Matches in SemOpenAlex for { <https://semopenalex.org/work/W2807420865> ?p ?o ?g. }
Showing items 1 to 100 of
100
with 100 items per page.
- W2807420865 abstract "ABSTRACT Predicting gene regulatory networks (GRNs) from gene expression profiles has become a common approach for identifying important biological regulators. Despite the increase in the use of inference methods, existing computational approaches do not integrate RNA-sequencing data analysis, are often not automated, and are restricted to users with bioinformatics and programming backgrounds. To address these limitations, we have developed TuxNet, an integrated user-friendly platform, which, with just a few selections, allows to process raw RNA-sequencing data (using the Tuxedo pipeline) and infer GRNs from these processed data. TuxNet is implemented as a graphical user interface and, using expression data from any organism with an existing reference genome, can mine the regulations among genes either by applying a dynamic Bayesian network inference algorithm, GENIST, or a regression tree-based pipeline that uses spatiotemporal data, RTP-STAR. To illustrate the use of TuxNet while getting insight into the regulatory cascade downstream of the Arabidopsis root stem cell regulator PERIANTHIA (PAN) , we obtained time course gene expression data of a PAN inducible line and inferred a GRN using GENIST. Using RTP-STAR, we then inferred the network of a PAN secondary downstream gene, ATHB13 , for which we obtained wildtype and mutant expression profiles. Our case studies feature the versatility of TuxNet to infer networks using different types of gene expression data (i.e time course and steady-state data) as well as how inference networks are used to identify important regulators. SUMMARY TuxNet offers a simple interface for non-computational biologists to infer GRNs from raw RNA-seq data." @default.
- W2807420865 created "2018-06-13" @default.
- W2807420865 creator A5001602562 @default.
- W2807420865 creator A5012552344 @default.
- W2807420865 creator A5014538327 @default.
- W2807420865 creator A5040624110 @default.
- W2807420865 creator A5066303839 @default.
- W2807420865 date "2018-06-03" @default.
- W2807420865 modified "2023-10-16" @default.
- W2807420865 title "TuxNet: A simple interface to process RNA sequencing data and infer gene regulatory networks" @default.
- W2807420865 cites W1899578943 @default.
- W2807420865 cites W1984197456 @default.
- W2807420865 cites W1989367702 @default.
- W2807420865 cites W2076513103 @default.
- W2807420865 cites W2094100452 @default.
- W2807420865 cites W2097065948 @default.
- W2807420865 cites W2098832713 @default.
- W2807420865 cites W2100305481 @default.
- W2807420865 cites W2103441770 @default.
- W2807420865 cites W2108234281 @default.
- W2807420865 cites W2114104545 @default.
- W2807420865 cites W2124985265 @default.
- W2807420865 cites W2128733118 @default.
- W2807420865 cites W2134526812 @default.
- W2807420865 cites W2159675211 @default.
- W2807420865 cites W2170551349 @default.
- W2807420865 cites W2174163589 @default.
- W2807420865 cites W2179438025 @default.
- W2807420865 cites W2554858735 @default.
- W2807420865 cites W2748889255 @default.
- W2807420865 cites W2787055899 @default.
- W2807420865 cites W3099289621 @default.
- W2807420865 doi "https://doi.org/10.1101/337147" @default.
- W2807420865 hasPublicationYear "2018" @default.
- W2807420865 type Work @default.
- W2807420865 sameAs 2807420865 @default.
- W2807420865 citedByCount "1" @default.
- W2807420865 countsByYear W28074208652018 @default.
- W2807420865 crossrefType "posted-content" @default.
- W2807420865 hasAuthorship W2807420865A5001602562 @default.
- W2807420865 hasAuthorship W2807420865A5012552344 @default.
- W2807420865 hasAuthorship W2807420865A5014538327 @default.
- W2807420865 hasAuthorship W2807420865A5040624110 @default.
- W2807420865 hasAuthorship W2807420865A5066303839 @default.
- W2807420865 hasBestOaLocation W28074208651 @default.
- W2807420865 hasConcept C104317684 @default.
- W2807420865 hasConcept C111919701 @default.
- W2807420865 hasConcept C124101348 @default.
- W2807420865 hasConcept C150194340 @default.
- W2807420865 hasConcept C154945302 @default.
- W2807420865 hasConcept C199360897 @default.
- W2807420865 hasConcept C2776214188 @default.
- W2807420865 hasConcept C41008148 @default.
- W2807420865 hasConcept C43521106 @default.
- W2807420865 hasConcept C54355233 @default.
- W2807420865 hasConcept C67339327 @default.
- W2807420865 hasConcept C70721500 @default.
- W2807420865 hasConcept C86803240 @default.
- W2807420865 hasConcept C98045186 @default.
- W2807420865 hasConceptScore W2807420865C104317684 @default.
- W2807420865 hasConceptScore W2807420865C111919701 @default.
- W2807420865 hasConceptScore W2807420865C124101348 @default.
- W2807420865 hasConceptScore W2807420865C150194340 @default.
- W2807420865 hasConceptScore W2807420865C154945302 @default.
- W2807420865 hasConceptScore W2807420865C199360897 @default.
- W2807420865 hasConceptScore W2807420865C2776214188 @default.
- W2807420865 hasConceptScore W2807420865C41008148 @default.
- W2807420865 hasConceptScore W2807420865C43521106 @default.
- W2807420865 hasConceptScore W2807420865C54355233 @default.
- W2807420865 hasConceptScore W2807420865C67339327 @default.
- W2807420865 hasConceptScore W2807420865C70721500 @default.
- W2807420865 hasConceptScore W2807420865C86803240 @default.
- W2807420865 hasConceptScore W2807420865C98045186 @default.
- W2807420865 hasLocation W28074208651 @default.
- W2807420865 hasOpenAccess W2807420865 @default.
- W2807420865 hasPrimaryLocation W28074208651 @default.
- W2807420865 hasRelatedWork W1581837830 @default.
- W2807420865 hasRelatedWork W17419921 @default.
- W2807420865 hasRelatedWork W1985899955 @default.
- W2807420865 hasRelatedWork W2042879528 @default.
- W2807420865 hasRelatedWork W2076513103 @default.
- W2807420865 hasRelatedWork W2103097715 @default.
- W2807420865 hasRelatedWork W2121937120 @default.
- W2807420865 hasRelatedWork W2135594369 @default.
- W2807420865 hasRelatedWork W2410978489 @default.
- W2807420865 hasRelatedWork W2621029911 @default.
- W2807420865 hasRelatedWork W2732684237 @default.
- W2807420865 hasRelatedWork W2771059120 @default.
- W2807420865 hasRelatedWork W2888079055 @default.
- W2807420865 hasRelatedWork W2891115924 @default.
- W2807420865 hasRelatedWork W2903067813 @default.
- W2807420865 hasRelatedWork W2936979086 @default.
- W2807420865 hasRelatedWork W2950163725 @default.
- W2807420865 hasRelatedWork W2979089085 @default.
- W2807420865 hasRelatedWork W3019620359 @default.
- W2807420865 hasRelatedWork W3186348651 @default.
- W2807420865 isParatext "false" @default.
- W2807420865 isRetracted "false" @default.
- W2807420865 magId "2807420865" @default.
- W2807420865 workType "article" @default.