HemAtlas
Mapping developmental hematopoiesis across stages, species and models

Core intrinsic regulatory model

TF Expression

The expression of the transcription factor (TF) that users are interested in, across three developmental stages in each species.

Stage highly enriched TFs

For each stage in the three species, TFs that had an average expression of more than 0.5 and were expressed in more than 25% of cells were regarded as highly enriched TFs of that stage for HSPCs.

Stage-common key TFs

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.

Stage-specific key 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.

TF Degree Centrality

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.

Gene Regulatory Network

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.