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 Rv1165/typA:

update plot	correlation	link to info on gene
Rv3920c/-	(cc=0.5499)	info on Rv3920c/-
Rv2983/-	(cc=0.535)	info on Rv2983/-
Rv3041c/-	(cc=0.5266)	info on Rv3041c/-
Rv2125/-	(cc=0.5228)	info on Rv2125/-
Rv2831/echA16	(cc=0.5129)	info on Rv2831/echA16
Rv2404c/lepA	(cc=0.4708)	info on Rv2404c/lepA
Rv2672/-	(cc=0.4557)	info on Rv2672/-
Rv3557c/-	(cc=0.4503)	info on Rv3557c/-
Rv3228/-	(cc=0.4443)	info on Rv3228/-
Rv2733c/-	(cc=0.4418)	info on Rv2733c/-

Correlation of Rv1165/typA with Rv2983/-

Normalized LFCs for Rv1165/typA:
(description and provenance of datasets)

	Rv1165/typA	Rv2983/-
Fe_supp_jason_reseq	-0.191	0.218
low_pH_jason_reseq	-0.015	0.0
NO_jason_reseq	0.764	0.0
B6_jason_reseq	0.078	0.292
MHCII_jason_reseq	0.896	0.135
Isoniazid02	1.302	2.89
Rifampicin4	0.818	2.142
Ethambutol3	0.083	1.249
Meropenem3	-0.504	0.189
Vancomycin16	0.825	2.183
Rv2680_day32	-0.932	0.0
H37Rv_KO_MarP	1.116	1.112
hypoxia_3wks	0.108	-0.502
hypoxia_6wks	-0.958	-0.549
glycerol	1.033	0.856
cholesterol	-0.015	1.504
AJ	0.182	0.232
Bibs02	-0.568	0.0
Bibs02c	-0.382	0.209
BL6	-0.653	0.0
BL6a	-0.397	0.0
BXD01	-0.344	0.0
BXD010	-0.13	0.0
BXD011	-0.136	0.0
BXD03	-0.861	0.0
BXD04	0.392	0.0
BXD05	-0.455	0.135
BXD06	-0.26	0.133
BXD07	-0.509	0.0
BXD08	0.097	0.0
BXD09	-0.408	0.0
CAST	-0.462	0.0
CCcont	-0.281	1.082
DS01	0.397	1.947
DS02	-0.282	0.0
DS04	-0.09	0.194
DS0c	0.086	0.596
GP01	-0.355	0.0
GP02	0.033	0.0
GP0c	-0.301	0.0
NOD	-0.89	0.0
NZO	-0.821	0.0
PWK	0.438	0.0
H37Rv_KO_CtpC	-0.297	0.0
H37Rv_KO_CtpD	-0.201	0.127
H37Rv_KO_Rv1272	-0.601	0.0
H37Rv_KO_SugABC	0.2	0.099
H37Rv_KO_MbtN	1.249	0.0
Trans05	-0.38	0.0
macrophage_unactivated	0.025	0.0
IL1	0.154	0.0
Rapamycin	0.092	0.0
Tcell	0.049	0.0
GMCSF	0.309	0.0
IFNab	0.248	0.0
IFNg	0.198	0.0
IFNg_GMCSF1	0.025	0.0
Rv1432_day32	-0.841	0.0
Rv1565c_day32	0.308	0.0
secA2_input	0.045	-0.485
delta_Rv3594	0.75	1.811
delta_Rv3717	0.43	0.0
delta_Rv3811	0.886	0.934
delta_Rv0954	0.373	0.811
PonA1	0.738	1.367
EccD1_KO	-0.056	-0.664
EspI_KO	0.26	-1.243
PE35_KO	0.359	1.52
PPE68_KO	-0.029	1.667
glycerol2	-1.391	-1.297
lignocerate	-0.374	-2.345
oleate	-1.202	-2.358
phosphatidylcholine	-0.462	-2.697
acetate	-0.387	-1.102
glucAc	-0.062	-1.49
Rv0950ko	-0.075	-1.294
Rv1096ko	0.386	-0.256
Rv3684ko	-0.4	-0.727
delta_otsA_trehalose	0.429	-0.111