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 Rv0303/-:

update plot	correlation	link to info on gene
Rv0276/-	(cc=0.5835)	info on Rv0276/-
Rv0592/mce2D	(cc=0.5553)	info on Rv0592/mce2D
Rv3839/-	(cc=0.5345)	info on Rv3839/-
Rv0918/-	(cc=0.5206)	info on Rv0918/-
Rv2771c/-	(cc=0.5135)	info on Rv2771c/-
Rv0071/-	(cc=0.4974)	info on Rv0071/-
Rv3788/-	(cc=0.4881)	info on Rv3788/-
Rv3103c/-	(cc=0.4749)	info on Rv3103c/-
Rv1453/-	(cc=0.461)	info on Rv1453/-
Rv0233/nrdB	(cc=0.4576)	info on Rv0233/nrdB

Correlation of Rv0303/- with Rv3839/-

Normalized LFCs for Rv0303/-:
(description and provenance of datasets)

	Rv0303/-	Rv3839/-
Fe_supp_jason_reseq	0.071	0.472
low_pH_jason_reseq	-0.577	0.549
NO_jason_reseq	-0.494	-2.263
B6_jason_reseq	0.857	1.347
MHCII_jason_reseq	-0.077	0.609
Isoniazid02	-0.162	-0.3
Rifampicin4	-0.13	-0.663
Ethambutol3	-0.206	-0.111
Meropenem3	-0.156	-0.047
Vancomycin16	-0.127	-0.302
Rv2680_day32	0.829	1.935
H37Rv_KO_MarP	0.241	-0.087
hypoxia_3wks	0.136	0.845
hypoxia_6wks	0.66	0.731
glycerol	-0.13	0.508
cholesterol	-0.764	-0.179
AJ	-0.343	1.933
Bibs02	-0.65	-0.517
Bibs02c	0.853	0.465
BL6	0.246	0.526
BL6a	0.098	0.703
BXD01	-0.735	0.967
BXD010	-0.357	0.4
BXD011	-0.805	0.465
BXD03	-0.487	1.4
BXD04	-0.092	0.555
BXD05	-0.316	0.772
BXD06	-0.356	0.561
BXD07	-0.369	0.759
BXD08	-1.018	0.434
BXD09	-0.325	0.749
CAST	0.317	1.71
CCcont	-0.969	-0.415
DS01	-0.075	0.922
DS02	0.325	0.914
DS04	0.24	1.138
DS0c	0.239	0.943
GP01	-0.658	0.099
GP02	-1.356	-0.391
GP0c	-0.727	-0.271
NOD	0.436	3.022
NZO	-0.376	1.585
PWK	0.159	0.354
H37Rv_KO_CtpC	-0.116	0.459
H37Rv_KO_CtpD	0.669	0.644
H37Rv_KO_Rv1272	0.418	0.448
H37Rv_KO_SugABC	-1.585	0.955
H37Rv_KO_MbtN	-1.073	0.685
Trans05	-0.511	0.949
macrophage_unactivated	-0.177	0.23
IL1	-0.092	-0.697
Rapamycin	-0.733	-0.104
Tcell	-0.287	-0.274
GMCSF	-0.301	0.359
IFNab	-0.856	1.034
IFNg	-0.083	-0.649
IFNg_GMCSF1	-0.984	0.0
Rv1432_day32	0.31	1.249
Rv1565c_day32	0.028	2.35
secA2_input	0.554	1.371
delta_Rv3594	-0.58	-0.109
delta_Rv3717	-0.312	-0.179
delta_Rv3811	-0.739	-0.086
delta_Rv0954	-0.868	-0.063
PonA1	-0.119	-0.082
EccD1_KO	-0.197	-0.227
EspI_KO	-0.836	-0.924
PE35_KO	-0.744	-0.945
PPE68_KO	-0.733	-1.081
glycerol2	-0.067	-0.073
lignocerate	-0.311	-0.589
oleate	0.024	0.062
phosphatidylcholine	-0.126	-0.265
acetate	-0.603	-0.593
glucAc	-0.315	-0.528
Rv0950ko	0.651	1.677
Rv1096ko	1.095	1.101
Rv3684ko	0.956	1.808
delta_otsA_trehalose	1.464	6.0