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 Rv0669c/-

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

	Rv2394/ggtB	Rv0669c/-
Fe_supp_jason_reseq	-1.01	-0.156
low_pH_jason_reseq	-0.616	-0.582
NO_jason_reseq	-0.047	0.039
B6_jason_reseq	-0.383	0.331
MHCII_jason_reseq	-0.607	0.163
Isoniazid02	0.581	0.247
Rifampicin4	0.764	0.0
Ethambutol3	2.847	1.07
Meropenem3	1.294	0.492
Vancomycin16	0.565	-0.019
Rv2680_day32	-1.556	0.483
H37Rv_KO_MarP	0.212	0.344
hypoxia_3wks	0.211	-0.231
hypoxia_6wks	0.111	0.092
glycerol	0.219	0.445
cholesterol	3.29	3.252
AJ	0.356	0.279
Bibs02	0.34	0.317
Bibs02c	0.053	-0.03
BL6	-0.117	-0.03
BL6a	0.135	-0.135
BXD01	0.016	0.134
BXD010	-0.418	-0.056
BXD011	0.523	0.12
BXD03	0.259	0.318
BXD04	0.454	0.164
BXD05	0.115	0.121
BXD06	-0.153	0.155
BXD07	0.337	0.013
BXD08	0.344	0.209
BXD09	-0.14	-0.161
CAST	0.058	0.237
CCcont	-0.214	-0.276
DS01	0.229	0.212
DS02	0.121	0.386
DS04	1.04	0.513
DS0c	0.198	0.138
GP01	0.043	0.31
GP02	0.164	-0.395
GP0c	0.096	-0.135
NOD	0.179	0.251
NZO	0.496	0.247
PWK	0.323	0.269
H37Rv_KO_CtpC	-0.011	-0.127
H37Rv_KO_CtpD	0.689	0.199
H37Rv_KO_Rv1272	0.044	0.534
H37Rv_KO_SugABC	0.608	1.096
H37Rv_KO_MbtN	0.599	-0.03
Trans05	0.389	-0.076
macrophage_unactivated	0.366	-0.174
IL1	0.4	-0.486
Rapamycin	-0.387	-0.718
Tcell	0.287	0.042
GMCSF	-0.19	-0.09
IFNab	-0.348	-0.405
IFNg	-0.166	-0.521
IFNg_GMCSF1	-0.295	-0.493
Rv1432_day32	-0.128	0.183
Rv1565c_day32	-0.019	-0.22
secA2_input	-0.26	-1.021
delta_Rv3594	-0.444	-0.32
delta_Rv3717	-0.927	-0.322
delta_Rv3811	-0.338	-0.103
delta_Rv0954	0.736	-0.91
PonA1	0.509	-0.372
EccD1_KO	0.763	0.385
EspI_KO	-0.031	0.642
PE35_KO	0.761	0.076
PPE68_KO	0.682	0.163
glycerol2	0.59	0.815
lignocerate	-0.108	0.919
oleate	0.713	0.333
phosphatidylcholine	0.363	0.944
acetate	-0.404	0.532
glucAc	-0.315	0.573
Rv0950ko	-0.211	0.265
Rv1096ko	-0.434	0.066
Rv3684ko	-0.164	0.265
delta_otsA_trehalose	1.096	-1.542