=== edge.ChIP_chip.tbl.txt.gz
##ColumnVariables[feature1_id] = (internal) feature_id of regulator (transcription factor)
##ColumnVariables[feature2_id] = (internal) feature_id of its target (bound by the regulator)
##ColumnVariables[weight] = the number of experiments that the TF has been observed binding at the target gene's promoter
#-----------------------------------------------
# this file is a dump of FANTOM4 EdgeExpressDB  
# with the following SQL                        
#-----------------------------------------------
# select
#   feature1_id
# , feature2_id
# , weight
# from
#   edge
# , edge_source
# where edge.edge_source_id = edge_source.edge_source_id
#   and edge.sub_type != "published"
#   and edge_source.name = "ChIP_chip"
# ;
# 
=== edge.GoldStd_TF.tbl.txt.gz
##ColumnVariables[feature1_id] = (internal) feature_id of regulator (transcription factor)
##ColumnVariables[feature2_id] = (internal) feature_id of its target (bound by the regulator)
##ColumnVariables[sym_value] = pubmed id of the publication, where the interaction is reported.
#-----------------------------------------------
# this file is a dump of FANTOM4 EdgeExpressDB  
# with the following SQL                        
#-----------------------------------------------
# select
#   feature1_id
# , feature2_id
# , symbol.sym_value
# from
#   edge
# , edge_source
# , edge_2_symbol
# , symbol
# where edge.edge_source_id = edge_source.edge_source_id
#   and edge_source.name = "GoldStd_TF"
#   and edge.edge_id = edge_2_symbol.edge_id
#   and edge_2_symbol.symbol_id = symbol.symbol_id
#   and symbol.sym_type = "PubmedID"
# ;
# 
=== edge.L2_to_L3_april08.tbl.txt.gz
##ColumnVariables[feature1_id] = (internal) feature_id of level2 promoter
##ColumnVariables[feature2_id] = (internal) feature_id of level3 promoter, which is associated with the level2.
#-----------------------------------------------
# this file is a dump of FANTOM4 EdgeExpressDB  
# with the following SQL                        
#-----------------------------------------------
# select
#   feature1_id
# , feature2_id
# from
#   edge
# , edge_source
# where edge.edge_source_id = edge_source.edge_source_id
#   and edge_source.name = "L2_to_L3_april08"
# ;
# 
=== edge.L3_promoter_Entrez_08May16_EvN.tbl.txt.gz
##ColumnVariables[feature1_id] = (internal) feature_id of level3 promoter
##ColumnVariables[feature2_id] = (internal) feature_id of gene, which is associated with the level3.
#-----------------------------------------------
# this file is a dump of FANTOM4 EdgeExpressDB  
# with the following SQL                        
#-----------------------------------------------
# select
#   feature1_id
# , feature2_id
# from
#   edge
# , edge_source
# where edge.edge_source_id = edge_source.edge_source_id
#   and edge_source.name = "L3_promoter_Entrez_08May16_EvN"
# ;
# 
=== edge.miRNA_pre2mature.tbl.txt.gz
##ColumnVariables[feature1_id] = (internal) feature_id of miRNA precursor
##ColumnVariables[feature2_id] = (internal) feature_id of mature miRNA, which is produced from the precursor
#-----------------------------------------------
# this file is a dump of FANTOM4 EdgeExpressDB  
# with the following SQL                        
#-----------------------------------------------
# select
#   feature1_id
# , feature2_id
# from
#   edge
# , edge_source
# where edge.edge_source_id = edge_source.edge_source_id
#   and edge_source.name = "miRNA_pre2mature"
# ;
# 
=== edge.miRNA_targets.tbl.txt.gz
##ColumnVariables[feature1_id] = (internal) feature_id of miRNA
##ColumnVariables[feature2_id] = (internal) feature_id of its target
##ColumnVariables[weight] = significance of the prediction
#
# Note that this data is based on ElMMo (PMID:17331257), and
# the latest predictions are available from MirZ web server (PMID:19468042):
#
#    http://www.mirz.unibas.ch/
#
#-----------------------------------------------
# this file is a dump of FANTOM4 EdgeExpressDB  
# with the following SQL                        
#-----------------------------------------------
# select
#   feature1_id
# , feature2_id
# , weight
# from
#   edge
# , edge_source
# where edge.edge_source_id = edge_source.edge_source_id
#   and edge_source.name = "miRNA_targets"
# ;
# 
=== edge.pre-miRNA_perturbation.tbl.txt.gz
##ColumnVariables[feature1_id] = (internal) feature_id of over-expressed miRNA
##ColumnVariables[feature2_id] = (internal) feature_id of gene, which is perturbed by the over expression
##ColumnVariables[weight] = logFC
#-----------------------------------------------
# this file is a dump of FANTOM4 EdgeExpressDB  
# with the following SQL                        
#-----------------------------------------------
# select
#   feature1_id
# , feature2_id
# , weight
# from
#   edge
# , edge_source
# where edge.edge_source_id = edge_source.edge_source_id
#   and edge_source.name = "pre-miRNA_perturbation"
# ;
# 
=== edge.public_ChIP_chip.tbl.txt.gz
##ColumnVariables[feature1_id] = (internal) feature_id of regulator (transcription factor)
##ColumnVariables[feature2_id] = (internal) feature_id of its target (bound by the regulator)
##ColumnVariables[weight] = the number of experiments that the TF has been observed binding at the target gene's promoter
##ColumnVariables[sym_value] = pubmed id of the publication, where the interaction is reported.
#-----------------------------------------------
# this file is a dump of FANTOM4 EdgeExpressDB  
# with the following SQL                        
#-----------------------------------------------
# select
#   feature1_id
# , feature2_id
# , weight
# , sym_value
# from
#   edge
# , edge_source
# , edge_2_symbol
# , symbol
# where edge.edge_source_id = edge_source.edge_source_id
#   and edge.sub_type = "published"
#   and edge_source.name = "ChIP_chip"
#   and edge.edge_id = edge_2_symbol.edge_id
#   and edge_2_symbol.symbol_id = symbol.symbol_id
#   and symbol.sym_type = "PubmedID"
# ;
# 
=== edge.siRNA_perturbation.tbl.txt.gz
##ColumnVariables[feature1_id] = (internal) feature_id of regulator (siRNA knockdown target)
##ColumnVariables[feature2_id] = (internal) feature_id of its target (perturbed gene by the knock down)
##ColumnVariables[weight] = Significance of the expression changes by the perturbation (B-statistics)
#-----------------------------------------------
# this file is a dump of FANTOM4 EdgeExpressDB  
# with the following SQL                        
#-----------------------------------------------
# select
#   feature1_id
# , feature2_id
# , weight
# from
#   edge
# , edge_source
# where edge.edge_source_id = edge_source.edge_source_id
#   and edge_source.name = "siRNA_perturbation"
# ;
# 
=== edge2hop.Entrez_TFmatrix_L2_may08.tbl.txt.gz
##ColumnVariables[feature1_id] = (internal) feature_id of regulator (transcription factor)
##ColumnVariables[feature2_id] = (internal) feature_id of its target
##ColumnVariables[weight1] = percent identity between the DNA binding domains of this entrez gene and the DNA binding domains of TFs known to bind to the motif
##ColumnVariables[weight2] = Z-value of the correlation between the expression profile of the promoter and the activity profile of the matrix. 
#-----------------------------------------------
# this file is a dump of FANTOM4 EdgeExpressDB  
# with the following SQL                        
#-----------------------------------------------
# select
#   edge1.feature1_id
# , edge2.feature2_id
# , edge1.weight
# , edge2.weight
# from
#   edge edge1
# , edge_source edge_source1
# , edge edge2
# , edge_source edge_source2
# where edge1.edge_source_id = edge_source1.edge_source_id
#   and edge_source1.name = "Entrez_TFmatrix_may08"
#   and edge1.feature2_id = edge2.feature1_id
#   and edge2.edge_source_id = edge_source2.edge_source_id
#   and edge_source2.name = "TFmatrix_L2_may08"
# ;
# 
# 
=== feature.CAGE_L1_promoter.tbl.txt.gz
##ColumnVariables[feature_id] = (internal) feature_id of the transcription starting site (or level1 promoter)
##ColumnVariables[primary_name] = name of the transcription starting site
#-----------------------------------------------
# this file is a dump of FANTOM4 EdgeExpressDB  
# with the following SQL                        
#-----------------------------------------------
# 
# select
#   feature.feature_id
# , primary_name
# 
# from
#   feature
# , feature_source
# 
# where feature_source.name = "CAGE_L1_promoter"
#   and feature_source.feature_source_id = feature.feature_source_id
# ;
# 
# 
# 
=== feature.CAGE_L2_promoter.tbl.txt.gz
##ColumnVariables[feature_id] = (internal) feature_id of the prmoter (or level2 promoter)
##ColumnVariables[primary_name] = name of the promoter
#-----------------------------------------------
# this file is a dump of FANTOM4 EdgeExpressDB  
# with the following SQL                        
#-----------------------------------------------
# 
# select
#   feature.feature_id
# , primary_name
# 
# from
#   feature
# , feature_source
# 
# where feature_source.name = "CAGE_L2_promoter_april2008"
#   and feature_source.feature_source_id = feature.feature_source_id
# ;
# 
# 
# 
=== feature.CAGE_L3_promoter.tbl.txt.gz
##ColumnVariables[feature_id] = (internal) feature_id of the prmoter region (or level3 promoter)
##ColumnVariables[primary_name] = name of the promoter region
#-----------------------------------------------
# this file is a dump of FANTOM4 EdgeExpressDB  
# with the following SQL                        
#-----------------------------------------------
# 
# select
#   feature.feature_id
# , primary_name
# 
# from
#   feature
# , feature_source
# 
# where feature_source.name = "CAGE_L3_promoter_april2008"
#   and feature_source.feature_source_id = feature.feature_source_id
# ;
# 
# 
# 
=== feature.entrez_gene.tbl.txt.gz
##ColumnVariables[feature_id] = (internal) feature_id of the entrez gene
##ColumnVariables[primary_name] = gene symbol
##ColumnVariables[sym_value] = entrez gene id
#-----------------------------------------------
# this file is a dump of FANTOM4 EdgeExpressDB  
# with the following SQL                        
#-----------------------------------------------
# 
# select
#   feature.feature_id
# , primary_name
# , sym_value
# 
# from
#   feature
# , feature_2_symbol
# , symbol
# , feature_source
# 
# where feature.feature_id = feature_2_symbol.feature_id
#   and feature_2_symbol.symbol_id = symbol.symbol_id
#   and symbol.sym_type = "EntrezID" 
#   and feature_source.name = "Entrez_gene"
#   and feature_source.feature_source_id = feature.feature_source_id
# ;
# 
# 
# 
=== feature.miRBase_mature.tbl.txt.gz
##ColumnVariables[feature_id] = (internal) feature_id of the mature miRNA
##ColumnVariables[primary_name] = name of the mature miRNA (in miRbase)
##ColumnVariables[sym_value] = accession of the mature miRNA (in miRbase)
#-----------------------------------------------
# this file is a dump of FANTOM4 EdgeExpressDB  
# with the following SQL                        
#-----------------------------------------------
# 
# select
#   feature.feature_id
# , primary_name
# , sym_value
# 
# from
#   feature
# , feature_2_symbol
# , symbol
# , feature_source
# 
# where feature_source.name = "miRBase_mature"
#   and feature_source.feature_source_id = feature.feature_source_id
#   and feature.feature_id = feature_2_symbol.feature_id
#   and feature_2_symbol.symbol_id = symbol.symbol_id
#   and symbol.sym_type = "miRBaseACC"
# ;
# 
# 
# 
=== feature.miRBase_pre.tbl.txt.gz
##ColumnVariables[feature_id] = (internal) feature_id of the mature miRNA
##ColumnVariables[primary_name] = name of the miRNA precursor (in miRbase)
##ColumnVariables[sym_value] = accession of the miRNA precursor (in miRbase)
#-----------------------------------------------
# this file is a dump of FANTOM4 EdgeExpressDB  
# with the following SQL                        
#-----------------------------------------------
# 
# select
#   feature.feature_id
# , primary_name
# , sym_value
# 
# from
#   feature
# , feature_2_symbol
# , symbol
# , feature_source
# 
# where feature_source.name = "miRBase_pre"
#   and feature_source.feature_source_id = feature.feature_source_id
#   and feature.feature_id = feature_2_symbol.feature_id
#   and feature_2_symbol.symbol_id = symbol.symbol_id
#   and symbol.sym_type = "miRBaseACC"
# ;
# 
# 
#-----------------------------------------------