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OmicsDB::Pathogens - A database for exploring functional networks of plant pathogens

https://doi.org/10.1101/2020.03.18.979971

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What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

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The FET3 gene of S. cerevisiae encodes a multicopper oxidase required for ferrous iron uptake

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A Proteome-wide Fission Yeast Interactome Reveals Network Evolution Principles from Yeasts to Human

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Current IUBMB recommendations on enzyme nomenclature and kinetics

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Gene Ontology: tool for the unification of biology

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Functional profiling of the Saccharomyces cerevisiae genome

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The genome sequence of the filamentous fungus Neurospora crassa

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Insights from the genome of the biotrophic fungal plant pathogen Ustilago maydis

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The genome sequence of Schizosaccharomyces pombe

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The wheat powdery mildew genome shows the unique evolution of an obligate biotroph

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SciPy 1.0: fundamental algorithms for scientific computing in Python

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The Iron Transporter Fth1p Forms a Complex with the Fet5 Iron Oxidase and Resides on the Vacuolar Membrane

inferredcites →https://doi.org/10.1093/bioinformatics/btp352openalex-snapshot

The Sequence Alignment/Map format and SAMtools

inferredcites →https://doi.org/10.1093/bioinformatics/btq671openalex-snapshot

Tabix: fast retrieval of sequence features from generic TAB-delimited files

inferredcites →https://doi.org/10.1093/bioinformatics/btt549openalex-snapshot

Are graph databases ready for bioinformatics?

inferredcites →https://doi.org/10.1093/bioinformatics/btu031openalex-snapshot

InterProScan 5: genome-scale protein function classification

inferredcites →https://doi.org/10.1093/bioinformatics/btu638openalex-snapshot

HTSeq—a Python framework to work with high-throughput sequencing data

inferredcites →https://doi.org/10.1093/bioinformatics/btv557openalex-snapshot

Cytoscape.js: a graph theory library for visualisation and analysis

inferredcites →https://doi.org/10.1093/database/bat042openalex-snapshot

eFG: an electronic resource for Fusarium graminearum

inferredcites →https://doi.org/10.1093/nar/26.1.73openalex-snapshot

SGD: Saccharomyces Genome Database

inferredcites →https://doi.org/10.1093/nar/gkn785openalex-snapshot

InterPro: the integrative protein signature database

inferredcites →https://doi.org/10.1093/nar/gkn807openalex-snapshot

ATTED-II provides coexpressed gene networks for Arabidopsis

inferredcites →https://doi.org/10.1093/nar/gkr853openalex-snapshot

PomBase: a comprehensive online resource for fission yeast

inferredcites →https://doi.org/10.1093/nar/gks1118openalex-snapshot

PANTHER in 2013: modeling the evolution of gene function, and other gene attributes, in the context of phylogenetic trees

inferredcites →https://doi.org/10.1093/nar/gkt1223openalex-snapshot

Pfam: the protein families database

inferredcites →https://doi.org/10.1093/nar/gku1057openalex-snapshot

ArrayExpress update—simplifying data submissions

inferredcites →https://doi.org/10.1093/nar/gkv007openalex-snapshot

limma powers differential expression analyses for RNA-sequencing and microarray studies

inferredcites →https://doi.org/10.1093/nar/gkv1007openalex-snapshot

MaizeGDB update: new tools, data and interface for the maize model organism database

inferredcites →https://doi.org/10.1093/nar/gkv1052openalex-snapshot

PhytoPath: an integrative resource for plant pathogen genomics

inferredcites →https://doi.org/10.1093/nar/gkv1248openalex-snapshot

eggNOG 4.5: a hierarchical orthology framework with improved functional annotations for eukaryotic, prokaryotic and viral sequences

inferredcites →https://doi.org/10.1093/nar/gky1049openalex-snapshot

UniProt: a worldwide hub of protein knowledge

inferredcites →https://doi.org/10.1093/nar/gky1055openalex-snapshot

The Gene Ontology Resource: 20 years and still GOing strong

inferredcites →https://doi.org/10.1093/nar/gky1079openalex-snapshot

The BioGRID interaction database: 2019 update

inferredcites →https://doi.org/10.1111/j.1365-3040.2009.02040.xopenalex-snapshot

Co‐expression tools for plant biology: opportunities for hypothesis generation and caveats

inferredcites →https://doi.org/10.1111/j.1365-3040.2012.02517.xopenalex-snapshot

Comparative co‐expression analysis in plant biology

inferredcites →https://doi.org/10.1126/science.1087447openalex-snapshot

A Gene-Coexpression Network for Global Discovery of Conserved Genetic Modules

inferredcites →https://doi.org/10.1126/science.1240230openalex-snapshot

Biosynthesis of Antinutritional Alkaloids in Solanaceous Crops Is Mediated by Clustered Genes

inferredcites →https://doi.org/10.1126/science.271.5255.1552openalex-snapshot

A Permease-Oxidase Complex Involved in High-Affinity Iron Uptake in Yeast

inferredcites →https://doi.org/10.1126/science.274.5292.1552openalex-snapshot

HLA Sequence Polymorphism and the Origin of Humans

inferredcites →https://doi.org/10.1126/science.277.5331.1453openalex-snapshot

The Complete Genome Sequence of Escherichia coli K-12

inferredcites →https://doi.org/10.1145/1383519.1383526openalex-snapshot

Amazon S3 for science grids

inferredcites →https://doi.org/10.1186/1471-2105-10-421openalex-snapshot

BLAST+: architecture and applications

inferredcites →https://doi.org/10.1186/1471-2105-6-227openalex-snapshot

Systematic survey reveals general applicability of "guilt-by-association" within gene coexpression networks

inferredcites →https://doi.org/10.1186/gb-2013-14-4-r36openalex-snapshot

TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions

inferredcites →https://doi.org/10.1186/s12864-015-1756-1openalex-snapshot

The completed genome sequence of the pathogenic ascomycete fungus Fusarium graminearum

inferredcites →https://doi.org/10.1186/s13059-014-0550-8openalex-snapshot

Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2

inferredcites →https://doi.org/10.17863/cam.64134openalex-snapshot

SciPy 1.0: fundamental algorithms for scientific computing in Python

inferredcites →https://doi.org/10.3389/fcimb.2019.00113openalex-snapshot

Magnaporthe oryzae CK2 Accumulates in Nuclei, Nucleoli, at Septal Pores and Forms a Large Ring Structure in Appressoria, and Is Involved in Rice Blast Pathogenesis

inferredcites →https://doi.org/10.3389/fpls.2014.00394openalex-snapshot

Elucidating gene function and function evolution through comparison of co-expression networks of plants

What points at this work

Incoming claims: where this work appears in other papers’ reference lists and arguments.

inferred← citeshttps://doi.org/10.1021/acs.jproteome.0c00448openalex-snapshot

Proteomics in Non-model Organisms: A New Analytical Frontier

inferred← citeshttps://doi.org/10.1109/codit55151.2022.9804139openalex-snapshot

Using Graph Databases for Portraying and Analysing Biological and Biomedical Networks

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