1) Select cell/tissue and a gene
Currently, a user can select up to five cell lines or tissues (Fig. 1.1). When a user types in the field Target, available options will be displayed to fill in the field, based on earlier typed values (Fig. 1.2). Leaving blank in the field will present all results from selected cell/tissue types. Extra options exomePeak Site Minimum, MACS2 Site Minimum and MeTPeak Site Minimum are used to further observe the counts of m6A peaks called in the three tools in a given gene. The option Supported Sample Minimum is useful for querying confident modified genes as they can be identified by multiple samples or datasets.
2) View the results of peak information
If a given gene is modified in one or more cell lines or tissues, the result is displayed in a five-column table (Fig. 2.1). Clicking on the figure of exomePeak Sites, MACS2 Sites or MeTPeak Sites directs users to a modal window to show peak information including the genomic position, tools that share the peak , peak length, fold enrichment, genomic feature where the peak is located, etc (Fig. 2.2). Clicking on Position, Dataset and Sample directs users to the built-in genome browser to visualize the peak position (Fig. 2.3) and to the SRA website to view the data source, respectively (Fig. 2.4 and 2.5).
3) View the results of sample information
If a user clicks on the figure of Supported Samples, he or she is directed to a modal window which displays sample information including cell/tissue type, treatment, GEO accession, reference, etc (Fig. 3.1). Clicking on Sample directs users to a modal window which illustrates read mapping statistics, region distribution, metagene profile and motif enrichment analysis (Fig. 3.2). Clicking on GSE Accession, GSM Accession and PMID directs users to the GEO website to view the data source (Fig. 3.3 and 3.4) and to the PubMed website to read the reference, respectively.
1) Select a genomic location and tracks
Like most popular genome browsers, a user can simply type an interested genomic location (chrom:start-end), a gene symbol or a GENCODE gene ID from Main Options (Fig. 4.1) and select up to three feature tracks from Epitranscriptomic Data Track Options (Fig. 4.2) and Epigenomic Data Track Options (Fig. 4.3) to investigate m6A and histone modifications and chromatin accessibility from different samples and conditions.
2) Multiple searches of tracks
Currently, there are a total of 3,225 tracks including seven distinct track types (Fig. 5.1) constitute the built-in genome browser. To exactly select interested tracks in such a large track set, a user can use regular expression searching in individual columns. For instance, | enables multiple searches to only present multiple specific tracks (Fig. 5.2). In the genome browser (Fig. 5.3), a user can drag horizontally on any tracks or the coordinates to move left/right, or use the mose wheel to zoom in/out, as described in How to navigate. Full screen browsing is available by clicking on in the top-right of the panel. Clicking on ADD TRACKS in the left of the panel displays available tracks of cell/tissue types that are related to previous selection in the track options.