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 Rv1954A/-:

update plot	correlation	link to info on gene
Rv1954c/-	(cc=0.6871)	info on Rv1954c/-
Rv2040c/-	(cc=0.5504)	info on Rv2040c/-
Rv2562/-	(cc=0.5253)	info on Rv2562/-
Rv3166c/-	(cc=0.5018)	info on Rv3166c/-
Rv1088/PE9	(cc=0.4774)	info on Rv1088/PE9
Rv1580c/-	(cc=0.4723)	info on Rv1580c/-
Rv1561/vapC11	(cc=0.4606)	info on Rv1561/vapC11
Rv1508A/-	(cc=0.4324)	info on Rv1508A/-
Rv1583c/-	(cc=0.4282)	info on Rv1583c/-
Rv2481c/-	(cc=0.4281)	info on Rv2481c/-

Correlation of Rv1954A/- with Rv1580c/-

Normalized LFCs for Rv1954A/-:
(description and provenance of datasets)

	Rv1954A/-	Rv1580c/-
Fe_supp_jason_reseq	-0.051	-0.401
low_pH_jason_reseq	-0.878	0.146
NO_jason_reseq	0.795	-0.473
B6_jason_reseq	-1.023	-0.826
MHCII_jason_reseq	-0.98	0.775
Isoniazid02	0.162	-0.326
Rifampicin4	0.699	0.116
Ethambutol3	-0.047	-0.322
Meropenem3	0.236	-0.473
Vancomycin16	0.034	0.287
Rv2680_day32	0.267	0.11
H37Rv_KO_MarP	0.679	0.635
hypoxia_3wks	-0.909	-0.897
hypoxia_6wks	-1.04	-0.226
glycerol	-1.412	-2.298
cholesterol	-1.382	-1.444
AJ	-0.906	0.452
Bibs02	-0.631	0.099
Bibs02c	-0.423	-0.132
BL6	1.662	1.101
BL6a	0.082	0.128
BXD01	-0.17	0.242
BXD010	0.235	0.871
BXD011	0.376	0.559
BXD03	1.021	0.28
BXD04	0.345	0.509
BXD05	1.009	1.022
BXD06	0.464	0.42
BXD07	0.734	0.089
BXD08	0.663	-0.12
BXD09	0.683	0.225
CAST	-0.352	-1.114
CCcont	-0.105	0.729
DS01	-0.441	-0.941
DS02	-0.199	0.487
DS04	0.049	1.079
DS0c	-0.137	-0.947
GP01	-0.69	-0.486
GP02	0.515	0.021
GP0c	-0.193	0.313
NOD	-0.351	-1.526
NZO	-1.113	-0.214
PWK	-0.756	0.557
H37Rv_KO_CtpC	-0.545	0.025
H37Rv_KO_CtpD	-0.004	0.852
H37Rv_KO_Rv1272	1.449	0.719
H37Rv_KO_SugABC	-2.115	-1.801
H37Rv_KO_MbtN	-1.266	-1.204
Trans05	0.628	0.629
macrophage_unactivated	-0.174	0.571
IL1	-0.065	0.501
Rapamycin	0.7	1.16
Tcell	0.414	0.795
GMCSF	0.121	-0.034
IFNab	0.78	0.771
IFNg	0.123	0.388
IFNg_GMCSF1	1.084	0.531
Rv1432_day32	0.746	-1.143
Rv1565c_day32	-0.839	1.502
secA2_input	-1.506	0.329
delta_Rv3594	0.021	-0.788
delta_Rv3717	0.461	-1.258
delta_Rv3811	-0.32	-0.522
delta_Rv0954	-0.605	-0.423
PonA1	-0.433	0.027
EccD1_KO	0.135	0.0
EspI_KO	0.713	-0.394
PE35_KO	0.12	0.496
PPE68_KO	0.32	0.71
glycerol2	-0.046	0.149
lignocerate	0.557	0.593
oleate	-0.437	-0.753
phosphatidylcholine	0.246	0.363
acetate	0.256	-0.11
glucAc	0.797	0.193
Rv0950ko	-0.326	0.256
Rv1096ko	-0.745	-0.89
Rv3684ko	-1.896	-0.295
delta_otsA_trehalose	-1.174	-1.07