The expression of the transcription factor (TF) that users are interested in, across three developmental stages in each species.
To identify HSPC-specific TFs at each developmental stage for each species, we utilized our constructed stage-specific atlases within the Hematopoietic References module. By comparing HSPCs against other cell types, we identified stage-specific TFs unique to HSPCs for each stage.
To identify both HSPC-specific and stage-common core TFs for each species, we initially compared HSPCs against other cell types in every hematopoietic stage to identify HSPC-specific TFs. Subsequently, the intersection of HSPC-specific TFs across three distinct developmental stages for each species was delineated as the set of HSPC-specific and stage-common core TFs.
Following the removal of stage-common core TFs for each species, we performed differential expression analysis on our constructed HSPC cross-stage atlas to identify HSPC differentially expressed TFs, termed as stage-specific TFs for HSPCs in each species.
Degree centrality differs from expression level of TFs in that it measures how many direct connections between certain TFs and other genes in a gene regulatory network (GRN). A higher degree centrality indicates a greater importance of the TF within the GRN.
After constructing TF-target gene networks of highly informative TFs, we visualized the regulatory relationships within the TF-target gene regulations using Cytoscape, where the thickness of the lines in the GRN indicates the absolute value of the regulatory strength.