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 Rv1896c/-

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

	Rv2040c/-	Rv1896c/-
Fe_supp_jason_reseq	0.032	0.508
low_pH_jason_reseq	0.291	-0.095
NO_jason_reseq	-0.399	0.845
B6_jason_reseq	-0.415	0.03
MHCII_jason_reseq	-1.451	0.458
Isoniazid02	-0.255	-0.78
Rifampicin4	0.252	-0.068
Ethambutol3	-0.27	0.512
Meropenem3	-0.266	-0.167
Vancomycin16	0.247	0.13
Rv2680_day32	0.687	0.736
H37Rv_KO_MarP	-0.052	-0.042
hypoxia_3wks	0.467	0.096
hypoxia_6wks	-0.065	-0.326
glycerol	-0.23	-0.177
cholesterol	-0.378	-0.141
AJ	0.513	0.259
Bibs02	-2.245	0.389
Bibs02c	-1.391	-0.364
BL6	1.183	0.701
BL6a	-0.03	0.528
BXD01	0.84	0.043
BXD010	0.656	0.718
BXD011	2.53	0.758
BXD03	0.755	0.162
BXD04	0.091	0.346
BXD05	0.598	0.991
BXD06	0.328	0.701
BXD07	0.042	0.36
BXD08	0.118	0.178
BXD09	0.87	0.0
CAST	-0.425	-0.591
CCcont	1.059	0.348
DS01	-1.131	-0.144
DS02	-0.792	-0.055
DS04	-0.468	0.555
DS0c	-0.247	-0.377
GP01	-0.601	0.647
GP02	-1.109	-0.941
GP0c	-0.865	0.011
NOD	0.76	0.182
NZO	-0.727	-0.175
PWK	0.06	0.377
H37Rv_KO_CtpC	0.567	0.535
H37Rv_KO_CtpD	0.039	1.04
H37Rv_KO_Rv1272	1.84	1.069
H37Rv_KO_SugABC	-0.918	0.579
H37Rv_KO_MbtN	-0.421	1.0
Trans05	1.52	0.666
macrophage_unactivated	0.325	0.088
IL1	0.089	0.24
Rapamycin	-0.046	0.427
Tcell	0.147	-0.528
GMCSF	0.729	0.673
IFNab	0.091	-0.26
IFNg	-0.385	0.457
IFNg_GMCSF1	0.826	0.399
Rv1432_day32	-0.415	-0.068
Rv1565c_day32	-0.584	0.659
secA2_input	-2.616	-0.894
delta_Rv3594	0.352	0.228
delta_Rv3717	0.044	-0.108
delta_Rv3811	0.696	0.12
delta_Rv0954	-0.439	0.252
PonA1	0.212	-0.165
EccD1_KO	0.605	1.098
EspI_KO	0.727	0.311
PE35_KO	1.164	1.091
PPE68_KO	1.072	1.286
glycerol2	-0.273	0.213
lignocerate	0.012	0.776
oleate	-0.597	-0.552
phosphatidylcholine	0.193	0.287
acetate	-0.032	0.74
glucAc	0.105	0.685
Rv0950ko	-0.645	0.169
Rv1096ko	-1.23	-0.265
Rv3684ko	-2.021	-0.56
delta_otsA_trehalose	-0.103	-0.533