The query results or the query history and default settings.
This page briefly describes the features of the List Mode and the Detail Mode. Besides, users are able to load previous successful query results or execute the query of specific filtering criteria by existing default settings in the bottom of this page.
The list mode in YNA presents the retrieved genes generated by genome-wide gene miner and analyze the biological significance of that list under multiple major considerations (details are described in the right section "Biological Significance Analyzer"). All of the displayed table contents and charts can be download in several file types (Excel table, CSV table, XML format and JSON format).
The detail mode exhibits the summary information of the 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. These coordinate-formatted maps contain all sequence-formatted datasets and are converted to log2 fold-change ratios to represent the enrichment or depletion of binding occupancy of histones and regulatory proteins. These sequence maps provide an overall view of chromatin modifications and the occupancy of regulatory proteins.
Biological Significance Analyzer
The Biological Significance Analyzer displays the transcriptional behaviors and chromatic characteristics shared by the gene list to present more comprehensive information of these system-generated lists. Four aspects are analyzed: histone modification, binding occupancy of regulatory proteins, gene transcription rates and functional categories.
The main algorithm to generate the significance reports is based on Fisher Exact Test, which is a statistical significance test used in the analysis of contingency tables. YNA adopts a statistic confidence level of α = 0.05. To gain more visual conception, the calculated p-values according to the score distributions in the four reports are converted into positive correlated scores by taking the negative logarithm then are displayed as the pie plots.
The biological significance analyzer resolves all deposited features in these four aspects and displays those significantly-enriched ones (we adopted a two times fold-change ratio as the enrichment threshold for all features). These analysis results demonstrate the tendency of those features shared by the retrieved genes. Beside those features defined as filtering criteria, there are also other significant features that may potentially regulate chromatin structure along with the given features. This provides hypotheses for the combinatorial effects of these significant chromatin-regulating features for downstream analysis.