README.md

Spatially Variable Genes

Spatially variable genes (SVGs) are genes whose expression levels vary significantly across different spatial regions within a tissue or across cells in a spatially structured context.

Repository: openproblems-bio/task_spatially_variable_genes

Description

Recent years have witnessed significant progress in spatially-resolved transcriptome profiling techniques that simultaneously characterize cellular gene expression and their physical position, generating spatial transcriptomic (ST) data. The application of these techniques has dramatically advanced our understanding of disease and developmental biology. One common task for all ST profiles, regardless of the employed protocols, is to identify genes that exhibit spatial patterns. These genes, defined as spatially variable genes (SVGs), contain additional information about the spatial structure of the tissues of interest, compared to highly variable genes (HVGs).

Identification of spatially variable genes is crucial to for studying spatial domains within tissue microenvironmnets, developmental gradients and cell signaling pathways. In this task we attempt to evaluate various methods for detecting SVGs using a number of realistic simulated datasets with diverse patterns derived from real-world spatial transcriptomics data using scDesign3. Synthetic data is generated by mixing a Gaussian Process (GP) model and a non-spatial model (obtained by shuffling mean parameters of the GP model to remove spatial correlation between spots) to generate gene expressions with various spatial variability. For more details, please refer to our manuscript and Github.

Authors & contributors

name	roles
Zhijian Li	author, maintainer
Zain M. Patel	author
Dongyuan Song	author
Guanao Yan	author
Jingyi Jessica Li	author
Luca Pinello	author
Robrecht Cannoodt	contributor
Sai Nirmayi Yasa	contributor

API

flowchart LR
  file_common_dataset("Common Dataset")
  file_dataset("Dataset")
  comp_control_method[/"Control method"/]
  comp_method[/"Method"/]
  file_output("Output")
  comp_metric[/"Metric"/]
  file_score("Score")
  file_simulated_dataset("Common Dataset")
  file_solution("Solution")
  file_dataset---comp_control_method
  file_dataset---comp_method
  comp_control_method-->file_output
  comp_method-->file_output
  file_output---comp_metric
  comp_metric-->file_score
  file_solution---comp_control_method
  file_solution---comp_metric

Loading

File format: Common Dataset

A subset of the common dataset.

Example file: resources_test/common/mouse_brain_coronal/dataset.h5ad

Format:

AnnData object
 var: 'feature_id', 'feature_name'
 obsm: 'spatial'
 layers: 'counts', 'counts'
 uns: 'dataset_id', 'dataset_name', 'dataset_url', 'dataset_reference', 'dataset_summary', 'dataset_description', 'dataset_organism'

Data structure:

Slot	Type	Description
var["feature_id"]	string	(Optional) Unique identifier for the feature, usually a ENSEMBL gene id.
var["feature_name"]	string	A human-readable name for the feature, usually a gene symbol.
obsm["spatial"]	double	Spatial coordinates for each spot.
layers["counts"]	integer	Raw counts.
layers["counts"]	double	Normalized expression values.
uns["dataset_id"]	string	A unique identifier for the dataset.
uns["dataset_name"]	string	(Optional) Nicely formatted name.
uns["dataset_url"]	string	(Optional) Link to the original source of the dataset.
uns["dataset_reference"]	string	(Optional) Bibtex reference of the paper in which the dataset was published.
uns["dataset_summary"]	string	(Optional) Short description of the dataset.
uns["dataset_description"]	string	(Optional) Long description of the dataset.
uns["dataset_organism"]	string	(Optional) The organism of the sample in the dataset.

File format: Dataset

The dataset without spatially variable genes.

Example file: resources_test/task_spatially_variable_genes/mouse_brain_coronal/dataset.h5ad

Format:

AnnData object
 var: 'feature_id', 'feature_name'
 obsm: 'spatial'
 layers: 'counts', 'normalized'
 uns: 'dataset_id', 'dataset_name'

Data structure:

Slot	Type	Description
var["feature_id"]	string	(Optional) Unique identifier for the feature, in this case a ENSEMBL gene id suffixed with alpha value.
var["feature_name"]	string	(Optional) A human-readable name for the feature, in this case a gene symbol suffixed with alpha value.
obsm["spatial"]	double	Spatial coordinates for each spot.
layers["counts"]	integer	Raw counts.
layers["normalized"]	double	Normalised expression values.
uns["dataset_id"]	string	A unique identifier for the dataset.
uns["dataset_name"]	string	(Optional) Nicely formatted name.

Component type: Control method

Quality control methods for verifying the pipeline.

Arguments:

Name	Type	Description
--input_data	file	The dataset without spatially variable genes.
--input_solution	file	Anndata with true spatial variability.
--output	file	(Output) Anndata with estimate spatial variability.

Component type: Method

A spatially variable gene identification method.

Arguments:

Name	Type	Description
--input_data	file	The dataset without spatially variable genes.
--output	file	(Output) Anndata with estimate spatial variability.

File format: Output

Anndata with estimate spatial variability.

Example file: resources_test/task_spatially_variable_genes/mouse_brain_coronal/output.h5ad

Description:

Anndata with estimated spatial variability score for each gene.

Format:

AnnData object
 var: 'feature_id', 'feature_name', 'pred_spatial_var_score'
 uns: 'dataset_id', 'method_id'

Data structure:

Slot	Type	Description
var["feature_id"]	string	Feature ID.
var["feature_name"]	string	(Optional) Feature name.
var["pred_spatial_var_score"]	double	Predicted spatial variability score.
uns["dataset_id"]	string	A unique identifier for the dataset.
uns["method_id"]	string	A unique identifier for the method.

Component type: Metric

A spatially variable genes identification metric.

Arguments:

Name	Type	Description
--input_method	file	Anndata with estimate spatial variability.
--input_solution	file	Anndata with true spatial variability.
--output	file	(Output) Metric score file.

File format: Score

Metric score file.

Example file: resources_test/task_spatially_variable_genes/mouse_brain_coronal/score.h5ad

Format:

AnnData object
 uns: 'dataset_id', 'method_id', 'metric_ids', 'metric_values'

Data structure:

Slot	Type	Description
uns["dataset_id"]	string	A unique identifier for the dataset.
uns["method_id"]	string	A unique identifier for the method.
uns["metric_ids"]	string	One or more unique metric identifiers.
uns["metric_values"]	double	The metric values obtained for the given prediction. Must be of same length as ‘metric_ids’.

File format: Common Dataset

A subset of the common dataset.

Example file: resources_test/task_spatially_variable_genes/mouse_brain_coronal/simulated_dataset.h5ad

Format:

AnnData object
 var: 'feature_id', 'feature_name', 'orig_feature_id', 'orig_feature_name', 'true_spatial_var_score'
 obsm: 'spatial'
 layers: 'counts'
 uns: 'dataset_id', 'dataset_name', 'dataset_url', 'dataset_reference', 'dataset_summary', 'dataset_description', 'dataset_organism'

Data structure:

Slot	Type	Description
var["feature_id"]	string	(Optional) Unique identifier for the feature, in this case a ENSEMBL gene id suffixed with alpha value.
var["feature_name"]	string	A human-readable name for the feature, in this case a gene symbol suffixed with alpha value.
var["orig_feature_id"]	string	(Optional) Original unique identifier for the feature, usually a ENSEMBL gene id.
var["orig_feature_name"]	string	Original human-readable name for the feature, usually a gene symbol.
var["true_spatial_var_score"]	double	True spatial variability score.
obsm["spatial"]	double	Spatial coordinates for each spot.
layers["counts"]	integer	Raw counts.
uns["dataset_id"]	string	A unique identifier for the dataset.
uns["dataset_name"]	string	Nicely formatted name.
uns["dataset_url"]	string	Link to the original source of the dataset.
uns["dataset_reference"]	string	(Optional) Bibtex reference of the paper in which the dataset was published.
uns["dataset_summary"]	string	Short description of the dataset.
uns["dataset_description"]	string	Long description of the dataset.
uns["dataset_organism"]	string	The organism of the sample in the dataset.

File format: Solution

Anndata with true spatial variability.

Example file: resources_test/task_spatially_variable_genes/mouse_brain_coronal/solution.h5ad

Description:

Anndata with true spatial variability score for each gene.

Format:

AnnData object
 var: 'feature_id', 'feature_name', 'orig_feature_name', 'true_spatial_var_score'
 obsm: 'spatial'
 uns: 'dataset_id', 'dataset_name', 'dataset_url', 'dataset_reference', 'dataset_summary', 'dataset_description', 'dataset_organism'

Data structure:

Slot	Type	Description
var["feature_id"]	string	(Optional) Unique identifier for the feature (e.g., ESEMBL gene id suffixed with alpha value).
var["feature_name"]	string	A human-readable name for the feature, in this case a gene symbol suffixed with alpha value.
var["orig_feature_name"]	string	Original human-readable name for the feature, usually a gene symbol.
var["true_spatial_var_score"]	double	True spatial variability score.
obsm["spatial"]	double	Spatial coordinates for each spot.
uns["dataset_id"]	string	A unique identifier for the dataset.
uns["dataset_name"]	string	Nicely formatted name.
uns["dataset_url"]	string	Link to the original source of the dataset.
uns["dataset_reference"]	string	(Optional) Bibtex reference of the paper in which the dataset was published.
uns["dataset_summary"]	string	Short description of the dataset.
uns["dataset_description"]	string	Long description of the dataset.
uns["dataset_organism"]	string	The organism of the sample in the dataset.