Prioritizing Maize Metabolic Gene Regulators through Multi-Omic Network Integration - processed networks, embeddings, and TF-function predictions

Processed network layers and transcription-factor (TF) function predictions from the maize multi-omic network integration study (Gomez-Cano et al.). The deposit contains the four TF-target network layers (RFN: RF-inferred regulatory network from expression; GRN: protein-DNA-interaction network; eGRN: cis-eQTL-supported PDI network; GAN: trans-eQTL gene-association network), the integrated weighted union network used for embedding, the PecanPy node embeddings (50 dimensions, walk length 80, 10 walks, directed weighted), the network-based TF-function predictions, and the TF-GO prioritization network. All gene identifiers use the B73 AGPv4 annotation, restricted to sorghum-syntenic genes. Files: CoExp_NetworkFinal.10_11_2021.txt (RFN edge list); Only_PDI_NetworkFinal.10_14_2022.txt (GRN edge list); CisE_PDI_NetworkFinal.10_14_2022.txt (eGRN edge list); teQTL_NetworkFinal.10_11_2021.txt (GAN edge list); uniqFullNets_weighted.txt (integrated weighted union network, w = 0.5 + 0.125 x n supporting layers); Pecanpy_uFNetsW.Dim50_WL80_nW10.txt (node embeddings); Total_NetworkBased_predictions.txt (network-based TF-function predictions); Summary.Total.Annotation.txt (annotation summary across strategies); TFGO_4337_net.txt (prioritized TF-GO association network); Table_S7.txt.gz (per-peak PDI table underlying the GRN, provided here because it exceeds journal Supporting Information size limits). Table_S8.txt (the TF-function catalog: TF, annotation, and strategy class for all three annotation strategies, with a Threshold_stability_n_of_5 column for the network-based associations giving the number of neighborhood-similarity thresholds, out of five spanning D >= 0.005-0.20, at which the association is significant; all 23,796 TF-PWY associations are scored, TF-GO associations are scored for the 5,469 of 7,722 parents assessable under the current Gene Ontology release, and NA marks GO terms now obsolete or restructured in the ontology as well as strategies outside the sweep; 35 rows retain v3 (GRMZM) gene identifiers from the source annotations). Analysis code: github.com/gomezcan/Multi-Omic_Network_Integration_Maize (archived separately).