Healp with CreateNetwork edges.txt interpretation
c2b2pss opened this issue · comments
I ran CreateNetwork on a batch of " _bound.bed" files and got
- adjancent.txt
- edges.txt
- a paths and edges file for each TF for which inputted the bed file.
The edges.txt file output is attached.
- What are the column names?
- Is this the file to use for looking at the whole network?
- Which column is source and which is target?
- At the last column there is are names of TF matched to my input mapping files. However, in colmn 4 ="Sites 3" the original HOCOMOCO names are still retained.
If you can please clarify which file to use to build the network and how the connections go it would be very helpful!
edges.txt
Any comments?
Hi @c2b2pss,
yes, I realize that the CreateNetwork tool can be confusing. So here is a bit more detail based on the example run given here. Please also see the image in this link as it summarizes the intention of this tool very well.
The CreateNetwork tool builds a TF-TF network based on given TF binding sites. For this to work, it needs two additional pieces of information: the gene origin (the gene that creates the TF) and the target gene (TF is bound in the promoter). The gene origin is provided through the --origin
parameter. This is a two-column mapping file with the TF name (left) and the origin gene (right; see motif2gene_mapping.txt
). The target genes are provided through a column within the *_bound.bed
files. With this, you can run TOBIAS CreateNetwork
to create four file types:
1. adjacency.txt
This file contains all direct connections between a source TF and its target TFs. It can be read as "Source TF binds in the promoter of Target TF" (Supplementary Methods of the TOBIAS paper) and is recommended to be used for visualization.
Source Targets
AR
ARNT LIN54, ELF2, IRF2
...
2. edges.txt
This file contains the TF binding locations used to create the network. All *_bound.bed
files are combined but filtered for sites that target genes with a known TF motif. Columns named Site_x
come from the .bed
files and Origin_x
columns come from the TF-to-Gene mapping file (--origin
).
Sites_0 Sites_1 Sites_2 Sites_3 Sites_4 Sites_5 Sites_6 Sites_7 Sites_8 Sites_9 Sites_10 Sites_11 Sites_12 Sites_13 Sites_14 Origin_0 Origin_1
CHR4 83013103 83013109 ARNT 8.10161 - CHR4 83012435 83013425 BCELL,TCELL . . ENSG00000189308 LIN54 25.46566 LIN54 ENSG00000189308
CHR4 139177963 139177969 ARNT 8.10161 - CHR4 139176415 139178557 BCELL,TCELL . . ENSG00000109381 ELF2 27.12301 ELF2 ENSG00000109381
3. *_path_edges.txt
Similar to adjacency.txt
this file contains connections between TFs however, it is limited to only one source TF. The Level
column provides whether the connection between two TFs is direct or indirect (see graph theory level).
Source Target Level
ARNT LIN54 1
ARNT IRF2 1
ARNT ELF2 1
4. *_paths.txt
This file contains all paths with the respective TF. The n_nodes
column gives the number of nodes (TFs) involved in any given path.
Regulatory_path n_nodes
ARNT --> LIN54 2
ARNT --> ELF2 2
ARNT --> IRF2 2
I hope this clears things up!
Best wishes,
Hendrik
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