RWRtoolkit-data

Multiplex network (Rdata) objects for use with the kb_djornl RWRtools KBase app.

Multiplex Networks

Comprehensive Network Multiplex (Default Multiplex Network)

Const	Comprehensive_Network_AT_d0.5_v02.RData
Version	0.2
Description	Contains the following network layers with unweighted edges and delta value = 0.5: CoEvolution-DUO (DU) version 0.1 (AT-UU-DU-67-AA-01) Coexpression Gene-Atlas (GA) version 0.3 (AT-UU-GA-01-AA-01) Knockout Similarity (KS) version 0.3 (AT-UU-KS-00-AA-01) PPI-6merged (PP) version 0.3 (AT-UU-PP-00-AA-01) PEN-Diversity (PX) version 0.1 (AT-UU-PX-01-AA-01) Predictive CG Methylation (PY) version 0.1 (AT-UU-PY-01-LF-01) Regulation-ATRM (RE) version 0.3 (AT-UU-RE-00-AA-01) Regulation-Plantregmap (RP) version 0.3 (AT-UU-RP-03-AA-01) Metabolic-AraCyc (RX) version 0.3 (AT-UU-RX-00-AA-01)

Close to Phenotype Multiplex

Const	Close_To_Phenotype_AT_d0.5_v01.RData
Version	0.1
Description	Contains the following network layers with unweighted edges and delta value = 0.5: Knockout Similarity (KS) version 0.3 (AT-UU-KS-00-AA-01) PPI-6merged (PP) version 0.3 (AT-UU-PP-00-AA-01) Metabolic-AraCyc (RX) version 0.3 (AT-UU-RX-00-AA-01)

Expression/Regulation Multiplex

Const	Expression_Regulation_AT_d0.5_v01.RData
Version	0.1
Description	Contains the following network layers with unweighted edges and delta value = 0.5: Coexpression Gene-Atlas (GA) version 0.3 (AT-UU-GA-01-AA-01) PEN-Diversity (PX) version 0.1 (AT-UU-PX-01-AA-01) Regulation-ATRM (RE) version 0.3 (AT-UU-RE-00-AA-01)

GO Multiplex

Const	GO_AT_d0.5_v01.RData
Version	0.1
Description	Contains the following network layers with unweighted edges and delta value = 0.5: GO semantic similarity (GO) version 0.4 (AT-UU-GO-05-AA-01)

High Confidence Multiplex

Const	High_Confidence_AT_d0.5_v01.RData
Version	0.1
Description	Contains the following network layers with unweighted edges and delta value = 0.5: Knockout Similarity (KS) version 0.3 (AT-UU-KS-00-AA-01) PPI-6merged (PP) version 0.3 (AT-UU-PP-00-AA-01) Regulation-ATRM (RE) version 0.3 (AT-UU-RE-00-AA-01) Metabolic-AraCyc (RX) version 0.3 (AT-UU-RX-00-AA-01)

Ontology Multiplex

Const	Ontology_AT_d0.5_v01.RData
Version	0.1
Description	Contains the following network layers with unweighted edges and delta value = 0.5: GO semantic similarity (GO) version 0.4 (AT-UU-GO-05-AA-01) Knockout Similarity (KS) version 0.3 (AT-UU-KS-00-AA-01)

Metabolic Multiplex

Const	Metabolic_AT_d0.5_v01.RData
Version	0.1
Description	Contains the following network layers with unweighted edges and delta value = 0.5: Metabolic-AraCyc (RX) version 0.3 (AT-UU-RX-00-AA-01)

Predicted Regulation Multiplex

Const	Predicted_Regulation_AT_d0.5_v02.RData
Version	0.2
Description	Contains the following network layers with unweighted edges and delta value = 0.5: Coexpression Gene-Atlas (GA) version 0.3 (AT-UU-GA-01-AA-01) PEN-Diversity (PX) version 0.1 (AT-UU-PX-01-AA-01) Regulation-Plantregmap (RP) version 0.3 (AT-UU-RP-03-AA-01) Predictive CG Methylation (PY) version 0.1 (AT-UU-PY-01-LF-01)

Unknown Function Multiplex

Const	Unknown_Function_AT_d0.5_v01.RData
Version	0.1
Description	Contains the following network layers with unweighted edges and delta value = 0.5: CoDomain (CD) version 0.3 (AT-UU-CD-00-AA-01) CoEvolution-DUO (DU) version 0.1 (AT-UU-DU-67-AA-01) PPI-6merged (PP) version 0.3 (AT-UU-PP-00-AA-01) Metabolic-AraCyc (RX) version 0.3 (AT-UU-RX-00-AA-01)

Networks

Network files are located on the kbase exascale_data repository.

CoDomain Network

Const	AT-UU-CD-00-AA-01
Version	0.3
Description	GeneA connects to GeneB if they share one or more common protein domains. Network was obtained from AraNet2.
DOI	https://doi.org/10.1093/nar/gku1053
# Edges	25,000
# Nodes	7,634
Processing information	During to-spec processing no changes were made.

CoEvolution-DUO Network

Const	AT-UU-DU-67-AA-01
Version	0.1
Description	GeneA connects to GeneB if a SNP in or near GeneA is correlated with a SNP in or near GeneB using the DUO metric. SNP data is from the full 1001 Genomes. SNPs were mapped to nearest genes (left/right) so that edges are all gene to gene.
DOI	https://doi.org/10.1101/2020.01.28.923730
# Edges	13,514
# Nodes	2,283
Processing information	Edges between genes on the same chromosome (cis) were removed and edges with a DUO score < 0.67 were filtered out.

Coex Gene-Atlas Network

Const	AT-UU-GA-01-AA-01
Version	0.3
Description	Coexpression network obtained from AtGenie.org. It uses expression array data from multiple tissues to calculate the correlation between genes.
DOI	https://doi.org/10.1111/nph.13557
# Edges	84,959
# Nodes	7,683
Processing information	The network was already provided. It was thresholded as the top 1% of edges. During to-spec processing no changes were made.

GO Network

Const	AT-UU-GO-05-AA-01
Version	0.4
Description	GeneA connects to GeneB if the two genes have semantically similar GO terms (with a similarity score > 0). This network is used to evaluate other networks for functional biology content.
DOI	https://doi.org/10.1093/bioinformatics/btq064
# Edges	2,930,141
# Nodes	7,625
Processing information	Edges are thresholded at similarity > 0.5. During to-spec processing no changes were made. V0.3 -> v0.4: used 0.5 thresholding instead of 0.3 to limit file size.

Knockout Similarity Network

Const	AT-UU-KS-00-AA-01
Version	0.3
Description	GeneA connects to GeneB if the phenotypic effect of knocking out GeneA is similar to the phenotypic effect of knocking out GeneB. Similarity is based on Phenotype Ontology semantic similarity.
DOI	https://doi.org/10.1186/s13007-015-0053-y
# Edges	94,952
# Nodes	1,841
Processing information	This network was already provided in the paper. Edges with similarity score < 0.2 were culled. During to-spec processing no changes were made.

PPI-6merged Network

const	AT-UU-PP-00-AA-01
Version	0.3
Description	GeneA connects to GeneB if their protein products have been shown to bind to interact with each other, typically through experimental evidence. The PPI-6merged network is the union of 6 different A.thaliana PPI networks: AraNet2 LC, AraNet2 HT, AraPPInet2 0.60, BIOGRID 4.3.194 physical, AtPIN, Mentha. These 6 were all relatively high scoring with GOintersect. StringDB provided a low score and therefore was not included
DOI	n/a
# Edges	317,787
# Nodes	19,191
Processing information	During to-spec processing no changes were made.

PEN-Diversity Network

Const	AT-UU-PX-01-AA-01
Version	0.1
Description	GeneA connects to GeneB if the expression vector of GeneA is an important predictor of the expression vector of GeneB in an iRF model, where all other genes’ expression are included as covariates. The iRF model is an expansion on Random Forest, a feature selection model.
DOI	https://doi.org/10.1016/j.cell.2016.06.044
# Edges	97,819
# Nodes	17,907
Processing information	10,258 duplicate edges were removed (these edges are directed edges with different scores from A->B than B->A, in the unweighted version where all edges have scores of 1 these are duplicate edges and only one direction is maintained in the network). The top 0.1% of all edges were retained.

Predictive CG Methylation-1001 Epigenomes Network

Const	AT-UU-PY-01-LF-01
Version	0.1
Description	GeneA connects to GeneB if the CG methylation vector of GeneA is an important predictor of the CG methylation vector of GeneB in an iRF model, where all other genes’ CG methylation states are included as covariates. The iRF model is an expansion on Random Forest, a feature selection model.
DOI	https://doi.org/10.1016/j.cell.2016.06.044
# Edges	76,027
# Nodes	13,314
Processing information	4,740 duplicate edges were removed (these edges are directed edges with different scores from A->B than B->A, in the unweighted version where all edges have scores of 1 these are duplicate edges and only one direction is maintained in the network). Only standard conditions were kept and methylation vectors with NAs were removed. The top 0.1% of all edges were retained.

Regulation-ATRM Network

Const	AT-UU-RE-00-AA-01
Version	0.3
Description	GeneA connects to GeneB if GeneA is a Transcription Factor (TF) that is shown to interact with GeneB (which may or may not be a TF). This dataset contains literature mined and manually curated TF regulatory interactions for A.thaliana. Started from 1701 TFs from PlantTFDB 2.0 and retrieved 4663 TF-associated interactions. These were manually filtered (e.g. FPs, PPI interactions removed). They then added some from other sources. Final result is 1431 confirmed TF regulatory interactions, of which 637 are TF-TF.
DOI	https://doi.org/10.1093/molbev/msv058
# Edges	1,359
# Nodes	789
Processing information	During to-spec processing, removed 25 self-loops and 47 duplicate edges.

Regulation-Plantregmap Network

const	AT-UU-RP-03-AA-01
Version	0.3
Description	This network contains computationally predicted TF-Target relationships based on motifs, binding sites, ChipSeq data
DOI	https://doi.org/10.1093/nar/gkz1020
# Edges	167,851
# Nodes	16,014
Processing information	Removed all Lit curated edges and then gave one point to each line of evidence (e.g. Motif, TFBS, ChipSeq) for an edge. Then summed them up to give an edge weight. Highest scoring regulatory edges have 5. We thresholded this network at score >=3. During to-spec processing, 29 self-loops and 48 duplicate edges were removed.

Metabolic-AraCyc Network

Const	AT-UU-RX-00-AA-01
Version	0.3
Description	GeneA connects to GeneB if they are both enzymatic and are linked by a common substrate or product. E.g. RXNA (GeneA) → Compound1 → RXNB (GeneB). Here GeneA connects to GeneB due to Compound1.
DOI	https://doi.org/10.1104/pp.102.017236
# Edges	21,524
# Nodes	2,857
Processing information	All enzymatic reactions and associated genes (enzymes) and compounds were downloaded from AraCyc as smart tables, and transformed by custom R script to generate the appropriate network format linking gene to gene based on intermediary compounds.During to-spec processing, 24 non-standard nodes were removed (corresponding to 322 non-standard edges), and 3,243 duplicate edges were removed.