MAASE: an alternative splicing database designed for supporting splicing microarray applications

Abstract

Alternative splicing is a prominent feature of higher eukaryotes. Understanding of the function of mRNA isoforms and the regulation of alternative splicing is a major challenge in the post-genomic era. The development of mRNA isoform sensitive microarrays, which requires precise splice-junction sequence information, is a promising approach. Despite the availability of a large number of mRNAs and ESTs in various databases and the efforts made to align transcript sequences to genomic sequences, existing alternative splicing databases do not offer adequate information in an appropriate format to aid in splicing array design. Here we describe our effort in constructing the Manually Annotated Alternatively Spliced Events (MAASE) database system, which is specifically designed to support splicing microarray applications. MAASE comprises two components: (1) a manual/computational annotation tool for the efficient extraction of critical sequence and functional information for alternative splicing events and (2) a user-friendly database of annotated events that allows convenient export of information to aid in microarray design and data analysis. We provide a detailed introduction and a step-by-step user guide to the MAASE database system to facilitate future large-scale annotation efforts, integration with other alternative splicing databases, and splicing array fabrication.

FIGURE 1.

Screen shot of the Progress Page. The Progress Page tracks the progress of each target ID in a project. There are five possible status messages: “Queued,” “Processing,” “Complete,” “Error,” and “Need Information.” The last three messages are Web links containing detailed information on how to proceed. Users are also able to delete a project within this page. At the completion of each step, users are automatically returned to the Progress Page.

FIGURE 2.

MAASE annotation stepwise flowchart. The annotation procedure consists of three automatic/manual steps. Step 1 is the identification of transcript sequences. Step 2 is the alignment of transcript sequences (part 1) and the determination of splicing mode(s) (part 2). Step 3 concludes with the deposition of annotated information into MAASE.

FIGURE 3.

Screen shot of automatically collected information from Step 1. This page is separated into four sections: General Information, Related Sequences, Literature References, and User Input. “General Information” contains descriptive information about the gene such as gene name, protein name, and gene function. The information is within text boxes to allow users to edit/add if needed. “Related Sequences” contains a list of transcript sequences retrieved from NCBI. Users are able to choose which sequences are to be included/excluded. “User Input” provides space for users to provide additional information such as more literature references, more transcript sequences (i.e., mRNAs or ESTs), and alternative splicing events only found in the literature.

FIGURE 4.

Screen shot of processed information from Step 2. This page is separated into five sections: General Information, Global View, Exonic Region Alignment, Alternative Splicing Event, and Literature References. The “General Information” section contains information similar to that in Fig. 2, in addition to user additions (if any), a list of retained transcript sequences from Step 1, with Web links to their original database sources, and a text box for additional comments. The “Global View” section displays a graphical representation of each transcript sequence to the genomic sequence. The last sequence, depicted in red, is the super-sequence of all exonic regions. Alternative splicing events are indicated by yellow lines connecting different segments within the super-sequence. The “Exonic Region Alignment” section displays the presence of each exonic region in each transcript in alternating colors. The “Alternative Splicing Event(s)” section contains the identification and initial categorization of each internal alternative splicing event. Users are able to edit the information to refine the annotation.

FIGURE 5.

Construction of the super-sequence of exonic regions. Note that an exonic region involved in alternative splicing may represent an entire exon subject to inclusion or exclusion or a portion of an exon due to the use of alternative donors or acceptors.

FIGURE 6.

Systematic characterization of alternative splicing modes used in MAASE.

FIGURE 7.

A gene entry in the database. This page has sections that are similar to those of the previous annotation steps: General Information, Global View, Alternative Splicing Event(s), and Literature References.

FIGURE 8.

MAASE database schema. For simplicity, all relationships from/to [uid] are not shown.