FRINK Linked Data Fragments server

Matches in SemOpenAlex for { <https://semopenalex.org/work/W3136308181> ?p ?o ?g. }

• W3136308181 abstract "Abstract Background Enrichment or over-representation analysis is a common method used in bioinformatics studies of transcriptomics, metabolomics, and microbiome datasets. The key idea behind enrichment analysis is: given a set of significantly expressed genes (or metabolites), use that set to infer a smaller set of perturbed biological pathways or processes, in which those genes (or metabolites) play a role. Enrichment computations rely on collections of defined biological pathways and/or processes, which are usually drawn from pathway databases. Although practitioners of enrichment analysis take great care to employ statistical corrections (e.g., for multiple testing), they appear unaware that enrichment results are quite sensitive to the pathway definitions that the calculation uses. Results We show that alternative pathway definitions can alter enrichment p -values by up to nine orders of magnitude, whereas statistical corrections typically alter enrichment p -values by only two orders of magnitude. We present multiple examples where the smaller pathway definitions used in the EcoCyc database produces stronger enrichment p -values than the much larger pathway definitions used in the KEGG database; we demonstrate that to attain a given enrichment p -value, KEGG-based enrichment analyses require 1.3–2.0 times as many significantly expressed genes as does EcoCyc-based enrichment analyses. The large pathways in KEGG are problematic for another reason: they blur together multiple (as many as 21) biological processes. When such a KEGG pathway receives a high enrichment p -value, which of its component processes is perturbed is unclear, and thus the biological conclusions drawn from enrichment of large pathways are also in question. Conclusions The choice of pathway database used in enrichment analyses can have a much stronger effect on the enrichment results than the statistical corrections used in these analyses." @default.
• W3136308181 created "2021-03-29" @default.
• W3136308181 creator A5044919501 @default.
• W3136308181 creator A5049879477 @default.
• W3136308181 creator A5058185060 @default.
• W3136308181 creator A5082071104 @default.
• W3136308181 date "2021-03-16" @default.
• W3136308181 modified "2023-10-11" @default.
• W3136308181 title "Pathway size matters: the influence of pathway granularity on over-representation (enrichment analysis) statistics" @default.
• W3136308181 cites W2060880575 @default.
• W3136308181 cites W2099526830 @default.
• W3136308181 cites W2100980426 @default.
• W3136308181 cites W2102899487 @default.
• W3136308181 cites W2135000328 @default.
• W3136308181 cites W2152274187 @default.
• W3136308181 cites W2158485828 @default.
• W3136308181 cites W2559588208 @default.
• W3136308181 cites W2560707317 @default.
• W3136308181 cites W2749464300 @default.
• W3136308181 cites W2767914218 @default.
• W3136308181 cites W2781939187 @default.
• W3136308181 cites W2950595506 @default.
• W3136308181 cites W2977870980 @default.
• W3136308181 cites W2989619704 @default.
• W3136308181 cites W4233698560 @default.
• W3136308181 doi "https://doi.org/10.1186/s12864-021-07502-8" @default.
• W3136308181 hasPubMedCentralId "https://www.ncbi.nlm.nih.gov/pmc/articles/7967953" @default.
• W3136308181 hasPubMedId "https://pubmed.ncbi.nlm.nih.gov/33726670" @default.
• W3136308181 hasPublicationYear "2021" @default.
• W3136308181 type Work @default.
• W3136308181 sameAs 3136308181 @default.
• W3136308181 citedByCount "123" @default.
• W3136308181 countsByYear W31363081812021 @default.
• W3136308181 countsByYear W31363081812022 @default.
• W3136308181 countsByYear W31363081812023 @default.
• W3136308181 crossrefType "journal-article" @default.
• W3136308181 hasAuthorship W3136308181A5044919501 @default.
• W3136308181 hasAuthorship W3136308181A5049879477 @default.
• W3136308181 hasAuthorship W3136308181A5058185060 @default.
• W3136308181 hasAuthorship W3136308181A5082071104 @default.
• W3136308181 hasBestOaLocation W31363081811 @default.
• W3136308181 hasConcept C104317684 @default.
• W3136308181 hasConcept C119857082 @default.
• W3136308181 hasConcept C150194340 @default.
• W3136308181 hasConcept C152724338 @default.
• W3136308181 hasConcept C162317418 @default.
• W3136308181 hasConcept C177264268 @default.
• W3136308181 hasConcept C17744445 @default.
• W3136308181 hasConcept C199360897 @default.
• W3136308181 hasConcept C199539241 @default.
• W3136308181 hasConcept C21565614 @default.
• W3136308181 hasConcept C2776291640 @default.
• W3136308181 hasConcept C2776359362 @default.
• W3136308181 hasConcept C2779230013 @default.
• W3136308181 hasConcept C41008148 @default.
• W3136308181 hasConcept C54355233 @default.
• W3136308181 hasConcept C60644358 @default.
• W3136308181 hasConcept C70721500 @default.
• W3136308181 hasConcept C86803240 @default.
• W3136308181 hasConcept C94625758 @default.
• W3136308181 hasConcept C9927688 @default.
• W3136308181 hasConceptScore W3136308181C104317684 @default.
• W3136308181 hasConceptScore W3136308181C119857082 @default.
• W3136308181 hasConceptScore W3136308181C150194340 @default.
• W3136308181 hasConceptScore W3136308181C152724338 @default.
• W3136308181 hasConceptScore W3136308181C162317418 @default.
• W3136308181 hasConceptScore W3136308181C177264268 @default.
• W3136308181 hasConceptScore W3136308181C17744445 @default.
• W3136308181 hasConceptScore W3136308181C199360897 @default.
• W3136308181 hasConceptScore W3136308181C199539241 @default.
• W3136308181 hasConceptScore W3136308181C21565614 @default.
• W3136308181 hasConceptScore W3136308181C2776291640 @default.
• W3136308181 hasConceptScore W3136308181C2776359362 @default.
• W3136308181 hasConceptScore W3136308181C2779230013 @default.
• W3136308181 hasConceptScore W3136308181C41008148 @default.
• W3136308181 hasConceptScore W3136308181C54355233 @default.
• W3136308181 hasConceptScore W3136308181C60644358 @default.
• W3136308181 hasConceptScore W3136308181C70721500 @default.
• W3136308181 hasConceptScore W3136308181C86803240 @default.
• W3136308181 hasConceptScore W3136308181C94625758 @default.
• W3136308181 hasConceptScore W3136308181C9927688 @default.
• W3136308181 hasFunder F4320332161 @default.
• W3136308181 hasIssue "1" @default.
• W3136308181 hasLocation W31363081811 @default.
• W3136308181 hasLocation W31363081812 @default.
• W3136308181 hasLocation W31363081813 @default.
• W3136308181 hasOpenAccess W3136308181 @default.
• W3136308181 hasPrimaryLocation W31363081811 @default.
• W3136308181 hasRelatedWork W2083488242 @default.
• W3136308181 hasRelatedWork W2297026197 @default.
• W3136308181 hasRelatedWork W2378339845 @default.
• W3136308181 hasRelatedWork W2402286330 @default.
• W3136308181 hasRelatedWork W2895072526 @default.
• W3136308181 hasRelatedWork W2943650845 @default.
• W3136308181 hasRelatedWork W3089173564 @default.
• W3136308181 hasRelatedWork W3107361973 @default.
• W3136308181 hasRelatedWork W4224243421 @default.
• W3136308181 hasRelatedWork W4321600314 @default.
• W3136308181 hasVolume "22" @default.
• W3136308181 isParatext "false" @default.

• next