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Usage of ASIP Tables and Functions

Function list:

• Search
• Group by
• Sort by
• Show only

Search - look for records in a certain table. The searchable column name must exist in the desired table. Currently, only the TUG (TUG name) and Alignment (AlignCode) in the Maize Intron Retention table and the Query column and AtModel column in the Conserved Intron Retention table can be searched. For example, if we want to know if the maize TUG ZMtuc03-04-07.21801 retains an intron, we can select to search the "TUG name", enter TUG ZMtuc03-04-07.21801 in the "for" text box, and select "in Maize Intron Retention", then click "Search!". The results are shown below.

To see if the maize TUG (or an Arabidopsis gene model) has been associated with a case of intron retention in the homologous genes in other plant species (maize, Arabidopsis, rice), choose to search "Query" (or "AtModel"), input the query name, e.g. ZMtuc03-04-07.21801 (or At gene model) and search the "Conserved Intron Retention" table. The results for the ZMtuc03-04-07.21801 search are shown below:

Group by - merge all rows having the same entry in the chosen column>. Only the first row will be shown after merging. A "count" column will be added to indicate how many rows have been merged. Clicking the numbers in the "count" column will expand the merged rows into individual rows and highlight them. The whole table will be sorted according to the "Group by" column. Example:

(1) Before grouping: There are 140 entries in the table. Many queries have multiple rows corresponding to alignments of different rice BACs:

(2) Grouping by Query: Select "Group by Query", click "Do!".

(3) After grouping:

(4) Expand group:

Sort by - order rows according to the chosen column. If the column contains all numbers, sorting will be in an increasing numeric order. If the column contains characters other than numbers, sorting will be in increasing alphabetic order. Descending order is not available at this moment.

Show only - change the number of rows shown in each page. Default is to show only 30 rows in each page, but the value can be set to show 60, 120, or all rows.