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 Rv1088/PE9

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

	Rv1954A/-	Rv1088/PE9
Fe_supp_jason_reseq	-0.051	1.621
low_pH_jason_reseq	-0.878	-2.414
NO_jason_reseq	0.795	-0.108
B6_jason_reseq	-1.023	-0.142
MHCII_jason_reseq	-0.98	-1.374
Isoniazid02	0.162	0.534
Rifampicin4	0.699	1.037
Ethambutol3	-0.047	0.505
Meropenem3	0.236	1.364
Vancomycin16	0.034	0.268
Rv2680_day32	0.267	-3.328
H37Rv_KO_MarP	0.679	-0.277
hypoxia_3wks	-0.909	0.299
hypoxia_6wks	-1.04	0.021
glycerol	-1.412	-2.147
cholesterol	-1.382	-0.961
AJ	-0.906	-0.827
Bibs02	-0.631	0.842
Bibs02c	-0.423	-0.981
BL6	1.662	0.674
BL6a	0.082	1.459
BXD01	-0.17	1.37
BXD010	0.235	1.021
BXD011	0.376	1.285
BXD03	1.021	1.652
BXD04	0.345	0.061
BXD05	1.009	1.745
BXD06	0.464	1.016
BXD07	0.734	0.866
BXD08	0.663	1.823
BXD09	0.683	1.547
CAST	-0.352	-0.445
CCcont	-0.105	0.882
DS01	-0.441	-1.567
DS02	-0.199	0.21
DS04	0.049	-0.316
DS0c	-0.137	-1.439
GP01	-0.69	-1.37
GP02	0.515	-0.065
GP0c	-0.193	0.253
NOD	-0.351	-1.189
NZO	-1.113	0.87
PWK	-0.756	-1.445
H37Rv_KO_CtpC	-0.545	0.971
H37Rv_KO_CtpD	-0.004	0.683
H37Rv_KO_Rv1272	1.449	1.354
H37Rv_KO_SugABC	-2.115	0.606
H37Rv_KO_MbtN	-1.266	-0.659
Trans05	0.628	2.476
macrophage_unactivated	-0.174	0.707
IL1	-0.065	0.406
Rapamycin	0.7	0.663
Tcell	0.414	1.896
GMCSF	0.121	0.446
IFNab	0.78	0.106
IFNg	0.123	0.759
IFNg_GMCSF1	1.084	-0.569
Rv1432_day32	0.746	0.265
Rv1565c_day32	-0.839	0.414
secA2_input	-1.506	-1.772
delta_Rv3594	0.021	-0.278
delta_Rv3717	0.461	0.54
delta_Rv3811	-0.32	0.776
delta_Rv0954	-0.605	-0.631
PonA1	-0.433	-0.248
EccD1_KO	0.135	-0.707
EspI_KO	0.713	0.0
PE35_KO	0.12	-1.683
PPE68_KO	0.32	-1.11
glycerol2	-0.046	0.266
lignocerate	0.557	0.911
oleate	-0.437	-0.588
phosphatidylcholine	0.246	0.585
acetate	0.256	0.198
glucAc	0.797	0.484
Rv0950ko	-0.326	-0.992
Rv1096ko	-0.745	-3.016
Rv3684ko	-1.896	-2.738
delta_otsA_trehalose	-1.174	0.539