Output files

This page is dedicated to output files created by ODAMNet, grouped by:

• Query result files

• Overlap analysis result files

• Active module identification (AMI) result files

• Random walk with restart (RWR) result files

Query output files

By default, ODAMNet retrieved input data from databases using queries. Chemical target genes are retrieved from the Comparative Toxicogenomics Database [1] (CTD). Rare disease pathways are retrieved from WikiPathways [2]. And biological networks are also downloaded from the Network Data Exchange [3].

It implies creation of output files that contain results of these queries.

CTD query output files

Chemical target genes are retrieved from CTD. Two files are created:

CTD_request_MeSHID_DATE.tsvCTD_requestFiltered_MeSHID_DATE.tsv

This file contains the raw query results.

These two files have the same format:

• Input: chemical query name (from the chemical file)

• ChemicalName: name of the query input or its descendant chemicals

• ChemicalId: MeSH ID of the query or its descendant chemicals

• CasRN: CasRN ID of the query or its descendant chemicals

• GeneSymbol: target gene name that is connected to the query or its descendant chemicals

• GeneId: target gene ID (HGCN)

• Organism: organism name where comes from the target gene

• OrganismId: organism ID

• PubMedIds: PubMed IDs of the publication associated to this connection

This is an example of this file:

Input       ChemicalName    ChemicalId      CasRN   GeneSymbol      GeneId  Organism        OrganismId      PubMedIds
d014801     Tretinoin       D014212 302-79-4        ZXDC    79364   Homo sapiens    9606    33167477
d014801     Tretinoin       D014212 302-79-4        ZYG11A  440590  Homo sapiens    9606    23724009|33167477
d014801     Tretinoin       D014212 302-79-4        ZYX     7791    Homo sapiens    9606    23724009
d014801     Tretinoin       D014212 302-79-4        ZZZ3    26009   Homo sapiens    9606    33167477
d014801     Vitamin A       D014801 11103-57-4      ACE2    59272   Homo sapiens    9606    32808185
d014801     Vitamin A       D014801 11103-57-4      AKR1B1  231     Homo sapiens    9606    19014918
d014801     Vitamin A       D014801 11103-57-4      AKR1B10 57016   Homo sapiens    9606    19014918

The file name is composed of the MeSHID and DATE that correspond to the query chemical and the query date (aaaa_mm_dd) respectively.

WikiPathways query output files

Rare disease pathways are retrieved from WikiPathways. Two GMT files are created:

WP_RareDiseases_request_DATE.gmtWP_allPathways_request_DATE.gmt

This file contains the rare disease pathways in GMT format.

GMT file is a tab-separated file:

• pathwayIDs: first column is the WikiPathways ID

• pathways: second column is the name of the WikiPathways

• HGNC: all the other columns contain genes inside the WikiPathways. The number of columns is different for each pathways and varies according the number of genes inside.

This is an example of this file:

pathwayIDs  pathways        HGNC
WP5195      Disorders in ketolysis  ACAT1   HMGCS1  OXCT1   BDH1    ACAT2
WP5189      Copper metabolism       ATP7B   ATP7A   SLC11A2 SLC31A1
WP5190      Creatine pathway        GAMT    SLC6A8  GATM    OAT     CK

The file name is composed of the query DATE (aaaa_mm_dd).

NDEx query output files

There are two ways to download biological network from NDEx in ODAMNet.

The first one is when you apply the active module identification (AMI) approach. You can use a biological network directly downloaded from NDEx. You need to provide the --netUUID identifier. A SIF file will be created. See Active Module Identification page for more details.

The second one is using the networkDownloading function. Providing the --netUUID identifier, you can download biological networks in both SIF and GR format. See Network downloading page for more details.

GR formatSIF format

MMP11       PRPF40A
ASB16-AS1   SHBG
KIAA0513    INTS4
KIAA0513    HAX1
RAVER2      PTBP1

Overlap analysis output files

In the Overlap analysis, only one type of file is created: Overlap_*.csv. Number of result files depends of the chemical number given in the chemicals file.

This file contains ten columns:

• PathwayIDs: Pathway ID

• PathwayNames: Pathway name

• PathwayBackgroundNames: Source of the pathway (e.g. Wikipathways)

• PathwaySizes: Number of genes inside the pathway

• TargetSize: Number of target genes (i.e. that interact with chemical) that are in the background gene set

• IntersectionSize: Number of target genes that are inside the pathway

• BackgroundSizes: Number of genes in the background gene sets (e.g. genes from all human pathways in WikiPathways)

• pValue: pvalue of the overlap between target genes and pathways/processes of interest (i.e. hypergeometric test)

• pAdjusted: adjusted pvalue (i.e. multitest correction)

• Intersection: list of genes shared between targeted genes and pathways/processes of interest (space-separated)

This is an example of this file:

PathwayIDs;PathwayNames;PathwayBackgroundNames;PathwaySizes;TargetSize;IntersectionSize;BackgroundSizes;pValue;pAdjusted;Intersection
WP4940;15q11.2 copy number variation syndrome;WikiPathway_2022_08_01;10;1721;0;12379;1.0;1.0;
WP4271;Vitamin B12 disorders;WikiPathway_2022_08_01;13;1721;0;12379;1.0;1.0;
WP4299;Lamin A-processing pathway;WikiPathway_2022_08_01;3;1721;0;12379;1.0;1.0;
WP4506;Tyrosine metabolism;WikiPathway_2022_08_01;4;1721;0;12379;1.0;1.0;
WP5223;2q21.1 copy number variation syndrome;WikiPathway_2022_08_01;42;1721;1;12379;0.9981605117974595;1.0;APC
WP4686;Leucine, isoleucine and valine metabolism;WikiPathway_2022_08_01;24;1721;2;12379;0.8660465002997586;1.0;BCAT1 BCAT2

See Overlap analysis page, Use-case 1 overlap analysis and Use-case 2 overlap analysis for more details.

AMI output files

The DOMINO_inputGeneList_*.txt file contains the input list of target genes using by DOMINO [4].

CCND1
CDKN1A
BAD
ESR1
KRT18

The three following files contain results of the AMI analysis. They give information about the identified active modules.

*_activeModulesNetwork.txt*_activeModulesMetrics.txt*_activeModules.txt

This file contains details about each identified active module found. It contains four columns:

• source: node 1

• target: node 2

• link: kind of link

• AMI_number: active module number

This is an example of the file:

source      target  link    AMI_number
CDT1        MCM6    ppi     1
CDT1        CDK1    ppi     1
CDT1        ORC1    ppi     1
CDT1        MCM2    ppi     1
CDT1        GMNN    ppi     1

The three following files contain results of the Overlap analysis between identified active modules and pathways/processes of interest.

Overlap_AM_*.csv*_signOverlap.txt*_overlapAMresults4Cytoscape.txt

There are as many overlap files as identified active modules. This file contains the Overlap analysis results. See Overlap analysis output files for more details.

See Active Module Identification page, Use-case 1 AMI analysis and Use-case 2 AMI analysis for more details.

RWR output files

In the RWR approach, the config_minimal.yml and seeds.txt input files are copy/paste into the output directory results. See Configuration file for more details.

The other created files contain RWR results.

multiplex_*.tsvUseCase1_RWR_network.sifRWR_top20.txt

There are as many multiplex output files as multiplexes used in the RWR analysis. It contains RWR scores for each node and three columns:

• multiplex: multiplex folder name

• node: name of node inside the multiplex (e.g. target genes, pathways …)

• score: score calculated by the walk

This is an example of this file:

multiplex   node    score
1   VCAM1   0.0002083975629882177
1   FN1     0.00020345404504599346
1   EGFR    0.00020244600248388192
1   HSP90AB1        0.00020195660880228006
1   CTNNB1  0.0002014264852242386
1   TP53    0.00019080205293178928
1   MED1    0.0001875608976608657
1   EP300   0.00018540571477254143
1   SMAD3   0.0001852022345355004

See Random Walk with Restart page, Use-case 1 RWR analysis and Use-case 2 RWR analysis for more details.

References

[1]

Davis AP, Grondin CJ, Johnson RJ et al.. The Comparative Toxicogenomics Database: update 2021. Nucleic acids research. 2021.

[2]

Martens M, Ammar A, Riutta A et al.. WikiPathways: connecting communities. Nucleic acids research. 2021.

[3]

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

[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.

[5] (1,2,3)

Shannon P, Markiel A, Ozier O et al.. Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome research. 2003.