1.
Header:
PLOS_Rank
Title:
Rank based on PLoS paper
Description:
Target priority based on PLoS paper (Hasan et al., 2006).
Values:
1-3924; 1 is best
Reference:
Date:
Nov 2007
2.
Header:
Gene
Title:
Rv Number
Description:
Rv Number for the H37Rv genome
Values:
Reference:
Date:
Nov 2007
3.
Header:
Name
Title:
Gene Name
Description:
Gene Name
Values:
Reference:
Date:
Nov 2007
4.
Header:
LipinskiDruggable
Title:
Druggability based on Lipinski's Rules
Description:
Target (or homolog) has been shown experimentally to bind small drug-like ligands (from Hasan data).
Values:
1/0, 0 also includes genes where no information is available
Reference:
Hopkins AL, Groom CR (2002) The druggable genome. Nat Rev Drug Discov 1: 727:730.
Date:
Nov 2007
5.
Header:
ECDruggable
Title:
Druggability based on Enzyme Classification
Description:
Whether any other member of the same EC family has been shown to bind small drug-like ligands (from Hasan data).
Values:
1/0, 0 includes hypothetical proteins where EC is not known
Reference:
Mulder NJ, Apweiler R, Attwood TK, Bairoch A, Bateman A, et al. (2005) InterPro, progress and status in 2005. Nucleic Acids Res 33: D201:205.
Date:
Nov 2007
6.
Header:
TRASH_in_vitro
Title:
In vitro essentiality (Sassetti and Rubin), thresholded
Description:
Whether gene disruption via transposon insertion inhibits growth in vitro (from Hasan data).
Values:
1,0,0.4: 1=hybridization ratio < 0.2, 0=hybridization ratio > 0.2, 0.4=hybridization ratio not measured
Reference:
Sassetti CM, Boyd DH, Rubin EJ (2003) Genes required for mycobacterial growth defined by high density mutagenesis. Mol Microbiol 48: 77:84.
Date:
Nov 2007
7.
Header:
DEADMAN_essential
Title:
In vitro essentiality (Bishai), thresholded
Description:
Statistical estimates of essentiality based on whether gene disruption inhibits growth in vitro (from Hasan data).
Values:
1,0,-1: 1=probability > 75%, 0=probability < 75%, -1=no information available regarding essentiality
Reference:
Lamichhnae G, Zignol M, Blades NJ, Geiman DE, Dougherty A, Grosset J, Broman KW , Bishai WR. (2003) A postgenomic method for predicting essential genes at subsaturation levels of mutagenesis: Application to Mycobacteriumtuberculosis. Proc Natl Acad Sci USA 100: 7213:7218.
Date:
Nov 2007
8.
Header:
isolate_deletion
Title:
Genes deleted in clinical isolates
Description:
Genes frequently observed to be deleted in clinical isolates; probably not essential (from Hasan data)
Values:
1/0
Reference:
Date:
Nov 2007
9.
Header:
UniqueProduct
Title:
Enzyme product is unique
Description:
Metabolic chokepoint - product not synthesized by other pathways (from Hasan data)
Values:
1/0
Reference:
Yeh I, Hanekamp T, Tsoka S, Karp PD, Altman RB (2004) Computational analysis of Plasmodium falciparum metabolism: Organizing genomic information to facilitate drug discovery. Genome Res 14: 917:924.
Date:
Nov 2007
10.
Header:
UniqueSubstrate
Title:
Enzyme substrate is unique
Description:
Metabolic chokepoint - substrate not utilized by other pathways (from Hasan data)
Values:
1/0
Reference:
Yeh I, Hanekamp T, Tsoka S, Karp PD, Altman RB (2004) Computational analysis of Plasmodium falciparum metabolism: Organizing genomic information to facilitate drug discovery. Genome Res 14: 917:924.
Date:
Nov 2007
11.
Header:
UniqueEC
Title:
Enzyme belongs to a unique Enzyme Class
Description:
Enzyme belongs to a unique Enzyme Class - possible metabolic chokepoint (from Hasan data).
Values:
1/0
Reference:
Yeh I, Hanekamp T, Tsoka S, Karp PD, Altman RB (2004) Computational analysis of Plasmodium falciparum metabolism: Organizing genomic information to facilitate drug discovery. Genome Res 14: 917:924.
Date:
Nov 2007
12.
Header:
pdb_structure
Title:
Is a PDB structure known?
Description:
Is a PDB structure known? (from Hasan data)
Values:
1/0
Reference:
Protein Data Bank: www.rcsb.org
Date:
Nov 2007
13.
Header:
smid_domain
Title:
Contains a small-molecule interaction domain
Description:
Contains a small-molecule interaction domain, based on orthologs in other genomes (from Hasan data).
Values:
1/0
Reference:
Alfarano C, Andrade CE, Anthony K, Bahroos N, Bajec M, et al. (2005) The Biomolecular Interaction Network Database and related tools 2005 update. Nucleic Acids Res 33: D418:D424.
Date:
Nov 2007
14.
Header:
PhysicalProperties
Title:
Desirable ranges for length, pI, and MW
Description:
Physical properties of protein are in desirable ranges for length, pI, and MW, based on Hasan et al. (2006).
Values:
1,0,-500: 1 means protein properties are in desirable ranges, -500 means data not available
Reference:
Terwilliger TC, Park MS, Waldo GS, Berendzen J, Hung LW, et al. (2003) The TB structural genomics consortium: A resource for Mycobacterium tuberculosis biology. Tuberculosis (Edinb) 83: 223:249.
Date:
Nov 2007
15.
Header:
Phylogeny
Title:
Sequence similarity to host proteins
Description:
Higher score if orthologs present in other Actinobacteria; lower score if orthologs present in human or gut flora (from hasan data).
Values:
continuous in range (0,1)
Reference:
Terwilliger TC, Park MS, Waldo GS, Berendzen J, Hung LW, et al. (2003) The TB structural genomics consortium: A resource for Mycobacterium tuberculosis biology. Tuberculosis (Edinb) 83: 223:249.
Date:
Nov 2007
16.
Header:
M0_ACT_48
Title:
Microarray data: activated macrophages, after 48 hours
Description:
Differential expression in activated macrophages after 48 hours. The microarray data was normalized to have a mean intensity of 0.0 and a variation of 1.0 (from Hasan data).
Values:
1/0/-0.5: 1= normalized microarray data > 0.7, -0.5=normalized microarray data < -0.1
Reference:
Schnappinger D, Ehrt S, Voskuil MI, Liu Y, Mangan JA, et al. (2003) Transcriptional Adaptation of Mycobacterium tuberculosis within macrophages: Insights into the phagosomal environment. J Exp Med 198: 693:704.
Date:
Nov 2007
17.
Header:
M0_ACT_OLIGO_24
Title:
Oligonucleotide arrays: activated macrophages, after 24 hours
Description:
Differential expression in activated macrophages after 24 hours measured using oligonucleotide arrays. The microarray data was normalized to have a mean intensity of 0.0 and a variation of 1.0 (from Hasan data)
Values:
1/0/-0.67: 1= normalized microarray data > 0.7, -0.67=normalized microarray data < -0.1
Reference:
Schnappinger D, Ehrt S, Voskuil MI, Liu Y, Mangan JA, et al. (2003) Transcriptional Adaptation of Mycobacterium tuberculosis within macrophages: Insights into the phagosomal environment. J Exp Med 198: 693:704.
Date:
Nov 2007
18.
Header:
M0_NAIVE_48
Title:
Microarray data: unactivated macrophages, after 48 hours
Description:
Differential expression in unactivated macrophages after 48 hours. The microarray data was normalized to have a mean intensity of 0.0 and a variation of 1.0 (from Hasan data).
Values:
1/0/-0.5: 1= normalized microarray data > 0.7, -0.5=normalized microarray data < -0.1
Reference:
Schnappinger D, Ehrt S, Voskuil MI, Liu Y, Mangan JA, et al. (2003) Transcriptional Adaptation of Mycobacterium tuberculosis within macrophages: Insights into the phagosomal environment. J Exp Med 198: 693:704.
Date:
Nov 2007
19.
Header:
M0_NAIVE_OLIGO
Title:
Oligonucleotide arrays: unactivated macrophages, after 24 hours
Description:
Differential expression in unactivated macrophages after 24 hours measured using oligonucleotide arrays. The microarray data was normalized to have a mean intensity of 0.0 and a variation of 1.0 (from Hasan data).
Values:
1/0/-0.5: 1= normalized microarray data > 0.7, -0.5=normalized microarray data < -0.1
Reference:
Schnappinger D, Ehrt S, Voskuil MI, Liu Y, Mangan JA, et al. (2003) Transcriptional Adaptation of Mycobacterium tuberculosis within macrophages: Insights into the phagosomal environment. J Exp Med 198: 693:704.
Date:
Nov 2007
20.
Header:
starvation_6
Title:
Microarray data: nutrient starvation after 6 hours
Description:
Differential expression of M.tb. in response to starvation conditions (transfer to phosphate buffer saline solution). The microarray data was normalized to have a mean intensity of 0.0 and a variation of 1.0 (from Hasan data).
Values:
1/0/-0.51: 1= normalized microarray data > 0.7, -0.51=normalized microarray data < -0.1
Reference:
Hampshire T, Soneji S, Bacon J, James BW, Hinds J, et al. (2004) Stationary phase gene expression of Mycobacterium tuberculosis following a progressive nutrient depletion: A model for persistent organisms? Tuberculosis (Edinb) 84: 228:238.
Date:
Nov 2007
21.
Header:
boshoff_starvation_6
Title:
Microarray data: nutrient starvation after 6 hours (Boshoff)
Description:
Differential expression of starved M.tb. were analysed to study the adaptation of M.tb. to nutrient starvation after 6 hours (transfer to phosphate buffer saline solution containing 0.05% of Tween 80). The microarray data was normalized to have a mean intensity of 0.0 and a variation of 1.0 (from Hasan data).
Values:
1/0/-0.51: 1= normalized microarray data > 0.7, -0.51=normalized microarray data < -0.1
Reference:
Boshoff HI, Myers TG, Copp BR, McNeil MR, Wilson MA, et al. (2004) The transcriptional responses of Mycobacterium tuberculosis to inhibitors of metabolism: Novel insights into drug mechanisms of action. J Biol Chem 279:40174:40184.
Date:
Nov 2007
22.
Header:
betts_starvation_96
Title:
Microarray data: nutrient starvation at 96 hours (Betts)
Description:
Differential expression of M.tb. in response to starvation conditions (transfer to phosphate buffer solution). The microarray data was normalized to have a mean intensity of 0.0 and a variation of 1.0 (from Hasan data).
Values:
1/0/-0.6: 1= normalized microarray data > 0.7, -0.6=normalized microarray data < -0.1
Reference:
Betts JC, Lukey PT, Robb LC, McAdam RA, Duncan K (2002) Evaluation of a nutrient starvation model of Mycobacterium tuberculosis persistence by gene and protein expression profiling. Mol Microbiol 43: 717:731.
Date:
Nov 2007
23.
Header:
nrp1_2
Title:
Microarray data: Nrp1
Description:
Differential expression in non-replicating persistance stage I (from Hasan data)
Values:
1,0: 1= normalized microarray data > 0.7
Reference:
Muttucumaru DG, Roberts G, Hinds J, Stabler RA, Parish T (2004) Gene expression profile of Mycobacterium tuberculosis in a non-replicating state. Tuberculosis (Edinb) 84: 239:246.
Date:
Nov 2007
24.
Header:
boshoff_nrp1_aerobic
Title:
Microarray data: Nrp1 Areobic (Boshoff)
Description:
Differential expression in non-replicating persistance stage I with oxygen levels at 1% saturation (from Hasan data)
Values:
1/0/-0.53 1= normalized microarray data > 0.7, -0.53= normalized microarray data < -0.1
Reference:
Boshoff HI, Myers TG, Copp BR, McNeil MR, Wilson MA, et al. (2004) The transcriptional responses of Mycobacterium tuberculosis to inhibitors of metabolism: Novel insights into drug mechanisms of action. J Biol Chem 279:40174:40184.
Date:
Nov 2007
25.
Header:
boshoff_nrp1_log_2
Title:
Boshoff Nrp1 Log
Description:
Differential expression in non-replicating persistance stage II (log phase growth) with oxygen levels below 0.06% (from Hasan data)
Values:
1/0/-0.5 1= normalized microarray data > 0.7, -0.5= normalized microarray data < -0.1
Reference:
Boshoff HI, Myers TG, Copp BR, McNeil MR, Wilson MA, et al. (2004) The transcriptional responses of Mycobacterium tuberculosis to inhibitors of metabolism: Novel insights into drug mechanisms of action. J Biol Chem 279:40174:40184.
Date:
Nov 2007
26.
Header:
hypoxia_1
Title:
Hypoxia
Description:
Differential regulation response to low oxygen conditions (hypoxic conditions) (from Hasan data)
Values:
1/0/-0.51 1= normalized microarray data > 0.7, -0.51= normalized microarray data < -0.1
Reference:
Sherman DR, Voskuil M, Schnappinger D, Liao R, Harrell MI, et al. (2001) Regulation of the Mycobacterium tuberculosis hypoxic differential regulation gene encoding alpha-crystallin. Proc Natl Acad Sci U S A 98: 7534:7539.
Date:
Nov 2007
27.
Header:
nrp2
Title:
Nrp2
Description:
Differential expression in non-replicating persistance stage II (log phase growth) (from Hasan data)
Values:
1/0/-0.51 1= normalized microarray data > 0.7, -0.51= normalized microarray data < -0.1
Reference:
Muttucumaru DG, Roberts G, Hinds J, Stabler RA, Parish T (2004) Gene expression profile of Mycobacterium tuberculosis in a non-replicating state. Tuberculosis (Edinb) 84: 239:246.
Date:
Nov 2007
28.
Header:
Boshoff_pH4_8
Title:
Boshoff ph4_8
Description:
Differential regulation in acidic conditions: pH 4.8 (from Hasan data)
Values:
1/0/-0.5 1= normalized microarray data > 0.7, -0.5= normalized microarray data < -0.1
Reference:
Boshoff HI, Myers TG, Copp BR, McNeil MR, Wilson MA, et al. (2004) The transcriptional responses of Mycobacterium tuberculosis to inhibitors of metabolism: Novel insights into drug mechanisms of action. J Biol Chem 279:40174:40184.
Date:
Nov 2007
29.
Header:
Boshoff_pH5_2
Title:
Boshoff ph5_2
Description:
Differential regulation in acidic conditions: pH 5.2 (from Hasan data)
Values:
1/0/-0.5 1= normalized microarray data > 0.7, -0.5= normalized microarray data < -0.1
Reference:
Boshoff HI, Myers TG, Copp BR, McNeil MR, Wilson MA, et al. (2004) The transcriptional responses of Mycobacterium tuberculosis to inhibitors of metabolism: Novel insights into drug mechanisms of action. J Biol Chem 279:40174:40184.
Date:
Nov 2007
30.
Header:
Boshoff_pH5_6
Title:
Boshoff ph5_6
Description:
Differential regulation in acidic conditions: pH 5.6 (from Hasan data)
Values:
1/0/-0.5 1= normalized microarray data > 0.7, -0.5= normalized microarray data < -0.1
Reference:
Boshoff HI, Myers TG, Copp BR, McNeil MR, Wilson MA, et al. (2004) The transcriptional responses of Mycobacterium tuberculosis to inhibitors of metabolism: Novel insights into drug mechanisms of action. J Biol Chem 279:40174:40184.
Date:
Nov 2007
31.
Header:
M_leprae
Title:
homolog in M. leprae
Description:
Whether a close homolog exists in M. leprae based on a BLAST search
Values:
1/0/-1: 1 meansE-value < 0.1; -1 means data not found
Reference:
Date:
Nov 2007
32.
Header:
C_glutamicum
Title:
homolog in C. glutamicum
Description:
Whether a close homolog exists in C. glutamicum based on a BLAST search
Values:
1/0/-1: 1 means E-value < 0.1; -1 means data not found
Reference:
Date:
Nov 2007
33.
Header:
M_E_coli
Title:
homolog in E. coli
Description:
Whether a close homolog exists in E. coli based on a BLAST search
Values:
1/0/-1: 1 means E-value < 0.1; -1 means data not found
Reference:
Date:
Nov 2007
34.
Header:
Human
Title:
homolog in Human
Description:
Whether a close homolog exists in Human based on a BLAST search
Values:
1/0/-1: 1 means E-value < 0.1; -1 means data not found
Reference:
Date:
Nov 2007
35.
Header:
D_109
Title:
Diamine#109
Description:
Shows the differential regulation of the gene in response to the drug
Values:
continuous, -1.3 to 1.8; negative values indicate down regulation and positive values indicate upregulation
Reference:
Personal Communication from H. Boshoff
Date:
Nov 2007
36.
Header:
D_111891
Title:
Pyridoacridine
Description:
Shows the differential regulation of the gene in response to the drug
Values:
continuous, -1.3 to 4.6; negative values indicate down regulation and positive values indicate upregulation
Reference:
Personal Communication from H. Boshoff
Date:
Nov 2007
37.
Header:
D_111895
Title:
Ascididemin
Description:
Shows the differential regulation of the gene in response to the drug
Values:
continuous, -2 to 3.5; negative values indicate down regulation and positive values indicate upregulation
Reference:
Personal Communication from H. Boshoff
Date:
Nov 2007
38.
Header:
D_121940
Title:
Pyridoacridine
Description:
Shows the differential regulation of the gene to the drug
Values:
continuous, -2.5 to 3.9; negative values indicate down regulation and positive values indicate upregulation
Reference:
Personal Communication from H. Boshoff
Date:
Nov 2007
39.
Header:
D_124196
Title:
Pyridoacridine
Description:
Shows the differential regulation of the gene in response to the drug
Values:
continuous, -1.8 to 3.3; negative values indicate down regulation and positive values indicate upregulation
Reference:
Personal Communication from H. Boshoff
Date:
Nov 2007
40.
Header:
D_241
Title:
Diamine#241
Description:
Shows the differential regulation of the gene in response to the drug
Values:
continuous, -1.7 to 1.9; negative values indicate down regulation and positive values indicate upregulation
Reference:
Personal Communication from H. Boshoff
Date:
Nov 2007
41.
Header:
D_59
Title:
Diamine#59
Description:
Shows the differential regulation of the gene in response to the drug
Values:
continuous, -3.14 to 3.4; negative values indicate down regulation and positive values indicate upregulation
Reference:
Personal Communication from H. Boshoff
Date:
Nov 2007
42.
Header:
5CL_PZA
Title:
Chloropyrazinamide
Description:
Shows the differential regulation of the gene in response to the drug
Values:
continuous, -3 to 3.6; negative values indicate down regulation and positive values indicate upregulation
Reference:
Personal Communication from H. Boshoff
Date:
Nov 2007
43.
Header:
ARP4
Title:
Antitubercular compound
Description:
Shows the differential regulation of the gene to the drug
Values:
continuous, -3.8 to 8; negative values indicate down regulation and positive values indicate upregulation
Reference:
Personal Communication from H. Boshoff
Date:
Nov 2007
44.
Header:
Amikacin
Title:
Amikacin
Description:
Shows the differential regulation of the gene in response to the drug
Values:
continuous, -3.4 to 3.4; negative values indicate down regulation and positive values indicate upregulation
Reference:
Personal Communication from H. Boshoff
Date:
Nov 2007
45.
Header:
Amp
Title:
Ampicillin
Description:
Shows the differential regulation of the gene in response to the drug
Values:
continuous, -2.15 to 2; negative values indicate down regulation and positive values indicate upregulation
Reference:
Personal Communication from H. Boshoff
Date:
Nov 2007
46.
Header:
Antimycin
Title:
Antimycin A
Description:
Shows the differential regulation of the gene in response to the drug
Values:
continuous, -2.13 to 6.3; negative values indicate down regulation and positive values indicate upregulation
Reference:
Personal Communication from H. Boshoff
Date:
Nov 2007
47.
Header:
Ascididemin_Nat_prod
Title:
Eudistoma Amplum
Description:
Shows the differential regulation of the gene in response to the drug
Values:
continuous, -2.25 to 4.2; negative values indicate down regulation and positive values indicate upregulation
Reference:
Personal Communication from H. Boshoff
Date:
Nov 2007
48.
Header:
BZA
Title:
Benzamide
Description:
Shows the differential regulation of the gene in response to the drug
Values:
continuous, -2.3 to 2.7; negative values indicate down regulation and positive values indicate upregulation
Reference:
Personal Communication from H. Boshoff
Date:
Nov 2007
49.
Header:
CCCP
Title:
Carbonyl cyanide 3-chlorophenylhydrazone
Description:
Shows the differential regulation of the gene in response to the drug
Values:
continuous, -4.3 to 5.2; negative values indicate down regulation and positive values indicate upregulation
Reference:
Personal Communication from H. Boshoff
Date:
Nov 2007
50.
Header:
CPZ
Title:
Chloropromazine
Description:
Shows the differential regulation of the gene in response to the drug
Values:
continuous, -1.6 to 3; negative values indicate down regulation and positive values indicate upregulation
Reference:
Personal Communication from H. Boshoff
Date:
Nov 2007
51.
Header:
Cap
Title:
Capreomycin
Description:
Shows the differential regulation of the gene in response to the drug
Values:
continuous, -3.6 to 3.9; negative values indicate down regulation and positive values indicate upregulation
Reference:
Personal Communication from H. Boshoff
Date:
Nov 2007
52.
Header:
Cephalexin
Title:
Cephalexin
Description:
Shows the differential regulation of the gene in response to the drug
Values:
continuous, -1.5 to 3.3; negative values indicate down regulation and positive values indicate upregulation
Reference:
Personal Communication from H. Boshoff
Date:
Nov 2007
53.
Header:
Cerulenin
Title:
Cerulenin
Description:
Shows the differential regulation of the gene in response to the drug
Values:
continuous, -1.6 to 3.6; negative values indicate down regulation and positive values indicate upregulation
Reference:
Personal Communication from H. Boshoff
Date:
Nov 2007
54.
Header:
Clofazimine
Title:
Clofazimine
Description:
Shows the differential regulation of the gene in response to the drug
Values:
continuous, -3.2 to 5.1; negative values indicate down regulation and positive values indicate upregulation
Reference:
Personal Communication from H. Boshoff
Date:
Nov 2007
55.
Header:
Clotrimazole
Title:
Clotrimazole
Description:
Shows the differential regulation of the gene in response to the drug
Values:
continuous, -1.7 to 2.8; negative values indicate down regulation and positive values indicate upregulation
Reference:
Personal Communication from H. Boshoff
Date:
Nov 2007
56.
Header:
DCCD
Title:
Dicyclohexylcarbodiimide
Description:
Shows the differential regulation of the gene in response to the drug
Values:
continuous, -5.3 to 8.3; negative values indicate down regulation and positive values indicate upregulation
Reference:
Personal Communication from H. Boshoff
Date:
Nov 2007
57.
Header:
DIPED
Title:
Dicyclohexylcarbodiimide
Description:
Shows the differential regulation of the gene in response to the drug
Values:
continuous, -2.4 to 2.3; negative values indicate down regulation and positive values indicate upregulation
Reference:
Personal Communication from H. Boshoff
Date:
Nov 2007
58.
Header:
DNP
Title:
Dinitrophenol
Description:
Shows the differential regulation of the gene in response to the drug
Values:
continuous, -4.8 to 9; negative values indicate down regulation and positive values indicate upregulation
Reference:
Personal Communication from H. Boshoff
Date:
Nov 2007
59.
Header:
DTNB
Title:
Dithiobis
Description:
Shows the differential regulation of the gene in response to the drug
Values:
continuous, -2.9 to 4.2; negative values indicate down regulation and positive values indicate upregulation
Reference:
Personal Communication from H. Boshoff
Date:
Nov 2007
60.
Header:
DTT
Title:
Dithio-DL-threitol
Description:
Shows the differential regulation of the gene in response to the drug
Values:
continuous, -3.1 to 6.9; negative values indicate down regulation and positive values indicate upregulation
Reference:
Personal Communication from H. Boshoff
Date:
Nov 2007
61.
Header:
Deferoxamine
Title:
Deferoxamine Mesylate
Description:
Shows the differential regulation of the gene in response to the drug
Values:
continuous, -2.2 to 1.8; negative values indicate down regulation and positive values indicate upregulation
Reference:
Personal Communication from H. Boshoff
Date:
Nov 2007
62.
Header:
Dipyridyl
Title:
Bipyridyl
Description:
Shows the differential regulation of the gene in response to the drug
Values:
continuous, -2.5 to 3.7; negative values indicate down regulation and positive values indicate upregulation
Reference:
Personal Communication from H. Boshoff
Date:
Nov 2007
63.
Header:
EMB
Title:
Ethambutol
Description:
Shows the differential regulation of the gene in response to the drug
Values:
continuous, -1.5 to 2.5; negative values indicate down regulation and positive values indicate upregulation
Reference:
Personal Communication from H. Boshoff
Date:
Nov 2007
64.
Header:
Econazole
Title:
Econazole
Description:
Shows the differential regulation of the gene in response to the drug
Values:
continuous, -2.2 to 3.4; negative values indicate down regulation and positive values indicate upregulation
Reference:
Personal Communication from H. Boshoff
Date:
Nov 2007
65.
Header:
Eta
Title:
Ethionamide
Description:
Shows the differential regulation of the gene in response to the drug
Values:
continuous, -2.4 to 3.2; negative values indicate down regulation and positive values indicate upregulation
Reference:
Personal Communication from H. Boshoff
Date:
Nov 2007
66.
Header:
GSNO
Title:
Nitrosoglutathione
Description:
Shows the differential regulation of the gene in response to the drug
Values:
continuous, -3.3 to 4.1; negative values indicate down regulation and positive values indicate upregulation
Reference:
Personal Communication from H. Boshoff
Date:
Nov 2007
67.
Header:
GSNO_CFZ
Title:
Nitrosoglutathione + Clofazimine
Description:
Shows the differential regulation of the gene in response to the drug
Values:
continuous, -3.9 to 3.6; negative values indicate down regulation and positive values indicate upregulation
Reference:
Personal Communication from H. Boshoff
Date:
Nov 2007
68.
Header:
GSNO_CPZ
Title:
Nitrosoglutathione + Chlorpromazine
Description:
Shows the differential regulation of the gene in response to the drug
Values:
continuous, -4.5 to 4.3; negative values indicate down regulation and positive values indicate upregulation
Reference:
Personal Communication from H. Boshoff
Date:
Nov 2007
69.
Header:
GSNO_KCN
Title:
Nitrosoglutathione + Potassium Cyanide
Description:
Shows the differential regulation of the gene in response to the drug
Values:
continuous, -5.3 to 7.5; negative values indicate down regulation and positive values indicate upregulation
Reference:
Personal Communication from H. Boshoff
Date:
Nov 2007
70.
Header:
GSNO_menadione
Title:
Nitrosoglutathione + Menadione
Description:
Shows the differential regulation of the gene in response to the drug
Values:
continuous, -3.0 to 4.9; negative values indicate down regulation and positive values indicate upregulation
Reference:
Personal Communication from H. Boshoff
Date:
Nov 2007
71.
Header:
H2O2
Title:
Hydrogen Peroxide
Description:
Shows the differential regulation of the gene in response to the drug
Values:
continuous, -1.9 to 2.2; negative values indicate down regulation and positive values indicate upregulation
Reference:
Personal Communication from H. Boshoff
Date:
Nov 2007
72.
Header:
INH
Title:
Isoniazid
Description:
Shows the differential regulation of the gene in response to the drug
Values:
continuous, -2.9 to 3.7; negative values indicate down regulation and positive values indicate upregulation
Reference:
Personal Communication from H. Boshoff
Date:
Nov 2007
73.
Header:
KCN
Title:
Potassium Cyanide
Description:
Shows the differential regulation of the gene in response to the drug
Values:
continuous, -3.2 to 4.5; negative values indicate down regulation and positive values indicate upregulation
Reference:
Personal Communication from H. Boshoff
Date:
Nov 2007
74.
Header:
Levo
Title:
Levofloxacin
Description:
Shows the differential regulation of the gene in response to the drug
Values:
continuous, -3.0 to 4.5; negative values indicate down regulation and positive values indicate upregulation
Reference:
Personal Communication from H. Boshoff
Date:
Nov 2007
75.
Header:
Min_med__succinate_
Title:
Minimal medium with succinate
Description:
Shows the differential regulation of the gene in response to the drug
Values:
continuous, -5.3 to 5.6; negative values indicate down regulation and positive values indicate upregulation
Reference:
Personal Communication from H. Boshoff
Date:
Nov 2007
76.
Header:
Mtm
Title:
Mitomycin C
Description:
Shows the differential regulation of the gene in response to the drug
Values:
continuous, -1.5 to 2.4; negative values indicate down regulation and positive values indicate upregulation
Reference:
Personal Communication from H. Boshoff
Date:
Nov 2007
77.
Header:
NRP_1
Title:
Non-replicating Persistence
Description:
Shows the differential regulation of the gene in response to the drug
Values:
continuous, -3.9 to 5.7; negative values indicate down regulation and positive values indicate upregulation
Reference:
Personal Communication from H. Boshoff
Date:
Nov 2007
78.
Header:
NaN3
Title:
Sodium Azide
Description:
Shows the differential regulation of the gene in response to the drug
Values:
continuous, -3.5 to 4; negative values indicate down regulation and positive values indicate upregulation
Reference:
Personal Communication from H. Boshoff
Date:
Nov 2007
79.
Header:
Nam
Title:
Nicotinamide
Description:
Shows the differential regulation of the gene in response to the drug
Values:
continuous, -2.2 to 2.2; negative values indicate down regulation and positive values indicate upregulation
Reference:
Personal Communication from H. Boshoff
Date:
Nov 2007
80.
Header:
Nigericin
Title:
Nigericin
Description:
Shows the differential regulation of the gene in response to the drug
Values:
continuous, -4.6 to 7.1; negative values indicate down regulation and positive values indicate upregulation
Reference:
Personal Communication from H. Boshoff
Date:
Nov 2007
81.
Header:
Novobiocin
Title:
Novobiocin
Description:
Shows the differential regulation of the gene in response to the drug
Values:
continuous, -4.6 to 7.1; negative values indicate down regulation and positive values indicate upregulation
Reference:
Personal Communication from H. Boshoff
Date:
Nov 2007
82.
Header:
Oflox
Title:
Ofloxacin
Description:
Shows the differential regulation of the gene in response to the drug
Values:
continuous, -2 to 4.4; negative values indicate down regulation and positive values indicate upregulation
Reference:
Personal Communication from H. Boshoff
Date:
Nov 2007
83.
Header:
PA_1
Title:
Antitubercular compound PA-1
Description:
Shows the differential regulation of the gene in response to the drug
Values:
continuous, -1.8 to 2.9; negative values indicate down regulation and positive values indicate upregulation
Reference:
Personal Communication from H. Boshoff
Date:
Nov 2007
84.
Header:
PA_21
Title:
Antitubercular compound PA-21
Description:
Shows the differential regulation of the gene in response to the drug
Values:
continuous, -1.9 to 2.3; negative values indicate down regulation and positive values indicate upregulation
Reference:
Personal Communication from H. Boshoff
Date:
Nov 2007
85.
Header:
PA824
Title:
PA-824
Description:
Shows the differential regulation of the gene in response to the drug
Values:
continuous, -3 to 3.9; negative values indicate down regulation and positive values indicate upregulation
Reference:
Personal Communication from H. Boshoff
Date:
Nov 2007
86.
Header:
PZA
Title:
Pyrazinamide
Description:
Shows the differential regulation of the gene in response to the drug
Values:
continuous, -1.7 to 2.8; negative values indicate down regulation and positive values indicate upregulation
Reference:
Personal Communication from H. Boshoff
Date:
Nov 2007
87.
Header:
Palmitate
Title:
Palmitate
Description:
Shows the differential regulation of the gene in response to the drug
Values:
continuous, -3.7 to 5.7; negative values indicate down regulation and positive values indicate upregulation
Reference:
Personal Communication from H. Boshoff
Date:
Nov 2007
88.
Header:
Procept_6776
Title:
Antitubercular compound Procept 6776
Description:
Shows the differential regulation of the gene in response to the drug
Values:
continuous, -3.7 to 4.6; negative values indicate down regulation and positive values indicate upregulation
Reference:
Personal Communication from H. Boshoff
Date:
Nov 2007
89.
Header:
Procept_6778
Title:
Antitubercular compound Procept 6778
Description:
Shows the differential regulation of the gene in response to the drug
Values:
continuous, -3.1 to 3.5; negative values indicate down regulation and positive values indicate upregulation
Reference:
Personal Communication from H. Boshoff
Date:
Nov 2007
90.
Header:
Rif
Title:
Rifampicin
Description:
Shows the differential regulation of the gene in response to the drug
Values:
continuous, -3.2 to 2.5; negative values indicate down regulation and positive values indicate upregulation
Reference:
Personal Communication from H. Boshoff
Date:
Nov 2007
91.
Header:
Rifp
Title:
Rifapentine
Description:
Shows the differential regulation of the gene in response to the drug
Values:
continuous, -3.4 to 2.4; negative values indicate down regulation and positive values indicate upregulation
Reference:
Personal Communication from H. Boshoff
Date:
Nov 2007
92.
Header:
Rox
Title:
Roxithromycin
Description:
Shows the differential regulation of the gene in response to the drug
Values:
continuous, -4.5 to 5.7; negative values indicate down regulation and positive values indicate upregulation
Reference:
Personal Communication from H. Boshoff
Date:
Nov 2007
93.
Header:
SM
Title:
Streptomycin
Description:
Shows the differential regulation of the gene in response to the drug
Values:
continuous, -2.1 to 4.1; negative values indicate down regulation and positive values indicate upregulation
Reference:
Personal Communication from H. Boshoff
Date:
Nov 2007
94.
Header:
Succinate
Title:
Succinate
Description:
Shows the differential regulation of the gene in response to the drug
Values:
continuous, -3.2 to 5.8; negative values indicate down regulation and positive values indicate upregulation
Reference:
Personal Communication from H. Boshoff
Date:
Nov 2007
95.
Header:
TLM
Title:
Thiolactomycin
Description:
Shows the differential regulation of the gene in response to the drug
Values:
continuous, -2.3 to 3.4; negative values indicate down regulation and positive values indicate upregulation
Reference:
Personal Communication from H. Boshoff
Date:
Nov 2007
96.
Header:
TRC
Title:
Triclosan
Description:
Shows the differential regulation of the gene in response to the drug
Values:
continuous, -2.3 to 4.0; negative values indicate down regulation and positive values indicate upregulation
Reference:
Personal Communication from H. Boshoff
Date:
Nov 2007
97.
Header:
TRZ
Title:
Thioridazine
Description:
Shows the differential regulation of the gene in response to the drug
Values:
continuous, -4.4 to 5.6; negative values indicate down regulation and positive values indicate upregulation
Reference:
Personal Communication from H. Boshoff
Date:
Nov 2007
98.
Header:
Tet
Title:
Tetracycline
Description:
Shows the differential regulation of the gene in response to the drug
Values:
continuous, -5.1 to 5.1; negative values indicate down regulation and positive values indicate upregulation
Reference:
Personal Communication from H. Boshoff
Date:
Nov 2007
99.
Header:
UV
Title:
UV-radiation
Description:
Shows the differential regulation of the gene in response to the drug
Values:
continuous, -2.4 to 3.2; negative values indicate down regulation and positive values indicate upregulation
Reference:
Personal Communication from H. Boshoff
Date:
Nov 2007
100.
Header:
Valinomycin
Title:
Valinomycin
Description:
Shows the differential regulation of the gene in response to the drug
Values:
continuous, -3.5 to 5.8; negative values indicate down regulation and positive values indicate upregulation
Reference:
Personal Communication from H. Boshoff
Date:
Nov 2007
101.
Header:
Verapamil
Title:
Verapamil
Description:
Shows the differential regulation of the gene in response to the drug
Values:
continuous, -5.0 to 5.1; negative values indicate down regulation and positive values indicate upregulation
Reference:
Personal Communication from H. Boshoff
Date:
Nov 2007
102.
Header:
ZnSO4
Title:
ZnSO4
Description:
Shows the differential regulation of the gene in response to the drug
Values:
continuous, -4.9 to 6.5; negative values indicate down regulation and positive values indicate upregulation
Reference:
Personal Communication from H. Boshoff
Date:
Nov 2007
103.
Header:
menadione
Title:
Menadione
Description:
Shows the differential regulation of the gene in response to the drug
Values:
continuous, -3.5 to 5.0; negative values indicate down regulation and positive values indicate upregulation
Reference:
Personal Communication from H. Boshoff
Date:
Nov 2007
104.
Header:
mercaptoethanol
Title:
Mercaptoethanol
Description:
Shows the differential regulation of the gene in response to the drug
Values:
continuous, -4.1 to 3.7; negative values indicate down regulation and positive values indicate upregulation
Reference:
Personal Communication from H. Boshoff
Date:
Nov 2007
105.
Header:
methoxatin
Title:
Methoxatin
Description:
Shows the differential regulation of the gene in response to the drug
Values:
continuous, -4.5 to 5.7; negative values indicate down regulation and positive values indicate upregulation
Reference:
Personal Communication from H. Boshoff
Date:
Nov 2007
106.
Header:
anova_pprob
Title:
Anov_Prob
Description:
Analysis of Variance in Microarray data obtained from H. Boshoff
Values:
continuous, 0 to 103
Reference:
Date:
Nov 2007
107.
Header:
Operon_Name
Title:
Operon
Description:
The operon definitions were obtained from www.webtb.org, which were derived based on a combination of proximity, experimental evidence, and
other information (Moreno-Hagelsieb and Collado-Vides, 2002)
Values:
Reference:
www.webtb.org
Date:
Nov 2007
108.
Header:
Original_TRASH_in_vitro
Title:
In vitro essentiality (Sassetti and Rubin), unthresholded
Description:
Whether gene disruption via transposon insertion inhibits growth in vitro.
Values:
continuous, hybridization ratios range from 0.01 to 5.9; gene essential when hybridization ratio < 0.2
Reference:
Sassetti CM, Boyd DH, Rubin EJ (2003) Genes required for mycobacterial growth defined by high density mutagenesis. Mol Microbiol 48: 77:84.
Date:
Nov 2007
109.
Header:
Original_TRASH_in_vivo
Title:
In vitro essentiality (Sassetti and Rubin), unthresholded
Description:
Whether gene disruption via transposon insertion inhibits growth in vivo.
Values:
continuous, hybridization ratios range from 0.045 to 4.2; gene essential when hybridization ratio < 0.4
Reference:
Sassetti CM, Boyd DH, Rubin EJ (2001) Comprehensive identification of conditionally essential genes in mycobacteria. Proc Natl Acad Sci USA 98: 12712:12717
Date:
Nov 2007
110.
Header:
Annotation
Title:
Annotation
Description:
Annotations for the genes obtained from NCBI
Values:
Reference:
www.ncbi.nlm.nih.gov
Date:
Nov 2007
111.
Header:
Functional_Category
Title:
Functional category
Description:
Definitions obtained from www.webtb.org
Values:
cell wall and cell processes;
conserved hypotheticals;
conserved hypotheticals with an orthologue in M. bovis;
information pathways;
insertion seqs and phages;
intermediary metabolism and respiration; lipid metabolism; PE/PPE; regulatory proteins; unknown; virulence, detoxification, adaptation
Reference:
www.webtb.org
Date:
Nov 2007
112.
Header:
Kegg_Pathway
Title:
Kegg Pathway
Description:
Pathway information obtained from Kegg
Values:
Fatty acid metabolism;
Thiamine metabolism;
Riboflavin metabolism
Reference:
Kanehisa M. and Goto S. (2000) KEGG: Kyoto Encyclopedia of Genes and Genomes. Nucleic Acids Res. 28, 27-30.
Date:
Jan 2008
113.
Header:
Membrane
Title:
Membrane protein
Description:
TMHMM, a web server was used to predict if a given protein has transmembrane helices. These predictions are based on a Hidden Markov Model.
Values:
1/0/-1, 1 if membrane protein, 0 if not and -1 if no data is available
Reference:
Date:
Nov 2007
114.
Header:
PDB_code
Title:
known structure(s) in PDB
Description:
A list of of the structures in the PDB solved for a particular gene (from www.webtb.org)
Values:
Reference:
www.webtb.org
Date:
Nov 2007
115.
Header:
Length
Title:
Residues
Description:
Length of the sequence for each gene (from www.webtb.org)
Values:
Reference:
www.webtb.org
Date:
Nov 2007
116.
Header:
Vosk_Day_0
Title:
Day 0
Description:
Differential regulation on day 0
Values:
0.5 to 1.9, 'nd' refers to non-determined values
Reference:
Voskuil MI, Visconti KC, Schoolnik GK (2004) Mycobacterium tuberculosis gene expression during adaptation to stationary phase and low-oxygen dormancy. Tuberculosis (Edinb) 84: 218:227.
Date:
Nov 2007
117.
Header:
Vosk_Day_6
Title:
Day 6
Description:
Differential regulation on day 6
Values:
0.2 to 10.5, 'nd' refers to non-determined values
Reference:
Voskuil MI, Visconti KC, Schoolnik GK (2004) Mycobacterium tuberculosis gene expression during adaptation to stationary phase and low-oxygen dormancy. Tuberculosis (Edinb) 84: 218:227.
Date:
Nov 2007
118.
Header:
Vosk_Day_8
Title:
Day 8
Description:
Differential regulation on day 8
Values:
0.15 to 16, 'nd' refers to non-determined values
Reference:
Voskuil MI, Visconti KC, Schoolnik GK (2004) Mycobacterium tuberculosis gene expression during adaptation to stationary phase and low-oxygen dormancy. Tuberculosis (Edinb) 84: 218:227.
Date:
Nov 2007
119.
Header:
Vosk_Day_14
Title:
Day 14
Description:
Differential regulation on day 14
Values:
0.1 to 28, 'nd' refers to non-determined values
Reference:
Voskuil MI, Visconti KC, Schoolnik GK (2004) Mycobacterium tuberculosis gene expression during adaptation to stationary phase and low-oxygen dormancy. Tuberculosis (Edinb) 84: 218:227.
Date:
Nov 2007
120.
Header:
Vosk_Day_24
Title:
Day 24
Description:
Differential regulation on day 24
Values:
0 to 34, 'nd' refers to non-determined values
Reference:
Voskuil MI, Visconti KC, Schoolnik GK (2004) Mycobacterium tuberculosis gene expression during adaptation to stationary phase and low-oxygen dormancy. Tuberculosis (Edinb) 84: 218:227.
Date:
Nov 2007
121.
Header:
Vosk_Day_60
Title:
Day 60
Description:
Differential regulation on day 60
Values:
0 to 4, 'nd' refers to non-determined values
Reference:
Voskuil MI, Visconti KC, Schoolnik GK (2004) Mycobacterium tuberculosis gene expression during adaptation to stationary phase and low-oxygen dormancy. Tuberculosis (Edinb) 84: 218:227.
Date:
Nov 2007
122.
Header:
Vosk_Day_4_NRP
Title:
Day 4 NRP
Description:
Differential regulation on day 4 (non-replicating stage)
Values:
0 to 46, 'nd' refers to non-determined values
Reference:
Voskuil MI, Visconti KC, Schoolnik GK (2004) Mycobacterium tuberculosis gene expression during adaptation to stationary phase and low-oxygen dormancy. Tuberculosis (Edinb) 84: 218:227.
Date:
Nov 2007
123.
Header:
Vosk_Day_6_NRP
Title:
Day 6 NRP
Description:
Differential regulation on day 6 (non-replicating stage)
Values:
0 to 108, 'nd' refers to non-determined values
Reference:
Voskuil MI, Visconti KC, Schoolnik GK (2004) Mycobacterium tuberculosis gene expression during adaptation to stationary phase and low-oxygen dormancy. Tuberculosis (Edinb) 84: 218:227.
Date:
Nov 2007
124.
Header:
Vosk_Day_8_NRP
Title:
Day 8 NRP
Description:
Differential regulation on day 8 (non-replicating stage)
Values:
0 to 75, 'nd' refers to non-determined values
Reference:
Voskuil MI, Visconti KC, Schoolnik GK (2004) Mycobacterium tuberculosis gene expression during adaptation to stationary phase and low-oxygen dormancy. Tuberculosis (Edinb) 84: 218:227.
Date:
Nov 2007
125.
Header:
Vosk_Day_10_NRP
Title:
Day 10 NRP
Description:
Differential regulation on day 10 (non-replicating stage)
Values:
0 to 95, 'nd' refers to non-determined values
Reference:
Voskuil MI, Visconti KC, Schoolnik GK (2004) Mycobacterium tuberculosis gene expression during adaptation to stationary phase and low-oxygen dormancy. Tuberculosis (Edinb) 84: 218:227.
Date:
Nov 2007
126.
Header:
Vosk_Day_12_NRP
Title:
Day 12 NRP
Description:
Differential regulation on day 12 (non-replicating stage)
Values:
0 to 40, 'nd' refers to non-determined values
Reference:
Voskuil MI, Visconti KC, Schoolnik GK (2004) Mycobacterium tuberculosis gene expression during adaptation to stationary phase and low-oxygen dormancy. Tuberculosis (Edinb) 84: 218:227.
Date:
Nov 2007
127.
Header:
Vosk_Day_14_NRP
Title:
Day 14 NRP
Description:
Differential regulation on day 14 (non-replicating stage)
Values:
0 to 64, 'nd' refers to non-determined values
Reference:
Voskuil MI, Visconti KC, Schoolnik GK (2004) Mycobacterium tuberculosis gene expression during adaptation to stationary phase and low-oxygen dormancy. Tuberculosis (Edinb) 84: 218:227.
Date:
Nov 2007
128.
Header:
Vosk_Day_20_NRP
Title:
Day 20 NRP
Description:
Differential regulation on day 20 (non-replicating stage)
Values:
0 to 38, 'nd' refers to non-determined values
Reference:
Voskuil MI, Visconti KC, Schoolnik GK (2004) Mycobacterium tuberculosis gene expression during adaptation to stationary phase and low-oxygen dormancy. Tuberculosis (Edinb) 84: 218:227.
Date:
Nov 2007
129.
Header:
Vosk_Day_30_NRP
Title:
Day 30 NRP
Description:
Differential regulation on day 30 (non-replicating stage)
Values:
0 to 23, 'nd' refers to non-determined values
Reference:
Voskuil MI, Visconti KC, Schoolnik GK (2004) Mycobacterium tuberculosis gene expression during adaptation to stationary phase and low-oxygen dormancy. Tuberculosis (Edinb) 84: 218:227.
Date:
Nov 2007
130.
Header:
Vosk_Day_80_NRP
Title:
Day 80 NRP
Description:
Differential regulation on day 80 (non-replicating stage)
Values:
0 to 8, 'nd' refers to non-determined values
Reference:
Voskuil MI, Visconti KC, Schoolnik GK (2004) Mycobacterium tuberculosis gene expression during adaptation to stationary phase and low-oxygen dormancy. Tuberculosis (Edinb) 84: 218:227.
Date:
Nov 2007
131.
Header:
Naive_Macrophage_4hrs
Title:
Naive Macrophage (4 hrs)
Description:
Differential regulation after 4 hrs
Values:
0 to 8.6, 'na' refers to non-deterministic values
Reference:
Schnappinger D, Ehrt S, Voskuil MI, Liu Y, Mangan JA, et al. (2003) Transcriptional Adaptation of Mycobacterium tuberculosis within macrophages: Insights into the phagosomal environment. J Exp Med 198: 693:704.
Date:
Nov 2007
132.
Header:
Naive_Macrophage_24hrs
Title:
Naive Macrophage (24 hrs)
Description:
Differential regulation after 24 hrs measured using amplicon arrays
Values:
0 to 25, 'na' refers to non-deterministic values
Reference:
Schnappinger D, Ehrt S, Voskuil MI, Liu Y, Mangan JA, et al. (2003) Transcriptional Adaptation of Mycobacterium tuberculosis within macrophages: Insights into the phagosomal environment. J Exp Med 198: 693:704.
Date:
Nov 2007
133.
Header:
Naive_Macrophage_24hrs_oligo
Title:
Naive Macrophage (24 hrs)
Description:
Differential regulation after 24 hrs measured using oligonucleotide arrays
Values:
0 to 47, 'na' refers to non-deterministic values
Reference:
Schnappinger D, Ehrt S, Voskuil MI, Liu Y, Mangan JA, et al. (2003) Transcriptional Adaptation of Mycobacterium tuberculosis within macrophages: Insights into the phagosomal environment. J Exp Med 198: 693:704.
Date:
Nov 2007
134.
Header:
Naive_Macrophage_48hrs
Title:
Naive Macrophage (48 hrs)
Description:
Differential regulation after 48 hrs measured using amplicon arrays
Values:
0 to 32, 'na' refers to non-deterministic values
Reference:
Schnappinger D, Ehrt S, Voskuil MI, Liu Y, Mangan JA, et al. (2003) Transcriptional Adaptation of Mycobacterium tuberculosis within macrophages: Insights into the phagosomal environment. J Exp Med 198: 693:704.
Date:
Nov 2007
135.
Header:
Activated_Macrophage_4hrs
Title:
Activated Macrophage (4 hrs)
Description:
Differential regulation 4 hrs after activation
Values:
0 to 8.3, 'na' refers to non-deterministic values
Reference:
Schnappinger D, Ehrt S, Voskuil MI, Liu Y, Mangan JA, et al. (2003) Transcriptional Adaptation of Mycobacterium tuberculosis within macrophages: Insights into the phagosomal environment. J Exp Med 198: 693:704.
Date:
Nov 2007
136.
Header:
Activated_Macrophage_24hrs
Title:
Activated Macrophage (24 hrs)
Description:
Differential regulation 24 hrs after activation measured using amplicon arrays
Values:
0 to 28, 'na' refers to non-deterministic values
Reference:
Schnappinger D, Ehrt S, Voskuil MI, Liu Y, Mangan JA, et al. (2003) Transcriptional Adaptation of Mycobacterium tuberculosis within macrophages: Insights into the phagosomal environment. J Exp Med 198: 693:704.
Date:
Nov 2007
137.
Header:
Activated_Macrophage_24hrs_oligo
Title:
Activated Macrophage (24 hrs)
Description:
Differential regulation 24 hrs after activation measured using oligonucleotide arrays
Values:
0 to 72, 'na' refers to non-deterministic values
Reference:
Schnappinger D, Ehrt S, Voskuil MI, Liu Y, Mangan JA, et al. (2003) Transcriptional Adaptation of Mycobacterium tuberculosis within macrophages: Insights into the phagosomal environment. J Exp Med 198: 693:704.
Date:
Nov 2007
138.
Header:
Activated_Macrophage_48hrs
Title:
Activated Macrophage (48 hrs)
Description:
Differential regulation 48 hrs after macrophage has been activated
Values:
0 to 35, 'na' refers to non-deterministic values
Reference:
Schnappinger D, Ehrt S, Voskuil MI, Liu Y, Mangan JA, et al. (2003) Transcriptional Adaptation of Mycobacterium tuberculosis within macrophages: Insights into the phagosomal environment. J Exp Med 198: 693:704.
Date:
Nov 2007
139.
Header:
Betts_Starvation_4hrs
Title:
Starvation(4 hrs)
Description:
Gene expression profiles in response to nutrient starvation for 4 hours
Values:
-9.43 to 14.6; 0 indicates no data available
Reference:
Betts JC, Lukey PT, Robb LC, McAdam RA, Duncan K (2002) Evaluation of a nutrient starvation model of Mycobacterium tuberculosis persistence by gene and protein expression profiling. Mol Microbiol 43: 717:731.
Date:
Nov 2007
140.
Header:
Betts_Starvation_24hrs
Title:
Starvation(24 hrs)
Description:
Gene expression profiles in response to nutrient starvation for 24 hours
Values:
-10.64 to 64.11; 0 indicates no data available
Reference:
Betts JC, Lukey PT, Robb LC, McAdam RA, Duncan K (2002) Evaluation of a nutrient starvation model of Mycobacterium tuberculosis persistence by gene and protein expression profiling. Mol Microbiol 43: 717:731.
Date:
Nov 2007
141.
Header:
Betts_Starvation_96hrs
Title:
Starvation(96 hrs)
Description:
Gene expression profiles in response to nutrient starvation for 96 hours
Values:
-14.49 to 282.24; 0 indicates no data available
Reference:
Betts JC, Lukey PT, Robb LC, McAdam RA, Duncan K (2002) Evaluation of a nutrient starvation model of Mycobacterium tuberculosis persistence by gene and protein expression profiling. Mol Microbiol 43: 717:731.
Date:
Nov 2007