Please be advised that the site will be down for maintenance on Sunday, September 1, 2024, from 08:00 to 18:00, and again on Monday, September 2, 2024, from 08:00 to 09:00. We apologize for any inconvenience this may cause.
dc.contributor.author | Zwaenepoel, Arthur | |
dc.contributor.author | Diels, Tim | |
dc.contributor.author | Amar, David | |
dc.contributor.author | Van Parys, Thomas | |
dc.contributor.author | Shamir, Ron | |
dc.contributor.author | Van de Peer, Yves | |
dc.contributor.author | Tzfadia, Oren | |
dc.date.accessioned | 2019-11-13T12:56:27Z | |
dc.date.available | 2019-11-13T12:56:27Z | |
dc.date.issued | 2018-03-19 | |
dc.description.abstract | Recent times have seen an enormous growth of “omics” data, of which high-throughput gene expression data are arguably the most important from a functional perspective. Despite huge improvements in computational techniques for the functional classification of gene sequences, common similarity-based methods often fall short of providing full and reliable functional information. Recently, the combination of comparative genomics with approaches in functional genomics has received considerable interest for gene function analysis, leveraging both gene expression based guilt-by-association methods and annotation efforts in closely related model organisms. Besides the identification of missing genes in pathways, these methods also typically enable the discovery of biological regulators (i.e., transcription factors or signaling genes). A previously built guilt-by-association method is MORPH, which was proven to be an efficient algorithm that performs particularly well in identifying and prioritizing missing genes in plant metabolic pathways. Here, we present MorphDB, a resource where MORPH-based candidate genes for large-scale functional annotations (Gene Ontology, MapMan bins) are integrated across multiple plant species. Besides a gene centric query utility, we present a comparative network approach that enables researchers to efficiently browse MORPH predictions across functional gene sets and species, facilitating efficient gene discovery and candidate gene prioritization. MorphDB is available at http:// bioinformatics.psb.ugent.be/webtools/morphdb/morphDB/index/. We also provide a toolkit, named “MORPH bulk” (https://github.com/arzwa/morph-bulk), for running MORPH in bulk mode on novel data sets, enabling researchers to apply MORPH to their own species of interest. | en_ZA |
dc.description.department | Genetics | en_ZA |
dc.description.librarian | am2019 | en_ZA |
dc.description.sponsorship | AZ acknowledges financial support from the special research fund (BOF) of Ghent University. YV acknowledges the Multidisciplinary Research Partnership Bioinformatics: from nucleotides to networks Project (no. 01MR0310W) of Ghent University, and funding from the European Union Seventh Framework Programme (FP7/2007-2013) under European Research Council Advanced Grant Agreement 322739 – DOUBLEUP. | en_ZA |
dc.description.uri | http://www.frontiersin.org/Plant_Science | en_ZA |
dc.identifier.citation | Zwaenepoel A, Diels T, Amar D, Van Parys T, Shamir R, Van de Peer Y and Tzfadia O (2018) MorphDB: Prioritizing Genes for Specialized Metabolism Pathways and Gene Ontology Categories in Plants. Frontiers In Plant Science 9:352. DOI: 10.3389/fpls.2018.00352. | en_ZA |
dc.identifier.issn | 1664-462X (online) | |
dc.identifier.other | 10.3389/fpls.2018.00352 | |
dc.identifier.uri | http://hdl.handle.net/2263/72246 | |
dc.language.iso | en | en_ZA |
dc.publisher | Frontiers Media | en_ZA |
dc.rights | © 2018 Zwaenepoel, Diels, Amar, Van Parys, Shamir, Van de Peer and Tzfadia. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). | en_ZA |
dc.subject | Comparative co-expression networks | en_ZA |
dc.subject | Candidate gene prioritization | en_ZA |
dc.subject | Functional annotation | en_ZA |
dc.subject | MORPH | en_ZA |
dc.subject | Defense response | en_ZA |
dc.title | MorphDB : prioritizing genes for specialized metabolism pathways and gene ontology categories in plants | en_ZA |
dc.type | Article | en_ZA |