#### README ####


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Download--Transcription factor-Targets Interactions (TTI)
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TTI dumps
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FILE NAMES
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The files are consistently named following this pattern:
<species>_motif.txt

<species>: The abbreviated name of a species.
_motif: All files in these directories represent TTI database files


Column definitions
The column contents should be as follows:
　1.motif_id
　　　The name of the motif, which is unique in the motif database files.
　2.motif_alt_id
	An alternate name for the motif that may be provided in the motif database files.
　3.Target_gene
　　　The promoter of the gene matched to the motif.
　4.start
	The start position of the motif occurrence.
　5.stop
	The end position of the motif occurrence.
　6.Strand
　　　The strand '+' indicates the motif matched the forward strand, '-' the reverse strand.
　7.p-value
　　　The p-value of the motif occurrence. The p-value of a motif match is the probability of a single random subsequence of the length of the motif scoring at least as well as the observed match.
　8.matched_sequence
　　　The region of the sequence matched to the motif.
　9.motif_source
　　　Source of motif database files.
　10.motif_class
　　　Motif class annotations.
　11.Motif_family
　　　Motif family annotations.
　12.Data_type
　　　Methods for getting motif.
　13.TF_family
　　　Transcription factor (TF) family annotations.
　14.TF
　　　TF that regulates target genes.



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Download--Protein-Protein Interactions (PPI)
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PPI dumps
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FILE NAMES
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The files are consistently named following this pattern:
<species>_ppi.txt

<species>: The abbreviated name of a species.
_ppi: All files in these directories represent PPI database files


Column definitions
The column contents should be as follows:
　1.Gene1
　　　Interacting gene 1 (replacing protein ID with gene ID).
　2.Gene2
　　　Interacting gene 2.
　3.Combined_score
　　　The combined score is computed by combining the probabilities from the different evidence channels.
　4.Interaction type
　　　Types of interactions, including physical interactions and indirect interactions.


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Network construction methods
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The collection of regulatory gene associations in PPGR was obtained through several methods: 
　1.We mined transcriptional regulatory associations from literature and manually curated each interaction.
　2.We integrated PPI and TTI with experimental evidence imported from primary database repositories such as IntAct, Complex Portal, BioGRID, TAIR, and MINT.
　3.We integrated high-score associations evidence from databases like STRING, KEGG, and Meta-Cyc.
　4.We identified co-expression evidence from pre-computed transcriptome samples.
　5.We predicted TTI in silico through searching for potential binding sites of TFs.
　6.We integrated four different evidence types (experiment, database, text mining, and manually curated) of PPI with Naive Bayes method.