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PopGenIE Gene Search inside Galaxy
Let’s start with some input
You just got the number of gene that you have been working with on your experiment and you need to analyze it. Type in your gene list in main search text box in the Gene Search tool and click the search button. Tool is smart enough to recognize many input types by default (detect id type state). If you know the correct id type which belongs to your input list you can use right side pull down list to choose the correct input type. For instance if you want to search specific synonyms or description, type in specific synonyms or description in main search text input box and choose the correct id type (description or synonyms) in pull down list. Then click the search button.
As stated earlier tool can recognize many of your input id types for example PU,GO,PFAM, PANTHER, Gene, Transcript ids by default, which means if you choose “detect id type” in pull down list, tool can recognize your input type automatically.
Soon after, a Results list appears on the screen.
Many entries in the results list are clickable. For example GO,PANTHER,PFAM,Ensembl,Gene,Transcript ids, they are appear in a blue font of clickable hyperlinks. Clicking the link calls up a page containing a rather detailed summary of the value you choose.
Add/Remove columns from results list
You can use checkbox controls to visible many data columns .For example Ensemble id, Description, Synonyms once you check the check box, specific column will added to the results list. Same method you can use to remove results list column just un-check the specific check box.
Retrieve sequence results
To be complted
Export Results list
Once you see the results in the results list click the “Export results” button. Then you will see the popup window as below. If you search for gene information you can click the CSV icon then it will download CSV file locally. If you search for sequence you can download the FASTA file locally by clicking FASTA icon in export popup window. Also you can click other options for instance you can click Galaxy, GBrowse or Ensembl icon then results list will upload to the desired destination for in-depth analysis.
What is gene basket?
You can see the red dots appear on next to transcript values. When you move mouse over the red dot, you can see the tool-tip indicates “This gene isn’t added to the gene basket” Gene basket is the place where you can save interested gene temporally for further analysis with PopGenIE analysis tools (eFP,Epllant,PopNet,Heatmap.e.t.c), which is similar to shopping cart in most commercial websites. But here you go shopping in Populus database and pick interested gene .You can add, remove gene or even clear the gene basket using Gene Search tool controls.
Add interested gene in to the gene basket.
If you found some interested gene by looking at extra columns or detailed information pages, you can add gene into to gene basket. You can select gene using left side check boxes in results list. Once you selected few gene you can use “Add gene to gene basket” button or if you want to add all results gene into gene basket click “Send all results to gene basket” button. Soon after, gene list will be added to the gene basket and it will display in Gene Search tool results list with green dot beside on transcript ids. When you over the mouse on green dot it will indicates “gene is already added to the gene basket”. Which mean gene is saved in the gene basket for further analysis. Added gene will not be removed until you select unwanted gene and remove it by clicking the “remove selected gene” button or clear the gene list by clicking the “clear the gene basket” button.