Network downloading

Warning

• Gene IDs have to be consistent between input data (target genes, GMT and networks)

• When data are retrieved by queries, HGNC IDs are used.

Principle

You can download biological networks from the Network Data Exchange (NDEx) [1] using networkDownloading function available in ODAMNet. This function downloads biological networks using the NDEx2 Python client [2] and the network IDs.

Input parameters for network downloading

To download biological networks, you needs the network ID --netUUID and a name to save the network --networkFile. These two parameters are required.

--netUUID TEXT

NDEx network ID [required]

--networkFile FILENAME

Output file name to save the downloaded network [required]

--simple BOOLEAN

if TRUE, creates a file with two columns without header

if FALSE, creates a file with three columns with header

--simple TRUE--simple FALSE

• Two columns: node 1 and node 2

• Without header

• Network format file used by multiXrank [3] (random walk with restart (RWR) approach).

• GR format

MMP11       PRPF40A
ASB16-AS1   SHBG
KIAA0513    INTS4
KIAA0513    HAX1
RAVER2      PTBP1
CNGB1       PNN
CLDN3       POM121
CFD HDHD2
DENND10P1   TMEM256

Use-case command lines

Warning

If --simple FALSE, network file name should has .sif extension

odamnet networkDownloading  --netUUID bfac0486-cefe-11ed-a79c-005056ae23aa \
                            --networkFile useCases/InputData/multiplex/1/PPI_HiUnion_LitBM_APID_gene_names_190123.gr \
                            --simple True

References

[1]

Pratt D, Chen J, Welker et al.. NDEx, the Network Data Exchange. Cell Systems. 2015.

[2]

Pillich RT, Chen J, Churas C, et al.. NDEx: Accessing Network Models and Streamlining Network Biology Workflows. Current Protocol. 2021.

[3]

Baptista A, Gonzalez A & Baudot A. Universal multilayer network exploration by random walk with restart. Communications Physics. 2022.

[4]

Levi H, Elkon R & Shamir R. DOMINO: a network‐based active module identification algorithm with reduced rate of false calls. Molecular systems biology. 2021.