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Perturbation Phenotype Summary by Gene
This database includes the phenotypic data of 1,368 embryos under 204 gene perturbations. Phenotypes are represented by tissue-marker expression in single cells mapped onto the cell lineage of each perturbed embryo and are organized by genes.
A summary heatmap of the marker expression pattern across the lineage is provided for each embryo. Marker expression in the terminal cell (350-cell stage) is used is to show clonal expression of tissue markers. Different markers are in different colors and each block corresponds to a uniform and significant clone (sublineage) that expresses a tissue marker. For each gene, the heatmaps are compiled across multiple tissue markers and experiments to provide a quick view of the phenotypes for a gene of interest.
Detailed phenotypes for each embryo are provided in the gene page for in-depth analysis (available by clicking gene name). For each embryo, quantitative marker expression in individual cells at each time point (75 second interval) is visualized as a color-coded tree and the source data is available for download. Each tree shows the cell lineage and the tree branch color shows tissue marker expression levels.
Two types of visualization are provided. One shows the raw phenotype detection in which the tree topology is based on direct lineage tracing and the color gradient is proportional to marker expression level. The other shows the processed phenotypic detection results in which the tree topology is standardized and the expression status (on/off) is binarized for ease of comparison.
Cell Fate Change Phenotypes
A summary of phenotype per gene is also provided in the form of a cell lineage. Changes to each fate marker are merged to detect perturbed founder fates (marked with blue in the cell lineage). The subset of homeotic transformations are marked with red and a red arrow showing the transformation.
Differentiation Landscape
All inferred binary fate choices were integrated with normal fate progression to generate a landscape of lineage differentiation with 56 trajectories and 32 types of regulated fate choices. This directed graph summarizes all possible trajectories a cell can take to differentiate into a specific fate.
Multiscale Model of Lineage Differentiation
The multiscale model synthesizes all information regarding phenotype similarity, action site and fate transformations into a single multiscale model of fate regulation.
This database includes the phenotypic data of 1,368 embryos under 204 gene perturbations. Phenotypes are represented by tissue-marker expression in single cells mapped onto the cell lineage of each perturbed embryo and are organized by genes.
A summary heatmap of the marker expression pattern across the lineage is provided for each embryo. Marker expression in the terminal cell (350-cell stage) is used is to show clonal expression of tissue markers. Different markers are in different colors and each block corresponds to a uniform and significant clone (sublineage) that expresses a tissue marker. For each gene, the heatmaps are compiled across multiple tissue markers and experiments to provide a quick view of the phenotypes for a gene of interest.
Detailed phenotypes for each embryo are provided in the gene page for in-depth analysis (available by clicking gene name). For each embryo, quantitative marker expression in individual cells at each time point (75 second interval) is visualized as a color-coded tree and the source data is available for download. Each tree shows the cell lineage and the tree branch color shows tissue marker expression levels.
Two types of visualization are provided. One shows the raw phenotype detection in which the tree topology is based on direct lineage tracing and the color gradient is proportional to marker expression level. The other shows the processed phenotypic detection results in which the tree topology is standardized and the expression status (on/off) is binarized for ease of comparison.
Cell Fate Change Phenotypes
A summary of phenotype per gene is also provided in the form of a cell lineage. Changes to each fate marker are merged to detect perturbed founder fates (marked with blue in the cell lineage). The subset of homeotic transformations are marked with red and a red arrow showing the transformation.
Differentiation Landscape
All inferred binary fate choices were integrated with normal fate progression to generate a landscape of lineage differentiation with 56 trajectories and 32 types of regulated fate choices. This directed graph summarizes all possible trajectories a cell can take to differentiate into a specific fate.
Multiscale Model of Lineage Differentiation
The multiscale model synthesizes all information regarding phenotype similarity, action site and fate transformations into a single multiscale model of fate regulation.