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 Rv2959c/-:

update plot	correlation	link to info on gene
Rv0888/-	(cc=0.5389)	info on Rv0888/-
Rv1523/-	(cc=0.4859)	info on Rv1523/-
Rv3125c/PPE49	(cc=0.477)	info on Rv3125c/PPE49
Rv2107/PE22	(cc=0.4696)	info on Rv2107/PE22
Rv0109/PE_PGRS1	(cc=0.4534)	info on Rv0109/PE_PGRS1
Rv2338c/moeW	(cc=0.4521)	info on Rv2338c/moeW
Rv3116/moeB2	(cc=0.4454)	info on Rv3116/moeB2
Rv2730/-	(cc=0.4444)	info on Rv2730/-
Rv2993c/-	(cc=0.4435)	info on Rv2993c/-
Rv2954c/-	(cc=0.4238)	info on Rv2954c/-

Correlation of Rv2959c/- with Rv0888/-

Normalized LFCs for Rv2959c/-:
(description and provenance of datasets)

	Rv2959c/-	Rv0888/-
Fe_supp_jason_reseq	0.481	-0.245
low_pH_jason_reseq	-0.709	0.04
NO_jason_reseq	-0.559	-0.284
B6_jason_reseq	-0.96	0.32
MHCII_jason_reseq	-0.614	0.175
Isoniazid02	-1.796	-0.31
Rifampicin4	0.344	0.298
Ethambutol3	1.56	0.852
Meropenem3	-1.445	-0.719
Vancomycin16	-0.512	-0.257
Rv2680_day32	-0.348	0.477
H37Rv_KO_MarP	0.24	0.477
hypoxia_3wks	0.606	-0.275
hypoxia_6wks	-0.355	-0.196
glycerol	-1.249	-0.582
cholesterol	-0.535	-0.453
AJ	0.425	0.262
Bibs02	0.0	0.309
Bibs02c	-0.465	-0.255
BL6	0.849	0.675
BL6a	0.911	0.207
BXD01	0.262	0.515
BXD010	1.063	0.482
BXD011	0.511	0.18
BXD03	0.436	0.136
BXD04	-0.028	0.58
BXD05	1.019	0.473
BXD06	0.409	0.378
BXD07	0.03	0.392
BXD08	0.029	0.764
BXD09	1.152	0.353
CAST	-0.158	0.389
CCcont	0.158	0.327
DS01	-0.108	0.188
DS02	0.592	0.098
DS04	0.084	0.178
DS0c	-0.801	0.28
GP01	0.043	0.667
GP02	-0.391	0.806
GP0c	-0.325	-0.262
NOD	0.049	0.825
NZO	0.087	0.019
PWK	0.043	0.837
H37Rv_KO_CtpC	-0.879	-0.198
H37Rv_KO_CtpD	0.874	0.204
H37Rv_KO_Rv1272	0.82	0.094
H37Rv_KO_SugABC	-0.167	-0.162
H37Rv_KO_MbtN	-0.381	0.042
Trans05	-0.327	0.501
macrophage_unactivated	0.24	0.038
IL1	-0.828	-0.421
Rapamycin	-1.562	-0.436
Tcell	-0.681	-0.101
GMCSF	-0.995	-0.285
IFNab	-0.989	-0.49
IFNg	-0.214	-0.016
IFNg_GMCSF1	-0.383	-0.509
Rv1432_day32	0.462	0.79
Rv1565c_day32	0.351	0.687
secA2_input	-0.941	-0.402
delta_Rv3594	0.797	0.672
delta_Rv3717	1.258	0.586
delta_Rv3811	0.775	0.626
delta_Rv0954	1.521	1.119
PonA1	1.293	1.309
EccD1_KO	0.49	0.589
EspI_KO	-0.679	0.944
PE35_KO	0.35	0.683
PPE68_KO	-0.31	0.918
glycerol2	0.101	0.419
lignocerate	-0.189	0.659
oleate	0.571	0.193
phosphatidylcholine	0.64	0.45
acetate	-0.125	0.088
glucAc	-0.132	0.342
Rv0950ko	0.721	0.736
Rv1096ko	-0.971	0.847
Rv3684ko	-0.291	0.547
delta_otsA_trehalose	-0.588	0.916