YNA is too complicated? Let's start on a fantastic journey in YNA!
The YNA database provides three main functional modes for users to investigate the regulations for chromatin structure: (I) The Query Mode contains the manipulation panel of the genome-wide gene miner and the gene query engine; (II) The List Mode presents the list of retrieved genes that match the query criteria. The biological significance analyzer displays the analysis results of the retrieved genes as pie plots; (III) The Detail Mode exhibits the basic description and the chromatin-related patterns of the specified gene. The query mode is set up in the query page, and the other two modes are integrated in the result page. All processed plain text files of chromatic-regulation datasets are annotated with their source and are available for downloading in the statistics page. We also provided a detailed tutorial page so that users can fully utilize functions in YNA.
YNA provides the simple gene query engine for convenience, which is designed for users who need to search genes by systematic names or standard names. YNA supports query with multiple keywords. Users can separate the keywords by space, comma (,) or semicolon (;), and YNA will combine these keywords with union as the query criterion.
The genome-wide gene miner is the main function in the query mode. Users are able to specify demand filtering criteria for the three filter sets, i.e. chromatin structure regulation filter, expression level filter and functional category filter, and then execute the query to fetch the lists satisfying the combination. The chromatin structure regulation filter enables users to specify coding or promoter regions and fold-change ratios of specific histone modifications and binding occupancy of regulatory proteins. The expression level filter provides the options for users to designate the threshold values for specific expression levels. The functional category filter allows users to enter MIPS FunCat category keywords or numbers to retrieve genes that match the search criteria. YNA also provides query defaults, which are pre-defined filter settings, so that users can easily get started.
B-1. Chromatin Structure Regulation Filter
In this filter set , users can specify 1. Feature Type (the ratio of experimentally identified regulation over background assay), 2. Detecting Region (in promoter region, coding region or intersection/union of the two) and 3. Enrichment Threshold Ratio (fold-change value). Besides, users can enable multiple features at the same time and the specify the combination method: union or intersection (all the three filter sets have this option).
Figure 02: Chromatin Structure Regulation Filter.
For example, if the user select 'H3K4ac vs H3', 'Promoter', '2.0' then execute the query, the genome-wide gene miner will return those genes containing 'at least one sample whose value of H3K4ac / H3 is greater than 2.0 in promoter regions' back to the user.
This filter set is similar to Chromatin Structure Regulation Filter. Users can specify 1. Feature (the expression profiles, every gene should have one each), 2. Mathematical Operator and 3. Threshold Value. The filter will return those genes whose experimental expression profiles are matching the criterion.
This filter set is based on MIPS functional categories, the filter will select those genes whose function categories are matching the criterion. The filter support multiple query keywords as well, users can select given keywords from "Main Category List" (The parent category) or from "Function Category List" (all available entries). Alternatively, users can also enter the keywords on their own in the top of the interface. The auto-complete function is implemented to provide the hints if users enter something valid. This filter set limit the count of keywords to 10 due to the issue concerning program performance.
In the list mode, the retrieved genes are displayed in the table. The genes are also analyzed through the biological significance analyzer in terms of four aspects: histone modifications, binding occupancy of regulatory proteins, transcription rates, and functional categories. All of the displayed table contents and charts can be downloaded in multiple file types (Excel table, CSV table, XML format and JSON format).
C-1. Query Results
The table contains basic information and expression levels of the retrieved gene list. The list may be generated from the genome-wide gene miner or from the gene query engine if the keywords is implicit. The table also supports the sorting function and filtering function based on grid numbers or texts as well.
The Biological Significance Analyzer presents the tendency of transcriptional behaviors and chromatic characteristics shared by the retrieved gene list. Certainly, the whole analyzing results and the pie plot are downloadable.
The detail mode exhibits the information of specifically selected gene. The information includes two parts. The first part displays the summary information for the specified gene; and the second part contains the sequence maps of chromatin structure regulations in the region near this gene which are plotted as groups of coordinate charts. Users are able to achieve this page just by gene query engine or by clicking the gene name in the table of query results from the genome-wide gene miner.
D-1. Gene Summary
The section displays the gene information such as systematic name, alias name, description, expression profiles and functional categories.
The Chromatin Regulation Viewer displays all sequence-formatted datasets and these experimental data are converted to log2 fold-change ratios to distinguish the difference between induced and repressed expression. These coordinate-based datasets provide a quick view to these diverse regulations of chromatin structure.