1.2 Trajectory differential expression
Differential expression results are represented as a table, where each differential expression event is one row. Within a trajectory, there are different possible types of differential expression, ranging from “overall” differential expression anywhere in the trajectory, to very specific types such as
Each type of differential expression always contain the following columns:
- feature_id: Subset of features from the original datasets
At least one of:
- significant: \(\{\textrm{TRUE}, \textrm{FALSE}\}\)
- p_value: \(0 \leq \textrm{p_value} \leq 1\)
- effect_size
- rank: \(1 \leq \textrm{rank} \leq n\)
Any other columns are also allowed. If this column contains some commonly used type of data, feel free to add it to this list.
1.2.1 tde_overall.csv: Overall differential expression
Overall trajectory differential expression indicates that the feature is changing somewhere along the trajectory.
| feature_id | significant | effect_size | p_value | rank |
|---|---|---|---|---|
| G1 | TRUE | 1.0 | 0.050 | 2 |
| G2 | FALSE | 0.2 | 0.250 | 3 |
| G3 | TRUE | 2.5 | 0.001 | 1 |
1.2.2 tde_local.csv: Local differential expression
Local trajectory differential expression provides information on exactly where the expression of a feature changes.
Columns:
- branch_id: The milestone at the tip point
- progression_percentage: The location within the branch at which the expression changes
No duplicated feature_id, branch_id, and progression_percentages combinations are allowed.
1.2.3 tde_tip_point.csv: Tip point differential expression
Tip point trajectory differential expression indicates that a feature is differentially expressed at a tip point, either upward or downward, compared to other locations in the trajectory. A feature can be differentially expressed at multiple tip points.
Columns:
- milestone_id: The milestone at the tip point
No duplicated feature_id and milestone_id combinations are allowed.
| feature_id | milestone_id | significant | effect_size | p_value | rank |
|---|---|---|---|---|---|
| G1 | M1 | TRUE | 1.0 | 0.050 | 2 |
| G2 | M2 | FALSE | 0.2 | 0.250 | 3 |
| G3 | M3 | TRUE | 2.5 | 0.001 | 1 |
| G3 | M1 | TRUE | 2.5 | 0.001 | 1 |
1.2.4 tde_branch_point.csv: Branch point differential expression
- milestone_id: The milestone at the branch point
No duplicated feature_id and milestone_id combinations are allowed.
1.2.5 tde_branch.csv: Branch differential expression
- branch_id: The branch_id from the milestone_network
No duplicated feature_id and branch_id combinations are allowed.
1.2.6 tde_pseudotime.csv: Pseudotime differential expression
- turning_point: The pseudotime value at which the expression changed
No duplicated feature_id and turning_point values are allowed.
1.2.7 tde_oscilating.csv: Oscillatory differential expression
- turning_point: The pseudotime value at which the expression changed.
Each feature_id requires an even number of rows. No duplicated feature_id and turning_point values are allowed.