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 Rv2040c/-:

update plot	correlation	link to info on gene
Rv2274c/mazF8	(cc=0.5681)	info on Rv2274c/mazF8
Rv1954A/-	(cc=0.5504)	info on Rv1954A/-
Rv1430/PE16	(cc=0.5072)	info on Rv1430/PE16
Rv1980c/mpt64	(cc=0.5032)	info on Rv1980c/mpt64
Rv1561/vapC11	(cc=0.5004)	info on Rv1561/vapC11
Rv2500c/fadE19	(cc=0.4949)	info on Rv2500c/fadE19
Rv1526c/-	(cc=0.4938)	info on Rv1526c/-
Rv3669/-	(cc=0.4922)	info on Rv3669/-
Rv2481c/-	(cc=0.4885)	info on Rv2481c/-
Rv1896c/-	(cc=0.4875)	info on Rv1896c/-

Correlation of Rv2040c/- with Rv1561/vapC11

Normalized LFCs for Rv2040c/-:
(description and provenance of datasets)

	Rv2040c/-	Rv1561/vapC11
Fe_supp_jason_reseq	0.032	-0.437
low_pH_jason_reseq	0.291	-0.097
NO_jason_reseq	-0.399	-0.123
B6_jason_reseq	-0.415	-2.194
MHCII_jason_reseq	-1.451	-2.172
Isoniazid02	-0.255	0.183
Rifampicin4	0.252	0.829
Ethambutol3	-0.27	3.934
Meropenem3	-0.266	0.341
Vancomycin16	0.247	0.923
Rv2680_day32	0.687	0.775
H37Rv_KO_MarP	-0.052	0.358
hypoxia_3wks	0.467	0.303
hypoxia_6wks	-0.065	0.309
glycerol	-0.23	-0.592
cholesterol	-0.378	-0.847
AJ	0.513	-0.101
Bibs02	-2.245	0.57
Bibs02c	-1.391	-0.444
BL6	1.183	1.315
BL6a	-0.03	1.538
BXD01	0.84	0.998
BXD010	0.656	1.712
BXD011	2.53	2.321
BXD03	0.755	2.179
BXD04	0.091	1.765
BXD05	0.598	2.034
BXD06	0.328	1.128
BXD07	0.042	1.8
BXD08	0.118	1.92
BXD09	0.87	2.109
CAST	-0.425	-0.612
CCcont	1.059	1.704
DS01	-1.131	-0.38
DS02	-0.792	-1.115
DS04	-0.468	-0.462
DS0c	-0.247	-0.699
GP01	-0.601	0.275
GP02	-1.109	-0.871
GP0c	-0.865	0.425
NOD	0.76	0.475
NZO	-0.727	0.202
PWK	0.06	-0.22
H37Rv_KO_CtpC	0.567	-0.145
H37Rv_KO_CtpD	0.039	1.481
H37Rv_KO_Rv1272	1.84	0.059
H37Rv_KO_SugABC	-0.918	-0.022
H37Rv_KO_MbtN	-0.421	-0.565
Trans05	1.52	1.582
macrophage_unactivated	0.325	0.085
IL1	0.089	0.528
Rapamycin	-0.046	0.424
Tcell	0.147	0.782
GMCSF	0.729	1.365
IFNab	0.091	0.263
IFNg	-0.385	0.935
IFNg_GMCSF1	0.826	0.38
Rv1432_day32	-0.415	-1.304
Rv1565c_day32	-0.584	-0.393
secA2_input	-2.616	0.235
delta_Rv3594	0.352	1.762
delta_Rv3717	0.044	1.197
delta_Rv3811	0.696	1.389
delta_Rv0954	-0.439	1.797
PonA1	0.212	-0.076
EccD1_KO	0.605	-0.487
EspI_KO	0.727	0.585
PE35_KO	1.164	1.467
PPE68_KO	1.072	1.181
glycerol2	-0.273	0.429
lignocerate	0.012	0.793
oleate	-0.597	-0.089
phosphatidylcholine	0.193	0.84
acetate	-0.032	1.405
glucAc	0.105	1.081
Rv0950ko	-0.645	-1.263
Rv1096ko	-1.23	0.039
Rv3684ko	-2.021	-1.49
delta_otsA_trehalose	-0.103	0.441