TnSeqCorr

• These are correlations of TnSeq responses across 82 experimental conditions.
• LFCs (log2-fold-changes) were computed for each gene in each condition relative to a relevant control condition (e.g. H37Rv grown on 7H9).
• The LFCs were normalized by dividing by the standard deviation for each condition. (so roughly, |LFC|>2 are the outliers, i.e. tails of the distribution)
• Note that essential genes often have LFCs around 0.
• Data for some genes is not available if they have less than 3 TA sites, or the dynamic range of LFCs is less than 2.0 across all conditions. (This is the case for many essential genes.)
• 'leverage' on each plot is a statistical score that indicates how much the regression is influenced by a few outlier points; the traditional threshold is indicated on the plots (3p/n, which is about 0.07 for this dataset), but in practice, cases with leverage > ~0.2 seem to be the least reliable (most misleading) correlation coefficients.

Top 10 genes with highest correlation to Rv0069c/sdaA:

update plot	correlation	link to info on gene
Rv0338c/-	(cc=0.7502)	info on Rv0338c/-
Rv0320/-	(cc=0.5463)	info on Rv0320/-
Rv0191/-	(cc=0.4888)	info on Rv0191/-
Rv0373c/-	(cc=0.4568)	info on Rv0373c/-
Rv2189c/-	(cc=0.4479)	info on Rv2189c/-
Rv2715/-	(cc=0.4477)	info on Rv2715/-
Rv3068c/pgmA	(cc=0.4325)	info on Rv3068c/pgmA
Rv2394/ggtB	(cc=0.4302)	info on Rv2394/ggtB
Rv1317c/alkA	(cc=0.4268)	info on Rv1317c/alkA
Rv2073c/-	(cc=0.4251)	info on Rv2073c/-

Correlation of Rv0069c/sdaA with Rv3068c/pgmA

Normalized LFCs for Rv0069c/sdaA:
(description and provenance of datasets)

	Rv0069c/sdaA	Rv3068c/pgmA
Fe_supp_jason_reseq	0.205	-0.557
low_pH_jason_reseq	-1.367	-1.005
NO_jason_reseq	-1.265	-0.927
B6_jason_reseq	-0.208	0.188
MHCII_jason_reseq	0.127	-0.345
Isoniazid02	-0.049	-0.185
Rifampicin4	-0.233	-0.236
Ethambutol3	0.627	0.1
Meropenem3	0.278	0.365
Vancomycin16	0.836	0.127
Rv2680_day32	-0.372	0.223
H37Rv_KO_MarP	0.217	0.058
hypoxia_3wks	-0.319	-2.731
hypoxia_6wks	-0.299	-3.408
glycerol	2.392	-0.14
cholesterol	6.0	3.524
AJ	0.187	-0.21
Bibs02	-0.592	-0.619
Bibs02c	0.196	-0.483
BL6	0.084	0.179
BL6a	0.307	0.056
BXD01	-0.154	0.261
BXD010	-0.171	0.242
BXD011	0.68	0.659
BXD03	-0.631	0.39
BXD04	-0.425	0.157
BXD05	-0.223	0.455
BXD06	-0.038	0.289
BXD07	-0.207	0.188
BXD08	0.329	-0.127
BXD09	0.076	0.072
CAST	-0.976	-0.27
CCcont	0.176	-0.128
DS01	-0.279	-0.152
DS02	-0.325	0.082
DS04	-1.036	0.495
DS0c	0.363	-0.338
GP01	0.265	1.364
GP02	-0.138	0.758
GP0c	0.639	0.159
NOD	-1.596	-0.898
NZO	-1.472	-0.244
PWK	0.183	-0.057
H37Rv_KO_CtpC	0.213	0.069
H37Rv_KO_CtpD	-1.75	-0.262
H37Rv_KO_Rv1272	-0.72	-0.142
H37Rv_KO_SugABC	0.94	0.48
H37Rv_KO_MbtN	1.301	-0.62
Trans05	-0.5	-0.416
macrophage_unactivated	0.18	0.202
IL1	0.383	-0.288
Rapamycin	0.807	-0.347
Tcell	0.42	-0.094
GMCSF	-0.264	0.349
IFNab	1.167	-0.088
IFNg	0.249	-0.388
IFNg_GMCSF1	-0.512	0.069
Rv1432_day32	0.415	0.576
Rv1565c_day32	-0.355	-0.444
secA2_input	1.656	0.095
delta_Rv3594	-0.783	-0.075
delta_Rv3717	-0.2	-0.43
delta_Rv3811	0.299	-0.65
delta_Rv0954	0.399	-0.208
PonA1	0.943	0.167
EccD1_KO	0.802	0.431
EspI_KO	-0.645	0.374
PE35_KO	0.055	-0.257
PPE68_KO	0.781	-0.55
glycerol2	0.171	0.269
lignocerate	0.183	-2.53
oleate	-0.264	-2.101
phosphatidylcholine	-0.067	-3.003
acetate	-0.191	0.229
glucAc	-0.249	-0.089
Rv0950ko	0.582	0.419
Rv1096ko	0.582	0.709
Rv3684ko	-0.069	0.563
delta_otsA_trehalose	0.027	0.3