Add ppGpp regulation of tRNA synthetases (#1208)

Author: tahorst

reconstruction/ecoli/dataclasses/process/transcription.py

@@ -143,9 +143,13 @@ def read_value(d, k):
 			fc_dir = rna_fold_changes.get(rna, 0)
 
 			# Ignore inconsistent regulatory directions
-			if reg_dir == 0 or reg_dir * fc_dir < 0:
+			if reg_dir == 0:
 				continue
 
+			# Use default value if annotated direction does not match data direction
+			if reg_dir * fc_dir < 0:
+				fc_dir = 0
+
 			regulated_genes.append(rna)
 			regulation_direction.append(np.sign(reg_dir))
 			fold_changes.append(fc_dir)

reconstruction/ecoli/flat/ppgpp_regulation_added.tsv

@@ -0,0 +1,18 @@
+"Gene"	"ppGpp"	"DksA-ppGpp"	"DksA"	"sigma70"	"sigmaS"	"sigma32"	"sigma54"	"sigma24"	"Curated Gene"	"_notes"
+"alaS"	-1								"alaS"	"tRNA synthetases are expected to be negatively regulated by ppGpp"
+"asnS"	-1								"asnS"	"tRNA synthetases are expected to be negatively regulated by ppGpp"
+"aspS"	-1								"aspS"	"tRNA synthetases are expected to be negatively regulated by ppGpp"
+"cysS"	-1								"cysS"	"tRNA synthetases are expected to be negatively regulated by ppGpp"
+"glnS"	-1								"glnS"	"tRNA synthetases are expected to be negatively regulated by ppGpp"
+"gltX"	-1								"gltX"	"tRNA synthetases are expected to be negatively regulated by ppGpp"
+"glyS"	-1								"glyS"	"tRNA synthetases are expected to be negatively regulated by ppGpp"
+"hisS"	-1								"hisS"	"tRNA synthetases are expected to be negatively regulated by ppGpp"
+"ileS"	-1								"ileS"	"tRNA synthetases are expected to be negatively regulated by ppGpp"
+"leuS"	-1								"leuS"	"tRNA synthetases are expected to be negatively regulated by ppGpp"
+"lysU"	-1								"lysU"	"tRNA synthetases are expected to be negatively regulated by ppGpp"
+"metG"	-1								"metG"	"tRNA synthetases are expected to be negatively regulated by ppGpp"
+"proS"	-1								"proS"	"tRNA synthetases are expected to be negatively regulated by ppGpp"
+"serS"	-1								"serS"	"tRNA synthetases are expected to be negatively regulated by ppGpp"
+"trpS"	-1								"trpS"	"tRNA synthetases are expected to be negatively regulated by ppGpp"
+"tyrS"	-1								"tyrS"	"tRNA synthetases are expected to be negatively regulated by ppGpp"
+"valS"	-1								"valS"	"tRNA synthetases are expected to be negatively regulated by ppGpp"

reconstruction/ecoli/knowledge_base_raw.py

@@ -54,6 +54,7 @@
 	"molecular_weight_keys.tsv",
 	"ppgpp_fc.tsv",
 	"ppgpp_regulation.tsv",
+	"ppgpp_regulation_added.tsv",
 	"ppgpp_regulation_removed.tsv",
 	"protein_half_lives_measured.tsv",
 	"protein_half_lives_n_end_rule.tsv",
@@ -139,6 +140,7 @@
 	'equilibrium_reactions': 'equilibrium_reactions_added',
 	'metabolic_reactions': 'metabolic_reactions_added',
 	'metabolites': 'metabolites_added',
+	'ppgpp_regulation': 'ppgpp_regulation_added',
 	'trna_charging_reactions': 'trna_charging_reactions_added',
 	}