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 Rv2394/ggtB:

update plot	correlation	link to info on gene
Rv2189c/-	(cc=0.7011)	info on Rv2189c/-
Rv2715/-	(cc=0.6425)	info on Rv2715/-
Rv1807/PPE31	(cc=0.5055)	info on Rv1807/PPE31
Rv0338c/-	(cc=0.5008)	info on Rv0338c/-
Rv3154/nuoJ	(cc=0.4785)	info on Rv3154/nuoJ
Rv0669c/-	(cc=0.476)	info on Rv0669c/-
Rv2268c/cyp128	(cc=0.4724)	info on Rv2268c/cyp128
Rv1317c/alkA	(cc=0.471)	info on Rv1317c/alkA
Rv1800/PPE28	(cc=0.4631)	info on Rv1800/PPE28
Rv0465c/-	(cc=0.4589)	info on Rv0465c/-

Correlation of Rv2394/ggtB with Rv2268c/cyp128

Normalized LFCs for Rv2394/ggtB:
(description and provenance of datasets)

	Rv2394/ggtB	Rv2268c/cyp128
Fe_supp_jason_reseq	-1.01	-0.906
low_pH_jason_reseq	-0.616	-0.196
NO_jason_reseq	-0.047	-0.714
B6_jason_reseq	-0.383	-0.834
MHCII_jason_reseq	-0.607	-1.068
Isoniazid02	0.581	-0.105
Rifampicin4	0.764	-0.298
Ethambutol3	2.847	-0.134
Meropenem3	1.294	0.875
Vancomycin16	0.565	0.0
Rv2680_day32	-1.556	-0.874
H37Rv_KO_MarP	0.212	-0.11
hypoxia_3wks	0.211	-0.518
hypoxia_6wks	0.111	-0.161
glycerol	0.219	1.434
cholesterol	3.29	6.0
AJ	0.356	0.632
Bibs02	0.34	0.792
Bibs02c	0.053	1.299
BL6	-0.117	1.26
BL6a	0.135	0.623
BXD01	0.016	0.489
BXD010	-0.418	0.0
BXD011	0.523	0.29
BXD03	0.259	1.271
BXD04	0.454	-0.408
BXD05	0.115	0.814
BXD06	-0.153	0.334
BXD07	0.337	0.377
BXD08	0.344	0.648
BXD09	-0.14	0.527
CAST	0.058	1.039
CCcont	-0.214	0.082
DS01	0.229	0.065
DS02	0.121	1.022
DS04	1.04	-1.248
DS0c	0.198	1.095
GP01	0.043	-0.802
GP02	0.164	1.79
GP0c	0.096	-0.836
NOD	0.179	1.595
NZO	0.496	1.329
PWK	0.323	0.108
H37Rv_KO_CtpC	-0.011	-0.473
H37Rv_KO_CtpD	0.689	1.684
H37Rv_KO_Rv1272	0.044	1.022
H37Rv_KO_SugABC	0.608	1.209
H37Rv_KO_MbtN	0.599	0.933
Trans05	0.389	0.982
macrophage_unactivated	0.366	-0.354
IL1	0.4	0.308
Rapamycin	-0.387	-0.718
Tcell	0.287	0.45
GMCSF	-0.19	0.774
IFNab	-0.348	-0.707
IFNg	-0.166	-0.299
IFNg_GMCSF1	-0.295	-0.735
Rv1432_day32	-0.128	0.287
Rv1565c_day32	-0.019	0.602
secA2_input	-0.26	-0.146
delta_Rv3594	-0.444	0.912
delta_Rv3717	-0.927	0.0
delta_Rv3811	-0.338	0.049
delta_Rv0954	0.736	-0.23
PonA1	0.509	-0.039
EccD1_KO	0.763	-1.059
EspI_KO	-0.031	-0.168
PE35_KO	0.761	0.904
PPE68_KO	0.682	0.442
glycerol2	0.59	0.144
lignocerate	-0.108	-0.346
oleate	0.713	-0.483
phosphatidylcholine	0.363	-0.132
acetate	-0.404	-0.183
glucAc	-0.315	-0.565
Rv0950ko	-0.211	-0.808
Rv1096ko	-0.434	-0.808
Rv3684ko	-0.164	-0.783
delta_otsA_trehalose	1.096	-0.838