Editing Sequence analysis (section)

=== Functional enrichment analysis === 

Functional enrichment analysis identifies biological processes, pathways, and functional impacts associated with differentially expressed genes obtained from the previous step. It uses tools like GOSeq<ref>{{cite journal |last1=Young |first1=M.D. |last2=Wakefield |first2=M.J |last3=Smythe |first3=G.K |display-authors=2 |title=Gene ontology analysis for RNA-seq: accounting for selection bias |journal=Genome Biology |date=February 2010 |volume=11 |issue=2 |pages=R14 |doi=10.1186/gb-2010-11-2-r14 |doi-access=free |pmid=20132535 |hdl=11343/56416 |hdl-access=free }}</ref> and Pathview.<ref>{{cite journal |last1=Luo |first1=Weijun |last2=Brouwer |first2=Cory |title=Pathview: an R/Bioconductor package for pathway-based data integration and visualization |journal=Bioinformatics |date=June 2013 |volume=29 |issue=14 |pages=1830–1831 |doi=10.1093/bioinformatics/btt285 |pmid=23740750 |pmc=3702256 |url=https://doi.org/10.1093/bioinformatics/btt285}}</ref> This creates a table with information about what pathways and molecular processes are associated with the differentially expressed genes, what genes are down or upregulated, and what [[gene ontology]] terms are recurrent or over-represented.<ref name=sequence_analysis/><ref name=galaxy1/><ref name=galaxy2/><ref name=galaxy3/> 

RNA sequence analysis explores gene expression dynamics and regulatory mechanisms underlying biological processes and diseases. Interpretation of images and tables are carried out within the context of the hypotheses being investigated.

''See also: [[Transcriptomic technologies]].''