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PhenoGeneRanker: A Tool for Gene Prioritization Using Complete Multiplex Heterogeneous Networks

https://doi.org/10.1101/651000
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What this work says

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

inferredcites →https://doi.org/10.1002/fes3.25openalex-snapshot
Avoiding damage and achieving cold tolerance in rice plants
inferredcites →https://doi.org/10.1007/978-1-4419-8819-5openalex-snapshot
Weighted Network Analysis
inferredcites →https://doi.org/10.1007/s00018-015-2089-6openalex-snapshot
Hormonal control of cold stress responses in plants
inferredcites →https://doi.org/10.1007/s00299-017-2234-9openalex-snapshot
Deep RNAseq indicates protective mechanisms of cold-tolerant indica rice plants during early vegetative stage
inferredcites →https://doi.org/10.1016/j.cell.2011.02.016openalex-snapshot
Interactome Networks and Human Disease
inferredcites →https://doi.org/10.1016/j.gde.2013.10.003openalex-snapshot
Genotype to phenotype via network analysis
inferredcites →https://doi.org/10.1038/ncomms10532openalex-snapshot
Open access resources for genome-wide association mapping in rice
inferredcites →https://doi.org/10.1038/nrg.2017.38openalex-snapshot
Network propagation: a universal amplifier of genetic associations
inferredcites →https://doi.org/10.1038/nrg3433openalex-snapshot
Computational solutions for omics data
inferredcites →https://doi.org/10.1038/nrg3868openalex-snapshot
Methods of integrating data to uncover genotype–phenotype interactions
inferredcites →https://doi.org/10.1038/s41467-018-05753-wopenalex-snapshot
Early selection of bZIP73 facilitated adaptation of japonica rice to cold climates
inferredcites →https://doi.org/10.1038/srep46598openalex-snapshot
A large-scale benchmark of gene prioritization methods
inferredcites →https://doi.org/10.1071/cp09006openalex-snapshot
Cold tolerance in rice varieties at different growth stages
inferredcites →https://doi.org/10.1073/pnas.0308067101openalex-snapshot
Protein ranking: From local to global structure in the protein similarity network
inferredcites →https://doi.org/10.1080/13102818.2014.978539openalex-snapshot
Mapping QTLs for cold tolerance at germination and the early seedling stage in rice (Oryza sativaL.)
inferredcites →https://doi.org/10.1093/bib/bbx066openalex-snapshot
Network approaches to systems biology analysis of complex disease: integrative methods for multi-omics data
inferredcites →https://doi.org/10.1093/bioinformatics/btr584openalex-snapshot
PRINCIPLE: a tool for associating genes with diseases via network propagation
inferredcites →https://doi.org/10.1093/bioinformatics/btu508openalex-snapshot
Walking the interactome for candidate prioritization in exome sequencing studies of Mendelian diseases
inferredcites →https://doi.org/10.1093/bioinformatics/bty637openalex-snapshot
Random walk with restart on multiplex and heterogeneous biological networks
inferredcites →https://doi.org/10.1093/nar/gkp427openalex-snapshot
ToppGene Suite for gene list enrichment analysis and candidate gene prioritization
inferredcites →https://doi.org/10.1093/nar/gks1193openalex-snapshot
NCBI GEO: archive for functional genomics data sets—update
inferredcites →https://doi.org/10.1093/nar/gkv1351openalex-snapshot
The Reactome pathway Knowledgebase
inferredcites →https://doi.org/10.1093/nar/gkx1132openalex-snapshot
The Reactome Pathway Knowledgebase
inferredcites →https://doi.org/10.1093/nar/gkx382openalex-snapshot
agriGO v2.0: a GO analysis toolkit for the agricultural community, 2017 update
inferredcites →https://doi.org/10.1093/nar/gky1131openalex-snapshot
STRING v11: protein–protein association networks with increased coverage, supporting functional discovery in genome-wide experimental datasets
inferredcites →https://doi.org/10.1093/pcp/pcs183openalex-snapshot
Rice Annotation Project Database (RAP-DB): An Integrative and Interactive Database for Rice Genomics
inferredcites →https://doi.org/10.1111/pce.12635openalex-snapshot
New insights into the genetic basis of natural chilling and cold shock tolerance in rice by genome‐wide association analysis
inferredcites →https://doi.org/10.1186/1471-2105-11-s1-s20openalex-snapshot
Integration of multiple data sources to prioritize candidate genes using discounted rating system
inferredcites →https://doi.org/10.1186/1471-2105-9-559openalex-snapshot
WGCNA: an R package for weighted correlation network analysis
inferredcites →https://doi.org/10.1186/1756-0381-4-19openalex-snapshot
DA DA: Degree-Aware Algorithms for Network-Based Disease Gene Prioritization
inferredcites →https://doi.org/10.1186/s12284-016-0133-2openalex-snapshot
Genome-wide Association Mapping of Cold Tolerance Genes at the Seedling Stage in Rice
inferredcites →https://doi.org/10.1186/s12284-018-0218-1openalex-snapshot
Identification of a cold-tolerant locus in rice (Oryza sativa L.) using bulked segregant analysis with a next-generation sequencing strategy
inferredcites →https://doi.org/10.1371/journal.pcbi.1001095openalex-snapshot
Identifying Causal Genes and Dysregulated Pathways in Complex Diseases
inferredcites →https://doi.org/10.1371/journal.pcbi.1002820openalex-snapshot
Chapter 5: Network Biology Approach to Complex Diseases
inferredcites →https://doi.org/10.1371/journal.pone.0043557openalex-snapshot
Exploiting Protein-Protein Interaction Networks for Genome-Wide Disease-Gene Prioritization
inferredcites →https://doi.org/10.1371/journal.pone.0058977openalex-snapshot
Prediction and Validation of Gene-Disease Associations Using Methods Inspired by Social Network Analyses
inferredcites →https://doi.org/10.1371/journal.pone.0172133openalex-snapshot
Genetic architecture of cold tolerance in rice (Oryza sativa) determined through high resolution genome-wide analysis
inferredcites →https://doi.org/10.2307/2528823openalex-snapshot
A General Coefficient of Similarity and Some of Its Properties
inferredcites →https://doi.org/10.3389/fpls.2017.00957openalex-snapshot
Assessment of Five Chilling Tolerance Traits and GWAS Mapping in Rice Using the USDA Mini-Core Collection
inferredcites →https://doi.org/10.5281/zenodo.19670360openalex-snapshot
Weighted Network Analysis: Applications in Genomics and Systems Biology
inferredcites →https://doi.org/10.7287/peerj.preprints.3179v2openalex-snapshot
rentrez: An R package for the NCBI eUtils API

What points at this work

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

inferred← citeshttps://doi.org/10.1016/j.csbj.2020.05.017openalex-snapshot
Constructing knowledge graphs and their biomedical applications
inferred← citeshttps://doi.org/10.1038/s41598-021-87987-1openalex-snapshot
MultiVERSE: a multiplex and multiplex-heterogeneous network embedding approach
inferred← citeshttps://doi.org/10.3389/fgene.2021.652189openalex-snapshot
Using Network-Based Machine Learning to Predict Transcription Factors Involved in Drought Resistance
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