links ==
*[https://www.gsea-msigdb.org/gsea/msigdb/ Molecular Signatures Database (MSigDB)]
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