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 Rv2562/-

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

	Rv1954A/-	Rv2562/-
Fe_supp_jason_reseq	-0.051	-0.226
low_pH_jason_reseq	-0.878	-0.87
NO_jason_reseq	0.795	-0.386
B6_jason_reseq	-1.023	-1.875
MHCII_jason_reseq	-0.98	-0.528
Isoniazid02	0.162	0.224
Rifampicin4	0.699	0.441
Ethambutol3	-0.047	0.045
Meropenem3	0.236	0.401
Vancomycin16	0.034	0.647
Rv2680_day32	0.267	0.503
H37Rv_KO_MarP	0.679	0.422
hypoxia_3wks	-0.909	-0.471
hypoxia_6wks	-1.04	0.044
glycerol	-1.412	-1.226
cholesterol	-1.382	-0.097
AJ	-0.906	-0.022
Bibs02	-0.631	0.743
Bibs02c	-0.423	-1.088
BL6	1.662	0.954
BL6a	0.082	-0.293
BXD01	-0.17	0.195
BXD010	0.235	0.7
BXD011	0.376	0.647
BXD03	1.021	0.533
BXD04	0.345	0.614
BXD05	1.009	0.613
BXD06	0.464	1.012
BXD07	0.734	0.602
BXD08	0.663	0.675
BXD09	0.683	0.787
CAST	-0.352	0.719
CCcont	-0.105	0.349
DS01	-0.441	-0.44
DS02	-0.199	-0.05
DS04	0.049	0.658
DS0c	-0.137	0.209
GP01	-0.69	0.295
GP02	0.515	0.362
GP0c	-0.193	0.024
NOD	-0.351	1.036
NZO	-1.113	-0.275
PWK	-0.756	0.371
H37Rv_KO_CtpC	-0.545	0.923
H37Rv_KO_CtpD	-0.004	1.291
H37Rv_KO_Rv1272	1.449	0.843
H37Rv_KO_SugABC	-2.115	0.168
H37Rv_KO_MbtN	-1.266	-0.83
Trans05	0.628	1.309
macrophage_unactivated	-0.174	1.446
IL1	-0.065	0.528
Rapamycin	0.7	0.712
Tcell	0.414	0.613
GMCSF	0.121	0.04
IFNab	0.78	-0.339
IFNg	0.123	0.858
IFNg_GMCSF1	1.084	0.575
Rv1432_day32	0.746	-0.332
Rv1565c_day32	-0.839	-0.423
secA2_input	-1.506	-1.929
delta_Rv3594	0.021	0.153
delta_Rv3717	0.461	-0.077
delta_Rv3811	-0.32	0.125
delta_Rv0954	-0.605	0.021
PonA1	-0.433	0.853
EccD1_KO	0.135	0.441
EspI_KO	0.713	0.476
PE35_KO	0.12	0.825
PPE68_KO	0.32	0.723
glycerol2	-0.046	1.247
lignocerate	0.557	1.249
oleate	-0.437	0.943
phosphatidylcholine	0.246	1.424
acetate	0.256	1.077
glucAc	0.797	0.617
Rv0950ko	-0.326	-0.585
Rv1096ko	-0.745	-0.368
Rv3684ko	-1.896	0.079
delta_otsA_trehalose	-1.174	-0.634