Module Documentation

STREAM.DetectLeafGenes


LSID
urn:lsid:broad.mit.edu:cancer.software.genepattern.module.analysis:00403
Author(s)
Huidong Chen, Massachussets General Hospital, wrapped as a module by Ted Liefeld, Mesirov Lab, UCSD School of Medicine.
Contact(s)

Algorithm and scientific questions: <Huidong.Chen  at mgh dot harvard dot edu>

Module wrapping issues:  Ted Liefeld  < jliefeld at cloud dot ucsd dot edu>

Introduction

STREAM (Single-cell Trajectories Reconstruction, Exploration And Mapping) is an interactive pipeline capable of disentangling and visualizing complex branching trajectories from both single-cell transcriptomic and epigenomic data. Within GenePattern STREAM is implemented as a collection of modules that cover the entire STREAM processing pipeline to allow individual steps to be performed interactively for data exploration.

STREAM.DetectLeafGenes is used to detect marker genes for each leaf branch.

Algorithm

For each gene E we scale the gene expression values to [0,1]. Then we calculate the average gene expressions for all leaf branches. Based on the average expressions, we calculate the Z-scores of all leaf branches. If there is any leaf branch with an absolute Z-score greater than 1.5, then the leaf branch with the highest absolute Z-score value will be picked as the candidate leaf branch. Next, Kruskal–Wallis H-test is computed for all the leaf branches to test if a significant difference of gene expression median value between leaf branches exists. If it is significant (p-value < 0.01), then a post-hoc pairwise Conover’s test is computed for multiple comparisons of mean rank sums test between all leaf branches. If the p-values between the candidate leaf branch and the other leaf branches are all below the specified threshold (0.01), then the gene E will be considered as leaf gene of the candidate leaf branch.

References

H Chen, L Albergante, JY Hsu, CA Lareau, GL Bosco, J Guan, S Zhou, AN Gorban, DE Bauer, MJ Aryee, DM Langenau, A Zinovyev, JD Buenrostro, GC Yuan, L Pinello Single-cell trajectories reconstruction, exploration and mapping of omics data with STREAM. Nature Communications, volume 10, Article number: 1903 (2019)

Nestorowa, S. et al. A single-cell resolution map of mouse hematopoietic stem and progenitor cell differentiation. Blood 128, e20-31 (2016).

Pinello Lab   STREAM Github Repository

Input Files

  1. data file *
    A STREAM pkl file containing an annotated AnnData matrix of gene expression data.

Output Files

  1. <output filename>_stream_result.pkl
    Output file in STREAM AnnData extended pickle (.pkl) file format suitable for passing to the next step of the STREAM analysis.
  2. leaf_genes/leaf_genes.tsv
    All the leaf genes from all branches. Columns include z score, H statistic, H pvalue, p values.
  3. leaf_genes/leaf_genesS#_S#.tsv
    The leaf genes for the specific branching. Columns include z score, H statistic, H pvalue, p values.

Example Data

Example data for the STREAM workflow can be downloaded from dropbox: Stream Example Data
Ref: Nestorowa, S. et al. A single-cell resolution map of mouse hematopoietic stem and progenitor cell differentiation. Blood 128, e20-31 (2016).

Example data for this specific step can be found at stream_epg_result.pkl

Requirements

GenePattern 3.9.11 or later (dockerized).

Parameters

Inputs and Outputs

Name Description
data file* A STREAM pkl file containing an annotated AnnData matrix of gene expression data/td>
output filename* The output filename prefix.

Marker Gene Detection

Parameters used if variable genes are to be selected as the feature.
Name Description
root The starting node.
preference The preference of nodes. The branch with speficied nodes are preferred and put on the top part of subway plot. The higher ranks the node have, the closer to the top the branch with that node is. e.g. S3,S4.
percentile expr* Between 0 and 100. Between 0 and 100. Specify the percentile of gene expression greater than 0 to filter out some extreme gene expressions.
use precomputed* If True, the previously computed scaled gene expression will be used.
cutoff zscore* The z-score cutoff used for mean values of all leaf branches.
cutoff pvalue The p value cutoff used for Kruskal-Wallis H-test and post-hoc pairwise Conover's test.

* - required