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 Rv3479/-:

update plot	correlation	link to info on gene
Rv3478/PPE60	(cc=0.5427)	info on Rv3478/PPE60
Rv3136A/-	(cc=0.5164)	info on Rv3136A/-
Rv2623/TB31.7	(cc=0.5071)	info on Rv2623/TB31.7
Rv1803c/PE_PGRS32	(cc=0.5045)	info on Rv1803c/PE_PGRS32
Rv0107c/ctpI	(cc=0.4478)	info on Rv0107c/ctpI
Rv1965/yrbE3B	(cc=0.443)	info on Rv1965/yrbE3B
Rv3060c/-	(cc=0.44)	info on Rv3060c/-
Rv2955c/-	(cc=0.4372)	info on Rv2955c/-
Rv0368c/-	(cc=0.4283)	info on Rv0368c/-
Rv3367/PE_PGRS51	(cc=0.4214)	info on Rv3367/PE_PGRS51

Correlation of Rv3479/- with Rv0107c/ctpI

Normalized LFCs for Rv3479/-:
(description and provenance of datasets)

	Rv3479/-	Rv0107c/ctpI
Fe_supp_jason_reseq	-0.426	0.148
low_pH_jason_reseq	-0.544	0.577
NO_jason_reseq	0.173	-0.053
B6_jason_reseq	0.097	0.902
MHCII_jason_reseq	0.155	0.669
Isoniazid02	0.955	-0.118
Rifampicin4	-0.428	0.325
Ethambutol3	1.175	0.451
Meropenem3	1.544	0.229
Vancomycin16	-0.419	0.241
Rv2680_day32	1.463	0.669
H37Rv_KO_MarP	0.374	0.089
hypoxia_3wks	-1.372	-0.395
hypoxia_6wks	-0.591	0.0
glycerol	0.212	0.24
cholesterol	-0.55	0.257
AJ	0.398	0.235
Bibs02	-0.658	0.427
Bibs02c	-0.596	-0.168
BL6	0.051	0.047
BL6a	-0.294	-0.244
BXD01	-0.009	0.0
BXD010	-0.15	-0.103
BXD011	-0.082	-0.257
BXD03	-0.168	-0.053
BXD04	0.357	0.023
BXD05	0.175	0.013
BXD06	-0.126	-0.384
BXD07	-0.119	0.026
BXD08	-0.241	-0.026
BXD09	0.0	-0.027
CAST	0.475	-0.068
CCcont	-0.118	0.24
DS01	-0.37	0.281
DS02	-0.046	0.421
DS04	-0.197	0.639
DS0c	-0.091	0.181
GP01	-0.071	-0.079
GP02	0.045	-0.076
GP0c	-0.765	-0.608
NOD	0.016	0.267
NZO	0.478	1.347
PWK	0.371	0.129
H37Rv_KO_CtpC	-0.294	-0.552
H37Rv_KO_CtpD	0.109	0.408
H37Rv_KO_Rv1272	-0.73	-1.165
H37Rv_KO_SugABC	0.17	0.574
H37Rv_KO_MbtN	0.594	0.217
Trans05	-0.055	-0.311
macrophage_unactivated	-0.278	-0.038
IL1	0.062	0.036
Rapamycin	-0.132	-0.077
Tcell	-0.593	-0.834
GMCSF	0.219	0.372
IFNab	-0.372	0.493
IFNg	0.056	0.192
IFNg_GMCSF1	-0.277	0.299
Rv1432_day32	2.477	0.714
Rv1565c_day32	0.603	0.408
secA2_input	0.33	0.285
delta_Rv3594	-0.106	0.031
delta_Rv3717	-0.064	0.097
delta_Rv3811	0.073	0.196
delta_Rv0954	0.318	0.39
PonA1	0.701	0.421
EccD1_KO	0.918	0.22
EspI_KO	0.91	0.419
PE35_KO	1.114	0.563
PPE68_KO	0.675	0.214
glycerol2	0.202	0.625
lignocerate	0.25	0.798
oleate	-0.457	0.051
phosphatidylcholine	-0.14	0.451
acetate	-0.19	0.559
glucAc	0.096	0.653
Rv0950ko	-0.621	-0.262
Rv1096ko	0.434	0.151
Rv3684ko	-0.524	-0.056
delta_otsA_trehalose	-0.083	0.032