Ontology-based Pattern Identification
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Biological Process 46
Cellular Component 24
Molecular Function 28
Literature 47
Literature Combined 11

User Manual [HTML] [PDF]
Literature Mining Pipeline
Publication Site
Literature Database
Using the Database
Step 1: paste in a list of words in the left query box, then click the 'Submit Query' button.
Step 2: click on the heat map in the resultant page to browse the gene expression pattern and the gene list of the corresponding GO group.
Note: You may use GO IDs, gene names or description keywords (comma- or space- separated). To search a phrase, enclose words by double quote, such as "cell invasion". Otherwise, it finds GO groups containing either "cell" or "invasion".
For an example, click on the 'Example' button, then 'Smart Find'

References

OPI Algorithm: Zhou et al. In silico gene function prediction using ontology-based pattern identification. Bioinformatics 2005, 21(7):1237-45. [GNF Web Site | PubMed ID: 15531612]

P. falciparum Asexual cell cycle gene expression data: Le Roch et al. Discovery of gene function by expression profiling of the malaria parasite life cycle. Science 2003, 301(5639):1503-8. [GNF Web Site | PubMed ID: 12893887]

P. falciparum gametocyte gene expression data: Young et al. Mol Biochem Parasitol. 2005 Sep;143(1):67-79. The Plasmodium falciparum sexual development transcriptome: a microarray analysis using ontology-based pattern identification.. Mol. Biochem. Parasitol. 2005, 143(1):67-79. [GNF Web Site| PubMed ID: 16005087]

P. yoelii life cycle and P. falciparum zygote & ookinete gene expression data: [GNF Web Site]

P. falciparum protein-protein interaction data: LaCount et al. A protein interaction network of the malaria parasite Plasmodium falciparum. Nature. 2005, 438(7064):103-7. [PubMed ID: 16267556]

S. cerevisiae gene expression data: 74 samples accumulated at GNF [CSV file]

Human Tissue Atlas data: Su et al. PNAS. A gene atlas of the mouse and human protein-encoding transcriptomes. PNAS 2004, 101(16)6062-7. [GNF Web Site| PubMed ID: 15075390]