Dahlquist:MAPP Archive

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This page is used to keep track of GenMAPP MAPPs being built by the Dahlquist Lab for eventual submission to the MAPP Archive at GenMAPP.org.

Contents

Escherichia coli K12 MAPPs

Metabolic Pathway MAPPs

These MAPPs are based on the pathways curated by EcoCyc.

Karp, P.D., Keseler, I.M., Shearer, A., Latendresse, M., Krummenacker, M., Paley, S.M., Paulsen, I., Collado-Vides, J., Gama-Castro, S., Peralta-Gil, M., Santos-Zavaleta, A., Penaloza-Spinola, M.I., Bonavides-Martinez, C., and Ingraham, J., "Multidimensional annotation of the Escherichia coli K-12 genome" Nucleic Acids Research 35:7577-7590 2007.

This list is based on the EcoCyc Pathway List as of 2008-09-08.

Chad: Will you please note on the list which are the 104 MAPPs that we submitted to GenMAPP.org? Also, from now on, instead of just using "Ec_" as the prefix for all the filenames, change it to "Ec-K12_". Thanks! Kam D. Dahlquist 21:40, 22 October 2008 (EDT)


Pathways

  • Biosynthesis
  • Amines and Polyamines Biosynthesis
  • Betaine Biosynthesis
  • glycine betaine biosynthesis I (Gram-negative bacteria)(done)
  • Putrescine Biosynthesis
  • putrescine biosynthesis I (done)
  • putrescine biosynthesis III (done)
  • UDP-N-acetyl-D-glucosamine Biosynthesis
  • UDP-N-acetyl-D-glucosamine biosynthesis I (done)
  • aminopropylcadaverine biosynthesis
  • arginine degradation III (arginine decarboxylase/agmatinase pathway
  • spermidine biosynthesis (done)
  • superpathway of arginine and polyamine biosynthesis (done)
  • superpathway of polyamine biosynthesis I
  • Amino acids Biosynthesis
  • Individual Amino Acids Biosynthesis
  • β Alanine Biosynthesis
  • β-alanine biosynthesis (done)
  • Alanine Biosynthesis
  • alanine biosynthesis I (done)
  • alanine biosynthesis II (done)
  • alanine biosynthesis III (done)
  • superpathway of alanine biosynthesis
  • Arginine Biosynthesis
  • arginine biosynthesis I
  • Asparagine Biosynthesis
  • asparagine biosynthesis I
  • asparagine biosynthesis III (done)
  • superpathway of asparagine biosynthesis
  • Aspartate Biosynthesis
  • aspartate biosynthesis (done)
  • glutamate degradation II (done)
  • Cysteine Biosynthesis
  • cysteine biosynthesis I (done)
  • Glutamate Biosynthesis
  • glutamate biosynthesis I (done)
  • glutamate biosynthesis III (done)
  • Glutamine Biosynthesis
  • glutamine biosynthesis I (done)
  • Glycine Biosynthesis
  • glycine biosynthesis I (done)
  • superpathway of threonine metabolism
  • Histidine Biosynthesis
  • histidine biosynthesis I (done)
  • Isoleucine Biosynthesis
  • isoleucine biosynthesis from threonine (done)
  • Leucine Biosynthesis
  • leucine biosynthesis (done)
  • Lysine Biosynthesis
  • lysine biosynthesis I (done)
  • Methionine Biosynthesis
  • homoserine and methionine biosynthesis (done)
  • methionine and methyl-donor-molecule biosynthesis (done)
  • methionine biosynthesis I (done)
  • Other Amino Acid Biosynthesis
  • homoserine biosynthesis (done)
  • ornithine biosynthesis (done)
  • Phenylalanine Biosynthesis (done)
  • phenylalanine biosynthesis I
  • Proline Biosynthesis
  • proline biosynthesis I (done)
  • Selenocysteine Biosynthesis
  • selenocysteine biosynthesis (done)
  • Serine Biosynthesis
  • serine biosynthesis (done)
  • Threonine Biosynthesis
  • threonine biosynthesis(done)
  • threonine biosynthesis from homoserine (done)
  • Tryptophan Biosynthesis
  • tryptophan biosynthesis (done)
  • Tyrosine Biosynthesis
  • tyrosine biosynthesis I (done)
  • Valine Biosynthesis
  • valine biosynthesis (done)
  • superpathway of biosynthesis of aspartate and asparagine; interconversion of aspartate and asparagine.
  • superpathway of leucine, valine, and isoleucine biosynthesis
  • superpathway of lysine, threonine, methionine, and S-adenosyl-L-methionine biosynthesis
  • superpathway of phenylalanine, tyrosine, and tryptophan biosynthesis
  • superpathway of serine and glycine biosynthesis
  • Aminoacyl-tRNA Charging
  • tRNA charging pathway (done)
  • Aromatic Compounds Biosynthesis
  • Chorismate Biosynthesis
  • chorismate biosynthesis (done)
  • 2,3-dihydroxybenzoate biosynthesis
  • Carbohydrates Biosynthesis
  • Polysaccharides Biosynthesis
  • Glucogen and starch biosynthesis
  • glycogen biosynthesis I (from ADP-D-Glucose)(done)
  • CMP-KDO biosynthesis I (done)
  • Sugars Biosynthesis
  • Sugar Nucleotides Biosynthesis
  • Rhamnose Biosynthesis
  • dTDP-L-rhamnose biosynthesis I (done)
  • ADP-L-glycero-β-D-manno-heptose biosynthesis (done)
  • CMP-KDO biosynthesis I
  • UDP-galactose biosynthesis (salvage pathway from galactose using UDP-glucose)(done)
  • Trehalose biosynthesis
  • trehalose biosynthesis I (done)
  • gluconeogenesis (done)
  • glycogen degradation I
  • Cell structures Biosynthesis
  • O-antigen Biosynthesis
  • dTDP-L-rhamnose biosynthesis I
  • O-antigen biosynthesis (done)
  • UDP-N-acetyl-D-glucosamine biosynthesis I
  • Peptidoglycan Biosynthesis (done)
  • peptidoglycan biosynthesis I
  • colanic acid building blocks biosynthesis (done)
  • enterobacterial common antigen biosynthesis (done)
  • GDP-mannose metabolism (done)
  • KDO transfer to lipid IVA
  • lipid-A-precursor biosynthesis (done)
  • superpathway of KDO2-lipid A biosynthesis
  • Cofactors, Prosthetic Groups, Electron Carriers Biosynthesis
  • Coenzyme A Biosynthesis
  • 2'-(5-phosphoribosyl)-3'-dephospho-CoA Biosynthesis
  • biosynthesis of 2'-(5-triphosphoribosyl)-3'-dephospho-CoA (done)
  • Coenzyme A biosynthesis (done)
  • superpathway of pantothenate and coenzyme A biosynthesis
  • Lipoate Biosynthesis
  • lipoate biosynthesis and incorporation I (done)
  • lipoate biosynthesis and incorporation II (done)
  • lipoate salvage and modification (done)
  • NAD Metabolism
  • NAD Biosynthesis
  • NAD biosynthesis I (from aspartate)(done)
  • NAD salvage pathway I
  • NAD phosphorylation and dephosphorylation (done)
  • Polyprenyl Biosynthesis
  • trans,trans-farnesyl diphosphate biosynthesis
  • methylerythritol phosphate pathway (done)
  • octaprenyl diphosphate biosynthesis
  • polyisoprenoid biosynthesis (E. coli)(done)
  • undecaprenyl diphosphate biosynthesis
  • Porphyrin Compounds Biosynthesis
  • Heme Biosynthesis
  • heme biosynthesis from uroporphyrinogen II
  • siroheme biosynthesis (done)
  • Quinone Biosynthesis
  • 1,4-dihydroxy-2-naphthoate biosynthesis
  • 1,4-dihydroxy-2-naphthoate biosynthesis I
  • Demethylmenaquinone Biosynthesis
  • demethylmenaquinone-8 biosynthesis
  • Menaquinone Biosynthesis
  • menaquinone biosynthesis (done)
  • superpathway of menaquinone-8 biosynthesis
  • Ubiquinone Biosynthesis
  • ubiquinone-8 biosynthesis (done)
  • Reductants
  • glutathione biosynthesis (done)
  • glutathione redox reactions II (done)
  • thioredoxin pathway (done)
  • Tetrapyrrole Biosynthesis
  • tetrapyrrole biosynthesis I (done)
  • Vitamins
  • Biotin
  • biotin biosynthesis I (done)
  • Cobalamin Biosynthesis
  • Adenosylcobalamin Biosynthesis'
  • adenosylcobalamin salvage from cobinamide and cobalamin
  • aminopropanol biosynthesis
  • Folate Biosynthesis
  • folate polyglutamylation I (done)
  • formylTHF biosynthesis I (done)
  • tetrahydrofolate biosynthesis I (done)
  • Pantothenate Biosynthesis
  • pantothenate biosynthesis I (done)
  • Vitamin B6 Biosynthesis
  • pyridoxal 5'-phosphate biosynthesis (done)
  • pyridoxal 5'-phosphate salvage pathway (done)
  • superpathway of pyridoxal 5'-phosphate biosynthesis and salvage (done)
  • coenzyme A biosynthesis
  • flavin biosynthesis (done)
  • superpathway of pantothenate and coenzyme A biosynthesis (done)
  • thiamine biosynthesis (done)
  • S-adenosylmethionine biosynthesis
  • Fatty Acids and Lipids Biosynthesis
  • Fatty Acid Biosynthesis
  • Unusual Fatty Acid Biosynthesis
  • Cyclopropane Fatty Acids Biosynthesis
  • cyclopropane fatty acid (CFA) biosynthesis (done)
  • fatty acid elongation -- unsaturated (done)
  • fatty acid biosynthesis - initial steps I (done)
  • fatty acid elongation -- saturated (done)
  • superpathway of fatty acid biosynthesis (done)
  • Phospholipid-Biosynthesis
  • Cardiolipin Biosynthesis
  • cardiolipin biosynthesis I
  • CDP-diacylglycerol biosynthesis I
  • CDP-diacylglycerol biosynthesis II
  • phosphatidyl-ethanolamine biosynthesis
  • phospholipid biosynthesis I (done)
  • biotin-carboxyl carrier protein (done)
  • KDO transfer to lipid IVA (done)
  • KDO2-lipid A biosynthesis I (done)
  • Lipid A-core biosynthesis (done)
  • lipid-A-precursor biosynthesis
  • superpathway of KDO2-lipid A biosynthesis
  • superpathway of lipopolysaccharide biosynthesis
  • Metabolic Regulators Biosynthesis
  • ppGpp biosynthesis (done)
  • Nucleosides and Nucleotides Biosynthesis
  • Purine Nucleotide Biosynthesis
  • Purine Nucleotide de novo Biosynthesis
  • purine nucleotides de novo biosynthesis I (done)
  • Purine Nucleotide Salvage
  • salvage pathways of adenine, hypoxanthine, and their nucleosides
  • salvage pathways of guanine, xanthine, and their nucleosides (done)
  • Pyrimidine Nucleotide Biosynthesis
  • de novo biosynthesis of pyrimidine deoxyribonucleotides
  • de novo biosynthesis of uridine-5'-monophosphate
  • de novo biosynthesis of pyrimidine ribonucleotides (done)
  • pyrimidine ribonucleotides interconversion
  • salvage pathways of pyrimidine deoxyribonucleotides (done)
  • salvage pathways of pyrimidine ribonucleotides
  • Other Biosynthesis
  • FRPP Biosynthesis
  • PRPP biosynthesis I (done)
  • PRPP biosynthesis II (done)
  • Siderophore Biosynthesis
  • enterobactin biosynthesis (done)
  • Degradation/Utilization/Assimilation
  • Alcohols Degradation
  • Ethanol Degradation
  • ethanol degradation (done)
  • Glycerol Degradation
  • glycerol degradation I (done)
  • glycerol degradation II (done)
  • ethylene glycol degradation (done)
  • superpathway of glycol metabolism and degradation
  • Aldehyde Degradation
  • Lactaldehyde Degradation
  • L-lactaldehyde degradation (aerobic)
  • L-lactaldehyde degradation (anaerobic)
  • methylglyoxal degradation I
  • methylglyoxal degradation II
  • methylglyoxal degradation III
  • methylglyoxal degradation IV
  • superpathway of methylglyoxal degradation
  • Amines and Polyamines Degradation
  • 4-Aminobutyrate Degradation
  • 4-aminobutyrate degradation I (done)
  • Allantoin Degradation
  • allantoin degradation IV (anaerobic)
  • allantoin degradation to ureidoglycolate II (ammonia producing)(done)
  • Carnitine Degradation
  • carnitine degradation I (done)
  • Putrescine Degradation
  • putrescine degradation I (done)
  • putrescine degradation II (done)
  • N-acetylglucosamine degradation (done)
  • N-acetylneuraminate and N-acetylmannosamine degradation
  • phenylethylamine degradation (done)
  • superpathway of N-acetylglucosamine, N-acetylmannosamine and N-::*acetylneuraminate degradation (done)
  • superpathway of ornithine degradation
  • Amino Acids Degradation
  • Alanine Degradation
  • alanine degradation I (done)
  • Arginine Degradation
  • arginine degradation II (AST pathway)(done)
  • arginine degradation III (arginine decarboxylase/agmatinase pathway)(done)
  • superpathway of arginine and ornithine degradation (done)
  • superpathway of arginine, putrescine, and 4-aminobutyrate degradation (done)
  • Aspartate Degradation
  • aspartate biosynthesis
  • Cysteine Degradation
  • L-cysteine degradation II (done)
  • Glutamate Degradation
  • glutamate degradation II
  • Glutamine Degradation
  • glutamine degradation I
  • Glycine Degradation (done)
  • glycine cleavage complex (done)
  • Lysine Degradation
  • lysine degradation I (done)
  • Miscellaneous Amino Acids Degradation
  • Taurine Degradation
  • taurine degradation IV
  • Proline Degradation
  • proline degradation I (done)
  • Serine Degradation
  • L-serine degradation (done)
  • Threonine Degradation
  • superpathway of threonine metabolism
  • threonine degradation I (done)
  • threonine degradation II
  • threonine degradation III (to methylglyoxal)
  • threonine degradation IV
  • Tryptophan Degradation
  • tryptophan degradation II (via pyruvate)(done)
  • 2-ketoglutarate dehydrogenase complex
  • Aromatic Compounds Degradation
  • Phenolic Compounds Degradation
  • Phenylacetate Degradation
  • phenylacetate degradation I (done)
  • 3-phenylpropionate and 3-(3-hydroxyphenyl)propionate degradation to 2-oxopent-4-enoate (done)
  • phenylethylamine degradation
  • 3-phenylpropionate and 3-(3-hydroxyphenyl)propionate degradation (done)
  • C1 Compounds Utilization and Assimilation
  • Formaldehyde Oxidation
  • formaldehyde oxidation II (glutathione-dependent)(done)
  • Carbohydrates Degradation
  • Polysaccharides Degradation
  • Glycogen Degradation
  • glycogen degradation I
  • Sugars Degradation
  • D-arabinose Degradation
  • D-arabinose degradation I (done)
  • L-arabinose Degradation
  • L-arabinose degradation I (done)
  • Lactose Degradation
  • lactose degradation III (done)
  • Trehalose Degradation
  • trehalose degradation I (low osmolarity)(done)
  • trehalose degradation II (trehalase)(done)
  • Xylose Degradation' (done)
  • xylose degradation I
  • 2-O-α-mannosyl-D-glycerate degradation
  • N-acetylneuraminate and N-acetylmannosamine degradation
  • D-allose degradation (done)
  • D-mannose degradation (done)
  • fructose degradation
  • fucose degradation (done)
  • glucose and glucose-1-phosphate degradation (done)
  • L-lyxose degradation (done)
  • melibiose degradation
  • rhamnose degradation (done)
  • ribose degradation (done)
  • UDP-galactose biosynthesis (salvage pathway from galactose using UDP-glucose)
  • 2-oxopentenoate degradation (done)
  • chitobiose degradation
  • Carboxylates Degradation
  • Acetate Formation
  • acetate formation from acetyl-CoA I
  • Propionate Degradation
  • 2-Methylcitrate Cycle (done)
  • 2-methylcitrate cycle I
  • methylmalonyl pathway (done)
  • Succinate Degradation
  • conversion of succinate to propionate (done)
  • acetate conversion to acetyl-CoA
  • acetyl-CoA biosynthesis (from pyruvate)
  • glycolate and glyoxylate degradation I (done)
  • glycolate and glyoxylate degradation II (done)
  • L-ascorbate degradation, anaerobic (done)
  • superpathway of acetate utilization and formation
  • Degradation/Utilization/Assimilation - Other
  • removal of superoxide radicals (done)
  • Fatty Acid and Lipids Degradation
  • Fatty Acids Degradation
  • fatty acid β-oxidation I (done)
  • acetoacetate degradation (to acetyl CoA)(done)
  • Inorganic Nutrients Metabolism
  • Nitrogen Compounds Metabolism
  • cyanate degradation (done)
  • superpathway of glutamate biosynthesis
  • Sulfur Compounds Metabolism
  • Sulfate Reduction
  • sulfate reduction I (assimilatory)
  • two-component alkanesulfonate monooxygenase (done)
  • Nucleosides and Nucleotides Degradation and Recycling
  • degradation of purine ribonucleosides
  • degradation of pyrimidine deoxyribonucleosides
  • degradation of pyrimidine ribonucleosides
  • purine deoxyribonucleosides degradation
  • Secondary Metabolites Degradation
  • Plant Secondary Metabolites Degradation
  • Sugar Derivatives Degradation
  • Sugar Acids Degradation
  • β-D-glucuronide and D-glucuronate degradation (done)
  • D-glucarate degradation (done)
  • D-galactarate degradation (done)
  • D-galactonate degradation
  • D-galacturonate degradation (done)
  • ketogluconate metabolism (done)
  • L-galactonate degradation
  • L-idonate degradation (done)
  • Sugar Alcohols Degradation
  • galactitol degradation
  • mannitol degradation I (done)
  • sorbitol degradation (done)
  • superpathway of hexitol degradation (done)
  • 1,6-anhydro-N-acetylmuramic acid recycling (done)
  • N-acetylglucosamine degradation
  • fructoselysine and psicoselysine degradation (done)
  • Detoxification
  • Acid Resistance
  • arginine dependent acid resistance
  • glutamate dependent acid resistance
  • Methylglyoxal Detoxification
  • methylglyoxal degradation I
  • methylglyoxal degradation II
  • methylglyoxal degradation III
  • methylglyoxal degradation IV
  • Generation of precursor metabolites and energy
  • Fermentation
  • mixed acid fermentation (done)
  • Glycolysis
  • glycolysis I (done)
  • superpathway of glycolysis, pyruvate dehydrogenase, TCA, and glyoxylate bypass
  • Pentose Phosphate Pathways
  • pentose phosphate pathway
  • pentose phosphate pathway (non-oxidative branch)(done)
  • pentose phosphate pathway (oxidative branch)(done)
  • Respiration
  • Aerobic Respiration
  • aerobic electron transfer (done)
  • aerobic respiration -- electron donors reaction list (done)
  • Anaerobic Respiration
  • electron transfer (anaerobic) (done)
  • respiration (anaerobic)(done)
  • respiration (anaerobic)-- electron acceptors reaction list
  • respiration (anaerobic)-- electron donors reaction list (done)
  • 2-ketoglutarate dehydrogenase complex
  • TCA cycle (done)
  • glyoxylate cycle (done)
  • pyruvate oxidation pathway (done)
  • superpathway of glycolysis, pyruvate dehydrogenase, TCA, and glyoxylate bypass
  • superpathway of glyoxylate bypass and TCA
  • TCA cycle
  • acetyl-CoA biosynthesis (from pyruvate)(done)
  • Entner-Doudoroff pathway I (done)
  • superpathway of glycolysis and Entner-Doudoroff
  • Signal transduction pathways
  • ArcAB Two-Component Signal Transduction System (done)
  • AtoSC Two-Component Signal Transduction System (done)
  • BaeSR Two-Component Signal Transduction System (done)
  • BarA-UvrY Two-Component Signal Transduction System (done)
  • BasSR Two-Component Signal Transduction System (done)
  • Chemotactic Signal Transduction System (done)
  • CpxAR Two-Component Signal Transduction System (done)
  • CreCB Two-Component Signal Transduction System (done)
  • EvgSA Two-Component Signal Transduction System (done)
  • KdpDE Two-Component Signal Transduction System (done)
  • NarQ Nitrate/Nitrite-Dependent Two-Component Regulatory System (done)
  • NarX Nitrate/Nitrite-Dependent Two-Component Regulatory System (done)
  • Nitrogen Regulation Two-Component System
  • Osmoregulatory Two-Component Signal Transduction System
  • PhoQP Two-Component Signal Transduction System (done)
  • PhoRB Two-Component Signal Transduction System (done)
  • RcsCB Two-Component Signal Transduction System (done)
  • RstBA Two-Component Signal Transduction System (done)
  • TorSR Two-Component Signal Transduction System (done)
  • UhpBA Two-Component Signal Transduction System (done)
  • ZraSR Two-Component Signal Transduction System (done)
  • Superpathways
  • 3-phenylpropionate and 3-(3-hydroxyphenyl)propionate degradation
  • arginine biosynthesis I
  • aspartate superpathway (done)
  • de novo biosynthesis of pyrimidine ribonucleotides
  • enterobactin biosynthesis
  • homoserine and methionine biosynthesis
  • methionine and methyl-donor-molecule biosynthesis
  • methylglyoxal degradation IV
  • O-antigen biosynthesis
  • pentose phosphate pathway
  • phospholipid biosynthesis I
  • polyisoprenoid biosynthesis (E. coli)
  • pyruvate oxidation pathway
  • superpathway of N-acetylglucosamine, N-acetylmannosamine and N-:*acetylneuraminate degradation
  • superpathway of acetate utilization and formation
  • superpathway of alanine biosynthesis (done)
  • superpathway of arginine and ornithine degradation
  • superpathway of arginine and polyamine biosynthesis
  • superpathway of arginine, putrescine, and 4-aminobutyrate degradation
  • superpathway of asparagine biosynthesis
  • superpathway of biosynthesis of aspartate and asparagine; interconversion of aspartate and asparagine.
  • superpathway of chorismate
  • superpathway of D-glucarate and D-galactarate degradation (done)
  • superpathway of fatty acid biosynthesis
  • superpathway of fucose and rhamnose degradation
  • superpathway of gluconate degradation
  • superpathway of glutamate biosynthesis
  • superpathway of glycol metabolism and degradation
  • superpathway of glycolysis and Entner-Doudoroff
  • superpathway of glycolysis, pyruvate dehydrogenase, TCA, and glyoxylate bypass
  • superpathway of glyoxylate bypass and TCA
  • superpathway of hexitol degradation
  • superpathway of hexuronide and hexuronate degradation
  • superpathway of histidine, purine, and pyrimidine biosynthesis
  • superpathway of KDO2-lipid A biosynthesis
  • superpathway of leucine, valine, and isoleucine biosynthesis
  • superpathway of lipopolysaccharide biosynthesis
  • superpathway of lysine, threonine, methionine, and S-adenosyl-L-methionine biosynthesis
  • superpathway of menaquinone-8 biosynthesis
  • superpathway of methylglyoxal degradation
  • superpathway of ornithine degradation
  • superpathway of pantothenate and coenzyme A biosynthesis
  • superpathway of phenylalanine, tyrosine, and tryptophan biosynthesis
  • superpathway of polyamine biosynthesis I (done)
  • superpathway of pyridoxal 5'-phosphate biosynthesis and salvage
  • superpathway of serine and glycine biosynthesis
  • superpathway of sulfate assimilation and cysteine biosynthesis (done)
  • superpathway of threonine metabolism
  • threonine biosynthesis

MAPPs Not Present in List Above

The following are the file names as they appear on our computer

  • methylglyoxal pathway
  • biosynthANandinterconv
  • polyamine biosynthesis I
  • pyridine nucleotide cycling
  • biosynthesis of proto- and siroheme
  • Ribose_Deoxyribose Phosphate Metabolism
  • degradation of short-chain fatty acids
  • superpathwayLVIsynth
  • glyoxylate degradation
  • fructoselysine degradation
  • superpathway ox + non ox pentose phos path
  • sulfate assimilation
  • ammonia assimilation cycle
  • KTMS-adenosyl-Lmet synthesis
  • Galactonate degradation
  • Galactitol degradation
  • FYW biosynthesis
  • acetate utilization
  • SGsynthesis
  • Glutamine degradation IV
  • lipoate biosynthesis and modification
  • (deoxy)ribose phosphate degradatoin
  • sulfate assimilation
  • glutathione redoxin

For MAPP Information Field

  • Make sure the Title of the MAPP matches the name of the EcoCyc pathway.
  • Add your name to the Author field if you have checked the pathway.
  • The Maintained by field should read "Kam Dahlquist"
  • The E-mail should read "kdahlquist@lmu.edu"
  • The Last modified field should read the current date
  • The Remarks field should read "Based on www.EcoCyc.org"
  • The Notes field should have the URL to the exact pathway page used:
e.g., http://biocyc.org/ECOLI/NEW-IMAGE?type=PATHWAY&object=BETSYN-PWY&detail-level=4&detail-level=3
  • In addition, create a label and locate it beneath the MAPP Information area that gives the reference as follows:
Karp et al. (2007) Nucl Acids Res 35:7577-7590.
  • Check that the MAPP Information area does not interfere with the pathway diagram.
  • Also check to see that the Legend does not interfere.

Saccharomyces cerevisiae MAPPs

Pathway MAPPs

  • zinc ion homeostasis — Liz and Olivia have completed, need to double-check it
  • ribosome biogenesis — Kevin has completed, need to fix layout to uncover gene value
  • lipid and phospholipid synthesis - Felicia did phospholipid synthesis, can now make larger MAPP based on metabolic reconstruction paper Nookaew et al. (2008)
  • oxidative stress
  • osmotic stress (hypo- and hyper-)
  • heat shock
  • high salt

Gene List MAPPs

  • cold shock responsive genes - Kevin has a version of this?
  • general environmental response genes - based off of Gasch et al. (2000) and Causton et al. (2001)

Transcription Factors

See Yeast Transcription Factors Page

  • Need to make final versions of MAPPs for Lee et al. (2002) data (Done)
    • 106 regulators
    • Autoregulatory
    • Single Input Motifs
    • Feed Forward Loops
    • Regulatory Chains
    • Multi-Input Motifs
  • Need to make final versions of MAPPs for Harbison et al. (2004) data. (Done)
    • 203 regulators
    • choose p value cut off and make MAPPs, see if Kevin has this already
  • Need to make final versions of MAPPs for Tan et al. (2008) data. (Done)
    • Looks like Kevin already has MAPP Builder files, confirm with him what they are.
    • They are Hu, Workman, TVSM and YEASTRACT (See Yeast Transcription Factors Page)
  • MacIsaac et al. (2006) TFs and Targets
  • A consolidated MAPP for Cin5p targets from Lee, Harbison, and Tan has been made by Kevin. (redundant, target appears multiple times if present in more than one paper.)
  • For all of these need to standardize file names, MAPP Information, layout on MAPP.
    • Total Cin5p Target MAPP has been created, saved as Cin5Targets_Total_Compiled.mapp on Desktop in folder "Database and Reference TF Search". Includes data from Lee, Harbison, Tan, Workman, Hu, TVSM and YEASTRACT.

WikiPathways

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