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 Rv1583c/-

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

	Rv1954A/-	Rv1583c/-
Fe_supp_jason_reseq	-0.051	0.515
low_pH_jason_reseq	-0.878	1.549
NO_jason_reseq	0.795	0.832
B6_jason_reseq	-1.023	-2.401
MHCII_jason_reseq	-0.98	-1.772
Isoniazid02	0.162	0.789
Rifampicin4	0.699	1.18
Ethambutol3	-0.047	0.676
Meropenem3	0.236	-0.246
Vancomycin16	0.034	0.324
Rv2680_day32	0.267	-1.26
H37Rv_KO_MarP	0.679	0.107
hypoxia_3wks	-0.909	-0.977
hypoxia_6wks	-1.04	0.672
glycerol	-1.412	0.0
cholesterol	-1.382	-0.46
AJ	-0.906	-1.071
Bibs02	-0.631	-0.991
Bibs02c	-0.423	0.743
BL6	1.662	3.191
BL6a	0.082	1.936
BXD01	-0.17	1.298
BXD010	0.235	1.592
BXD011	0.376	2.091
BXD03	1.021	2.033
BXD04	0.345	1.324
BXD05	1.009	1.302
BXD06	0.464	1.925
BXD07	0.734	2.073
BXD08	0.663	1.806
BXD09	0.683	1.625
CAST	-0.352	0.736
CCcont	-0.105	2.504
DS01	-0.441	0.962
DS02	-0.199	0.054
DS04	0.049	1.612
DS0c	-0.137	-1.798
GP01	-0.69	1.857
GP02	0.515	1.808
GP0c	-0.193	2.036
NOD	-0.351	0.797
NZO	-1.113	0.673
PWK	-0.756	-0.905
H37Rv_KO_CtpC	-0.545	1.404
H37Rv_KO_CtpD	-0.004	3.186
H37Rv_KO_Rv1272	1.449	0.795
H37Rv_KO_SugABC	-2.115	1.851
H37Rv_KO_MbtN	-1.266	0.987
Trans05	0.628	1.01
macrophage_unactivated	-0.174	0.559
IL1	-0.065	0.0
Rapamycin	0.7	0.862
Tcell	0.414	0.469
GMCSF	0.121	0.805
IFNab	0.78	-0.115
IFNg	0.123	1.219
IFNg_GMCSF1	1.084	0.537
Rv1432_day32	0.746	1.454
Rv1565c_day32	-0.839	0.526
secA2_input	-1.506	-0.227
delta_Rv3594	0.021	-1.637
delta_Rv3717	0.461	-0.945
delta_Rv3811	-0.32	-0.448
delta_Rv0954	-0.605	-0.472
PonA1	-0.433	-0.396
EccD1_KO	0.135	2.088
EspI_KO	0.713	1.141
PE35_KO	0.12	1.523
PPE68_KO	0.32	1.638
glycerol2	-0.046	1.813
lignocerate	0.557	2.527
oleate	-0.437	-2.562
phosphatidylcholine	0.246	1.909
acetate	0.256	2.818
glucAc	0.797	2.145
Rv0950ko	-0.326	0.826
Rv1096ko	-0.745	-1.197
Rv3684ko	-1.896	-1.251
delta_otsA_trehalose	-1.174	0.204