1. Retrieval
Published data is downloaded from its respective repository.
2. Noise reduction
Background noise is eliminated to ensure data accuracy.
3. Standardization
Author annotations, such as cell type and tissue, are mapped to a consistent, controlled vocabulary.
4. Expression threshold
A gene is considered expressed in a cell type or tissue if it has a non-zero value in at least 100 cells and 15% of the total cells.
5. Study Count
Count the number of studies reporting the gene as expressed in each cell type.
6. Biological process factorization
We divide gene sets specific to biological processes in gene ontology into groups of co-expressed genes specific to certain cell types. We demonstrate biological process factorization in the context of cell type interactions and gene cellular location, derived from gene ontology.