2.2 Gene Retrieval by Text Mining
Apart from the gene models present in your input genomic interval, you may wish to know if there are other genes that have been reported to be associated with the trait/phenotype you are studying. You can query our in-house dataset obtained by text mining PubMed abstracts on rice gene-trait associations, to obtain such genes reported in the literature. The co-expression and regulatory enrichment analyses automatically take as input the genes in the input interval, but you can supplement the list of genes by manually adding the genes you obtained from text-mining.
The screenshot below shows the user input interface for the text mining feature.
In the textbox, enter your query trait/phenotype of interest. For example: "anaerobic germination" or "pre-harvest sprouting". If you wish to filter results such that only genes in your input interval are retained, use the checkbox for the filtering the results. Click Search to search the query against our text-mining dataset.
The result of the query search is displayed as a table.
- The Gene column provides the gene name.
- The MSU ID column provides the MSU gene ID, which can be copy-pasted into the "Include additional genes" box of the co-expression or regulatory enrichment analyses.
- The column provides the PMID and a link to the PubMed entry.
- The title column provides the title of the paper, and the sentence column shows the context in which the gene occurred in the abstract.