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Description:

genewalk 1.6.3

GeneWalk

GeneWalk determines for individual genes the functions that are relevant in a
particular biological context and experimental condition. GeneWalk quantifies
the similarity between vector representations of a gene and annotated GO terms
through representation learning with random walks on a condition-specific gene
regulatory network. Similarity significance is determined through comparison
with node similarities from randomized networks.
Install GeneWalk
To install the latest release of GeneWalk (preferred):
pip install genewalk

To install the latest code from Github (typically ahead of releases):
pip install git+https://github.com/churchmanlab/genewalk.git

GeneWalk uses a number of resource files that it downloads as needed during
runtime. To optionally pre-download these resource files in the default resource folder,
the command
python -m genewalk.resources

can be run.
Using GeneWalk
Gene list file
GeneWalk always requires as input a text file containing a list with genes of
interest relevant to the biological context. For example, differentially
expressed genes from a sequencing experiment that compares an experimental
versus control condition. GeneWalk supports gene list files containing HGNC
human gene symbols, HGNC IDs, human Ensembl gene IDs, MGI mouse gene IDs, RGD
rat gene IDs, or human or mouse entrez IDs. GeneWalk internally maps these IDs
to human genes.
For organisms other than human, mouse or rat, there are two options. The first
is to map the genes to human orthologs yourself and then input the human ortholog
list as described above. Use this strategy if you consider the organism
sufficiently related to human. The second option is to provide an input gene file
with custom gene IDs. These are not mapped to human genes. Use custom gene IDs
for more divergent organisms, such as drosophila, worm, yeast, plants or bacteria.
In this case the user must also provide a custom gene network with GO annotations
as input. See section Custom input networks for more details.
Each line in the gene input file contains a gene identifier of one of the
above types.
GeneWalk command line interface
Once installed, GeneWalk can be run from the command line as genewalk, with
a set of required and optional arguments. The required arguments include the
project name, a path to a text file containing a list of genes, and an argument
specifying the type of gene identifiers in the file.
Example
genewalk --project context1 --genes gene_list.txt --id_type hgnc_symbol

Below is the full documentation of the command line interface:
genewalk [-h] [--version] --project PROJECT --genes GENES --id_type
{hgnc_symbol,hgnc_id,ensembl_id,mgi_id,rgd_id,entrez_human,entrez_mouse,custom}
[--stage {all,node_vectors,null_distribution,statistics}]
[--base_folder BASE_FOLDER]
[--network_source {pc,indra,edge_list,sif,sif_annot,sif_full}]
[--network_file NETWORK_FILE] [--nproc NPROC] [--nreps NREPS]
[--alpha_fdr ALPHA_FDR] [--save_dw SAVE_DW]
[--random_seed RANDOM_SEED]

required arguments:
--version Print the version of GeneWalk and exit.
--project PROJECT A name for the project which determines the folder
within the base folder in which the intermediate and
final results are written. Must contain only
characters that are valid in folder names.
--genes GENES Path to a text file with a list of differentially
expressed genes. Thetype of gene identifiers used in
the text file are provided in the id_type argument.
--id_type {hgnc_symbol,hgnc_id,ensembl_id,mgi_id,rgd_id,entrez_human,entrez_mouse,custom}
The type of gene IDs provided in the text file in the
genes argument. Possible values are: hgnc_symbol,
hgnc_id, ensembl_id, mgi_id, rgd_id, entrez_human,
entrez_mouse, and custom. If custom, a network_source
of sif_annot or sif_full must be used.

optional arguments:
--stage {all,node_vectors,null_distribution,statistics,visual}
The stage of processing to run. Default: all
--base_folder BASE_FOLDER
The base folder used to store GeneWalk temporary and
result files for a given project. Default:
~/genewalk
--network_source {pc,indra,edge_list,sif,sif_annot,sif_full}
The source of the network to be used.Possible values
are: pc, indra, edge_list, sif, sif_annot, and
sif_full. In case of indra, edge_list, sif, sif_annot,
and sif_full, the network_file argument must be
specified. Default: pc
--network_file NETWORK_FILE
If network_source is indra, this argument points to a
Python pickle file in which a list of INDRA Statements
constituting the network is contained. In case
network_source is edge_list, sif, sif_annot, or
sif_full, the network_file argument points to a text
file representing the network. See README section
Custom input networks for full description of file
format requirements.
--nproc NPROC The number of processors to use in a multiprocessing
environment. Default: 1
--nreps_graph NREPS_GRAPH
The number of repeats to run when calculating node
vectors on the GeneWalk graph. Default: 3
--nreps_null NREPS_NULL
The number of repeats to run when calculating node
vectors on the random network graphs for constructing
the null distribution. Default: 3
--alpha_fdr ALPHA_FDR
The false discovery rate to use when outputting the
final statistics table. If 1 (default), all
similarities are output, otherwise only the ones whose
false discovery rate are below this parameter are
included. Default: 1
For visualization a default value of 0.1 for both global
and gene-specific plots is used. Lower this value to
increase the stringency of the regulator gene selection
procedure.
--dim_rep DIM_REP Dimension of vector representations (embeddings). This
value should only be increased if genewalk with the
default value generates no statistically significant
results, for instance with very large (>2500) input
gene lists. Alternatively, it can be decreased in case
(nearly) all GO annotations are significant, for
instance with very short gene lists. Default: 8
--save_dw SAVE_DW If True, the full DeepWalk object for each repeat is
saved in the project folder. This can be useful for
debugging but the files are typically very large.
Default: False
--random_seed RANDOM_SEED
If provided, the random number generator is seeded
with the given value. This should only be used if the
goal is to deterministically reproduce a prior result
obtained with the same random seed.

Output files
GeneWalk automatically creates a genewalk folder in the user's home folder
(or the user specified base_folder).
When running GeneWalk, one of the required inputs is a project name.
A sub-folder is created for the given project name where all intermediate and
final results are stored. The files stored in the project folder are:

genewalk_results.csv - The main results table, a comma-separated values text file. See below for detailed description.
genes.pkl - A processed representation of the given gene list, in Python pickle (.pkl) binary file format.
multi_graph.pkl - A networkx MultiGraph resembling the GeneWalk network which was assembled based on the
given list of genes, an interaction network, GO annotations, and the GO ontology.
deepwalk_node_vectors_*.pkl - A set of learned node vectors for each analysis repeat for the graph.
deepwalk_node_vectors_rand_*.pkl - A set of learned node vectors for each analysis repeat for a random graph.
genewalk_rand_simdists.pkl - Distributions constructed from repeats.
deepwalk_*.pkl - A DeepWalk object for each analysis repeat on the graph
(only present if save_dw argument is set to True).
deepwalk_rand_*.pkl - A DeepWalk object for each analysis repeat on a random graph
(only present if save_dw argument is set to True).

Figure files
GeneWalk also automatically generates figures to visualize its results in the
project/figures sub-folder:

index.html: an HTML page that includes all the figures generated, as
described below.
barplots with GO annotations ranked by relevance for each input gene that
GeneWalk was able to generate results for. The filenames contain the
corresponding human gene symbol and input gene id: barplot_[symbol]_[gene id]_x_mlog10global_padj_y_GO.png.
regulators_x_gene_con_y_frac_rel_go(.png and .pdf): scatter plot to
identify regulator genes of interest. These have a large gene connectivity
and high fraction of relevant GO annotations. For more information see our
publication.
genewalk_regulators.csv: list with regulator genes that are named in the
regulators scatterplot.
moonlighters_x_go_con_y_frac_rel_go(.png and .pdf): scatter plot to
identify moonlighting genes: genes with many GO annotations of which a low
fraction are relevant. For more information see our publication.
genewalk_moonlighters.csv: list with moonlighting genes that are named in
the moonlighting scatterplot.
genewalk_scatterplots.csv: data corresponding to the regulator and
moonlighter scatter plots. This file can be used for further gene
prioritization analyses.

GeneWalk results file description
genewalk_results.csv is the main GeneWalk output table, a comma-separated values text file
with the following column headers:

hgnc_id - human gene HGNC identifier.
hgnc_symbol - human gene symbol.
go_name - GO term name.
go_id - GO term identifier.
go_domain - Ontology domain that GO term belongs to
(biological process, cellular component or molecular function).
ncon_gene - number of connections to gene in GeneWalk network.
ncon_go - number of connections to GO term in GeneWalk network.
global_padj - false discovery rate (FDR) adjusted p-value of the
similarity between gene and GO term, when correcting for testing over all
gene-GO term pairs present in the output file.
This is the key statistic that indicates how relevant the gene-GO term pair
(gene function) is in the particular biological context or tested condition.
Global_padj should be used for global analyses that
consider all the GeneWalk output simultaneously, such as gene prioritization
procedures. GeneWalk determines an adjusted p-value with Benjamini Hochberg FDR
correction for multiple testing of all connected GO term for each
nreps_graph repeat analysis. The value presented here is the average (mean
estimate) over all p-adjust values from all nreps_graph repeat analyses.
gene_padj - FDR adjusted p-value of the similarity between gene and
GO term, when correcting for multiple testing over all GO annotations of
that gene. This the key statistic when investigating the functions of one
(or a few) pre-defined gene(s) of interest. Gene_padj determines the statistical
significance of each GO annotation (function) and gene_padj can be used to
sensitively rank GO annotations to reflect the relevance to the gene of interest
in the particular biological context or tested condition. When you consider all
(or many) input genes simultaneously, use global_padj instead. Average
over nreps_graph repeat runs as for global_padj.
pval - p-value of gene - GO term similarity, not corrected for multiple
hypothesis testing. Average over nreps_graph repeat runs.
sim - gene - GO term (cosine) similarity, average over nreps_graph repeat runs.
sem_sim - standard error on sim (mean estimate).
cilow_global_padj - lower bound of 95% confidence interval on global_padj
(mean estimate) from the nreps_graph repeat analyses.
ciupp_global_padj - upper bound of 95% confidence interval on global_padj.
cilow_gene_padj - lower bound of 95% confidence interval on gene_padj
(mean estimate) from the nreps_graph repeat analyses.
ciupp_gene_padj - upper bound of 95% confidence interval on gene_padj.
cilow_pval - lower bound of 95% confidence interval on pval (mean estimate)
from the nreps_graph repeat analyses.
ciupp_pval - upper bound of 95% confidence interval on pval.
mgi_id, rgd_id, ensembl_id, entrez_human or entrez_mouse - in case one of
these gene identifiers were provided as input, the GeneWalk results table
starts with an additional column to indicate the gene identifiers. In the
case of mouse genes, the corresponding hgnc_id and hgnc_symbol resemble its
human ortholog gene used for the GeneWalk analysis.

Run time and stages of GeneWalk algorithm
Recommended number of processors (optional argument: nproc) for a short (1-2h)
run time is 4:
genewalk --project context1 --genes gene_list.txt --id_type hgnc_symbol --nproc 4

By default GeneWalk will run with 1 processor, resulting in a longer overall
run time: 6-12h.
Given a list of genes, GeneWalk runs three stages of analysis:

Assembling a GeneWalk network and learning node vector representations
by running DeepWalk on this network, for a specified number of repeats.
Typical run time: one to a few hours.
Learning random node vector representations by running DeepWalk on a set of
randomized versions of the GeneWalk network, for a specified number of
repeats. Typical run time: one to a few hours.
Calculating statistics of similarities between genes and GO terms, and
outputting the GeneWalk results in a table. Typical run time: a few minutes.
Visualization of the GeneWalk results generated in the project/figures subfolder.
Typical run time: 1-10 mins depending on the number of input genes.

GeneWalk can either be run once to complete all these stages (default), or
called separately for each stage (optional argument: stage). Recommended
memory availability on your operating system: 16Gb or 32Gb RAM. GeneWalk
outputs the uncertainty (95% confidence intervals) of the similarity
significance (global and gene p-adjust). Depending on the context-specific network
topology, this uncertainty can be large for individual gene - function
associations. However, if overall the uncertainties turn out very large, one
can set the optional arguments nreps_graph to 10 (or more) and nreps_null to 10
to increase the algorithm's precision. This comes at the cost of an increased
run time.
Custom input networks
By default, GeneWalk uses the PathwayCommons resource (--network_source pc)
to create a human gene network. It then automatically adds edges
representing GO annotations for input genes and ontology relations between
GO terms. However, there are options to run GeneWalk with a custom network as
an input.
First, specify the --network_source argument as one of the alternative sources:
{indra, edge_list, sif, sif_annot, sif_full}.
If custom gene IDs are used (--id_type custom) in the input gene list, for
instance from a model organism: choose as network source sif_annot or sif_full.
Then, include the argument --network_file with the path to the custom network
input file. The network file format has to correspond to the chosen
--network_source, as follows.
The sif/sif_annot/sif_full options require the network file in a simple
interaction file (SIF) format. Each row of the SIF text file consists of
three comma-separated entries representing source, relation type, and target.
The relation type is not explicitly used by GeneWalk, and can be set
to an arbitrary label.
The difference between the sif, sif_annot, and sif_full options:

sif: the input SIF can contain only human gene-gene relations.
Genes have to be encoded as human HGNC gene symbols (for example KRAS).
GO annotations for genes, as well as ontology relations
between GO terms are added automatically by GeneWalk.
sif_annot: the input SIF has to contain both
gene-gene relations, and GO annotations for genes: rows where the
source is a gene, and the target is a GO term. Use GO IDs with prefix
(for example GO:0000186) to encode GO terms. Genes should be encoded the same
as in the gene input list and do not have to correspond to human genes.
Ontology relations between GO terms are then added automatically by GeneWalk.
sif_full: the input SIF has to contain all GeneWalk network edges:
gene-gene relations, GO annotations for genes, and ontology relations between
GO terms. GeneWalk does not add any more edges to the network. Encode genes and
GO terms in the same manner as for sif_annot.

The edge_list option is a simplified version of the sif option. It requires
a network text file that contains rows with two columns each, a source and a target.
In other words, it omits the relation type column from the SIF format. Further file
preparation requirements are the same as for the sif option.
The indra option requires as custom network input file a Python pickle file
containing a list of INDRA Statements. These statements can represent human gene-gene,
as well as gene-GO relations from which network edges are derived. Human GO
annotations and ontology relations between GO terms are then added automatically
by GeneWalk during network construction.
Further documentation
For a tutorial and more general information see the
GeneWalk website.
For further code documentation see our readthedocs page.
Citation
Robert Ietswaart, Benjamin M. Gyori, John A. Bachman, Peter K. Sorger, and
L. Stirling Churchman
GeneWalk identifies relevant gene functions for a biological context using network
representation learning,
Genome Biology 22, 55 (2021). https://doi.org/10.1186/s13059-021-02264-8
Funding
This work was supported by National Institutes of Health grant 5R01HG007173-07
(L.S.C.), EMBO fellowship ALTF 2016-422 (R.I.), and DARPA grants W911NF-15-1-0544
and W911NF018-1-0124 (P.K.S.).