ArticlePloS one2013
CoCiter: an efficient tool to infer gene function by assessing the significance of literature co-citation.
Article in PloS one, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers.
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Who cites it
21 citing papers in PubMed.
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- IReNA: Integrated regulatory network analysis of single-cell transcriptomes and chromatin accessibility profiles.iScience · 2022Article
- DriverRWH: discovering cancer driver genes by random walk on a gene mutation hypergraph.BMC bioinformatics · 2022Article
- A random walk-based method to identify driver genes by integrating the subcellular localization and variation frequency into bipartite graph.BMC bioinformatics · 2019Article
- Revealing the Critical Regulators of Cell Identity in the Mouse Cell Atlas.Cell reports · 2018Article
- Recent Advances in the Systems Biology of Aging.Antioxidants & redox signaling · 2018Review
- Inter-nucleosomal communication between histone modifications for nucleosome phasing.PLoS computational biology · 2018Article
- Recently Evolved Tumor Suppressor Transcript TP73-AS1 Functions as Sponge of Human-Specific miR-941.Molecular biology and evolution · 2018Article
- Annotating gene sets by mining large literature collections with protein networks.Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing · 2018Article
- Inference of differentiation time for single cell transcriptomes using cell population reference data.Nature communications · 2017Article
- Data-Driven Approach To Determine Popular Proteins for Targeted Proteomics Translation of Six Organ Systems.Journal of proteome research · 2016Article
- A Systems Approach to Reverse Engineer Lifespan Extension by Dietary Restriction.Cell metabolism · 2016Article
- An integrated structure- and system-based framework to identify new targets of metabolites and known drugs.Bioinformatics (Oxford, England) · 2015Article
- Genetics of Rapid and Extreme Size Evolution in Island Mice.Genetics · 2015Article
- Finding optimal interaction interface alignments between biological complexes.Bioinformatics (Oxford, England) · 2015Article
- Partial depletion of yolk during zebrafish embryogenesis changes the dynamics of methionine cycle and metabolic genes.BMC genomics · 2015Article
- Single-cell-level spatial gene expression in the embryonic neural differentiation niche.Genome research · 2015Article
- Systematic identification of cancer driving signaling pathways based on mutual exclusivity of genomic alterations.Genome biology · 2015Article
- Deep sequencing reveals a novel class of bidirectional promoters associated with neuronal genes.BMC genomics · 2014Article
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Authors and funding
5 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
A routine approach to inferring functions for a gene set is by using function enrichment analysis based on GO, KEGG or other curated terms and pathways. However, such analysis requires the existence of overlapping genes between the query gene set and those annotated by GO/KEGG. Furthermore, GO/KEGG databases only maintain a very restricted vocabulary. Here, we have developed a tool called "CoCiter" based on literature co-citations to address the limitations in conventional function enrichment analysis. Co-citation analysis is widely used in ranking articles and predicting protein-protein interactions (PPIs). Our algorithm can further assess the co-citation significance of a gene set with any other user-defined gene sets, or with free terms. We show that compared with the traditional approaches, CoCiter is a more accurate and flexible function enrichment analysis method. CoCiter is freely available at www.picb.ac.cn/hanlab/cociter/.
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