ArticleGenome biology2012
RIDDLE: reflective diffusion and local extension reveal functional associations for unannotated gene sets via proximity in a gene network.
Article in Genome biology, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
14 citing papers in PubMed.
- Identification of antimicrobial resistance genes in Escherichia coli through network diffusion.The Journal of antimicrobial chemotherapy · 2026Article
- KiRNet: Kinase-centered network propagation of pharmacological screen results.Cell reports methods · 2021Article
- NGSEA: Network-Based Gene Set Enrichment Analysis for Interpreting Gene Expression Phenotypes with Functional Gene Sets.Molecules and cells · 2019Article
- Network propagation: a universal amplifier of genetic associations.Nature reviews. Genetics · 2017Review
- Article
- Algorithms for modeling global and context-specific functional relationship networks.Briefings in bioinformatics · 2016Article
- Jumping across biomedical contexts using compressive data fusion.Bioinformatics (Oxford, England) · 2016Article
- Applications of comparative evolution to human disease genetics.Current opinion in genetics & development · 2015Review
- Determining microbial products and identifying molecular targets in the human microbiome.Cell metabolism · 2014Review
- MORPHIN: a web tool for human disease research by projecting model organism biology onto a human integrated gene network.Nucleic acids research · 2014Article
- REGNET: mining context-specific human transcription networks using composite genomic information.BMC genomics · 2014Article
- Bayesian pathway analysis of cancer microarray data.PloS one · 2014Article
- GeneMANIA prediction server 2013 update.Nucleic acids research · 2013Article
- Genome-scale co-evolutionary inference identifies functions and clients of bacterial Hsp90.PLoS genetics · 2013Article
Corrections and comments
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Authors and funding
6 authors.
Funding
Abstract
The growing availability of large-scale functional networks has promoted the development of many successful techniques for predicting functions of genes. Here we extend these network-based principles and techniques to functionally characterize whole sets of genes. We present RIDDLE (Reflective Diffusion and Local Extension), which uses well developed guilt-by-association principles upon a human gene network to identify associations of gene sets. RIDDLE is particularly adept at characterizing sets with no annotations, a major challenge where most traditional set analyses fail. Notably, RIDDLE found microRNA-450a to be strongly implicated in ocular diseases and development. A web application is available at http://www.functionalnet.org/RIDDLE.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.