| Content Provider | Springer Nature : BioMed Central |
|---|---|
| Author | Peng, Jiajie Wang, Honggang Lu, Junya Hui, Weiwei Wang, Yadong Shang, Xuequn |
| Abstract | Background The Gene Ontology (GO) is a community-based bioinformatics resource that employs ontologies to represent biological knowledge and describes information about gene and gene product function. GO includes three independent categories: molecular function, biological process and cellular component. For better biological reasoning, identifying the biological relationships between terms in different categories are important. However, the existing measurements to calculate similarity between terms in different categories are either developed by using the GO data only or only take part of combined gene co-function network information. Results We propose an iterative ranking-based method called C r o G O2 to measure the cross-categories GO term similarities by incorporating level information of GO terms with both direct and indirect interactions in the gene co-function network. Conclusions The evaluation test shows that C r o G O2 performs better than the existing methods. A genome-specific term association network for yeast is also generated by connecting terms with the high confidence score. The linkages in the term association network could be supported by the literature. Given a gene set, the related terms identified by using the association network have overlap with the related terms identified by GO enrichment analysis. |
| Related Links | https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-017-1959-3.pdf |
| Ending Page | 74 |
| Page Count | 8 |
| Starting Page | 67 |
| File Format | HTM / HTML |
| ISSN | 14712105 |
| DOI | 10.1186/s12859-017-1959-3 |
| Journal | BMC Bioinformatics |
| Issue Number | 16 |
| Volume Number | 18 |
| Language | English |
| Publisher | BioMed Central |
| Publisher Date | 2017-12-28 |
| Access Restriction | Open |
| Subject Keyword | Bioinformatics Microarrays Computational Biology Computer Appl. in Life Sciences Algorithms Gene Ontology Term similarity Cross categories Computational Biology/Bioinformatics |
| Content Type | Text |
| Resource Type | Article |
| Subject | Molecular Biology Biochemistry Computer Science Applications Applied Mathematics Structural Biology |
| Journal Impact Factor | 2.9/2023 |
| 5-Year Journal Impact Factor | 3.6/2023 |
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