Matches in SemOpenAlex for { <https://semopenalex.org/work/W3136285258> ?p ?o ?g. }
- W3136285258 abstract "The NCBI Gene Expression Omnibus (GEO) provides tools to query and download transcriptomic data. However, less than 4% of microbial experiments include the sample group annotations required to assess differential gene expression for high-throughput reanalysis, and data deposited after 2014 universally lack these annotations. Our algorithm GAUGE (general annotation using text/data group ensembles) automatically annotates GEO microbial data sets, including microarray and RNA sequencing studies, increasing the percentage of data sets amenable to analysis from 4% to 33%. Eighty-nine percent of GAUGE-annotated studies matched group assignments generated by human curators. To demonstrate how GAUGE annotation can lead to scientific insight, we created GAPE (GAUGE-annotated Pseudomonas aeruginosa and Escherichia coli transcriptomic compendia for reanalysis), a Shiny Web interface to analyze 73 GAUGE-annotated P. aeruginosa studies, three times more than previously available. GAPE analysis revealed that PA3923, a gene of unknown function, was frequently differentially expressed in more than 50% of studies and significantly coregulated with genes involved in biofilm formation. Follow-up wet-bench experiments demonstrate that PA3923 mutants are indeed defective in biofilm formation, consistent with predictions facilitated by GAUGE and GAPE. We anticipate that GAUGE and GAPE, which we have made freely available, will make publicly available microbial transcriptomic data easier to reuse and lead to new data-driven hypotheses.IMPORTANCE GEO archives transcriptomic data from over 5,800 microbial experiments and allows researchers to answer questions not directly addressed in published papers. However, less than 4% of the microbial data sets include the sample group annotations required for high-throughput reanalysis. This limitation blocks a considerable amount of microbial transcriptomic data from being reused easily. Here, we demonstrate that the GAUGE algorithm could make 33% of microbial data accessible to parallel mining and reanalysis. GAUGE annotations increase statistical power and, thereby, make consistent patterns of differential gene expression easier to identify. In addition, we developed GAPE (GAUGE-annotated Pseudomonas aeruginosa and Escherichia coli transcriptomic compendia for reanalysis), a Shiny Web interface that performs parallel analyses on P. aeruginosa and E. coli compendia. Source code for GAUGE and GAPE is freely available and can be repurposed to create compendia for other bacterial species." @default.
- W3136285258 created "2021-03-29" @default.
- W3136285258 creator A5000952507 @default.
- W3136285258 creator A5006474038 @default.
- W3136285258 creator A5009010756 @default.
- W3136285258 creator A5017023395 @default.
- W3136285258 creator A5030383333 @default.
- W3136285258 creator A5041236219 @default.
- W3136285258 creator A5045250449 @default.
- W3136285258 creator A5058782541 @default.
- W3136285258 creator A5089692722 @default.
- W3136285258 date "2021-04-27" @default.
- W3136285258 modified "2023-10-15" @default.
- W3136285258 title "GAUGE-Annotated Microbial Transcriptomic Data Facilitate Parallel Mining and High-Throughput Reanalysis To Form Data-Driven Hypotheses" @default.
- W3136285258 cites W1972602976 @default.
- W3136285258 cites W1995924159 @default.
- W3136285258 cites W2013106856 @default.
- W3136285258 cites W2020541351 @default.
- W3136285258 cites W2024605770 @default.
- W3136285258 cites W2030955639 @default.
- W3136285258 cites W2038329167 @default.
- W3136285258 cites W2055613435 @default.
- W3136285258 cites W2057873642 @default.
- W3136285258 cites W2070238977 @default.
- W3136285258 cites W2100239923 @default.
- W3136285258 cites W2110055456 @default.
- W3136285258 cites W2110256992 @default.
- W3136285258 cites W2114104545 @default.
- W3136285258 cites W2118258530 @default.
- W3136285258 cites W2133425351 @default.
- W3136285258 cites W2139744939 @default.
- W3136285258 cites W2141012198 @default.
- W3136285258 cites W2146512944 @default.
- W3136285258 cites W2156247618 @default.
- W3136285258 cites W2164003656 @default.
- W3136285258 cites W2168027558 @default.
- W3136285258 cites W2179324586 @default.
- W3136285258 cites W2259632819 @default.
- W3136285258 cites W2294470506 @default.
- W3136285258 cites W2302501749 @default.
- W3136285258 cites W2734646376 @default.
- W3136285258 cites W2781236732 @default.
- W3136285258 cites W2793422535 @default.
- W3136285258 cites W2883251903 @default.
- W3136285258 cites W2930906415 @default.
- W3136285258 cites W2951403620 @default.
- W3136285258 cites W2969054306 @default.
- W3136285258 cites W2991449692 @default.
- W3136285258 cites W2994526781 @default.
- W3136285258 doi "https://doi.org/10.1128/msystems.01305-20" @default.
- W3136285258 hasPubMedCentralId "https://www.ncbi.nlm.nih.gov/pmc/articles/8547006" @default.
- W3136285258 hasPubMedId "https://pubmed.ncbi.nlm.nih.gov/33758032" @default.
- W3136285258 hasPublicationYear "2021" @default.
- W3136285258 type Work @default.
- W3136285258 sameAs 3136285258 @default.
- W3136285258 citedByCount "9" @default.
- W3136285258 countsByYear W31362852582021 @default.
- W3136285258 countsByYear W31362852582022 @default.
- W3136285258 countsByYear W31362852582023 @default.
- W3136285258 crossrefType "journal-article" @default.
- W3136285258 hasAuthorship W3136285258A5000952507 @default.
- W3136285258 hasAuthorship W3136285258A5006474038 @default.
- W3136285258 hasAuthorship W3136285258A5009010756 @default.
- W3136285258 hasAuthorship W3136285258A5017023395 @default.
- W3136285258 hasAuthorship W3136285258A5030383333 @default.
- W3136285258 hasAuthorship W3136285258A5041236219 @default.
- W3136285258 hasAuthorship W3136285258A5045250449 @default.
- W3136285258 hasAuthorship W3136285258A5058782541 @default.
- W3136285258 hasAuthorship W3136285258A5089692722 @default.
- W3136285258 hasBestOaLocation W31362852581 @default.
- W3136285258 hasConcept C104317684 @default.
- W3136285258 hasConcept C121332964 @default.
- W3136285258 hasConcept C124101348 @default.
- W3136285258 hasConcept C141231307 @default.
- W3136285258 hasConcept C150194340 @default.
- W3136285258 hasConcept C162317418 @default.
- W3136285258 hasConcept C166957645 @default.
- W3136285258 hasConcept C177212765 @default.
- W3136285258 hasConcept C198531522 @default.
- W3136285258 hasConcept C205649164 @default.
- W3136285258 hasConcept C23123220 @default.
- W3136285258 hasConcept C2776321320 @default.
- W3136285258 hasConcept C2908923196 @default.
- W3136285258 hasConcept C40976572 @default.
- W3136285258 hasConcept C41008148 @default.
- W3136285258 hasConcept C54355233 @default.
- W3136285258 hasConcept C60644358 @default.
- W3136285258 hasConcept C70721500 @default.
- W3136285258 hasConcept C77088390 @default.
- W3136285258 hasConcept C86803240 @default.
- W3136285258 hasConcept C97355855 @default.
- W3136285258 hasConceptScore W3136285258C104317684 @default.
- W3136285258 hasConceptScore W3136285258C121332964 @default.
- W3136285258 hasConceptScore W3136285258C124101348 @default.
- W3136285258 hasConceptScore W3136285258C141231307 @default.
- W3136285258 hasConceptScore W3136285258C150194340 @default.
- W3136285258 hasConceptScore W3136285258C162317418 @default.
- W3136285258 hasConceptScore W3136285258C166957645 @default.
- W3136285258 hasConceptScore W3136285258C177212765 @default.
- W3136285258 hasConceptScore W3136285258C198531522 @default.