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 Rv1430/PE16

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

	Rv2040c/-	Rv1430/PE16
Fe_supp_jason_reseq	0.032	0.302
low_pH_jason_reseq	0.291	-0.125
NO_jason_reseq	-0.399	0.113
B6_jason_reseq	-0.415	-0.171
MHCII_jason_reseq	-1.451	0.083
Isoniazid02	-0.255	-0.851
Rifampicin4	0.252	-1.099
Ethambutol3	-0.27	-0.067
Meropenem3	-0.266	-0.836
Vancomycin16	0.247	-0.74
Rv2680_day32	0.687	-0.018
H37Rv_KO_MarP	-0.052	-0.229
hypoxia_3wks	0.467	0.69
hypoxia_6wks	-0.065	0.226
glycerol	-0.23	0.161
cholesterol	-0.378	0.209
AJ	0.513	0.45
Bibs02	-2.245	-0.183
Bibs02c	-1.391	-0.838
BL6	1.183	1.033
BL6a	-0.03	0.306
BXD01	0.84	0.813
BXD010	0.656	0.928
BXD011	2.53	0.727
BXD03	0.755	1.269
BXD04	0.091	1.496
BXD05	0.598	1.203
BXD06	0.328	0.868
BXD07	0.042	1.106
BXD08	0.118	1.299
BXD09	0.87	0.941
CAST	-0.425	0.47
CCcont	1.059	0.585
DS01	-1.131	0.216
DS02	-0.792	-0.52
DS04	-0.468	-0.046
DS0c	-0.247	-0.363
GP01	-0.601	-1.111
GP02	-1.109	0.305
GP0c	-0.865	-0.218
NOD	0.76	0.727
NZO	-0.727	-0.225
PWK	0.06	0.179
H37Rv_KO_CtpC	0.567	0.47
H37Rv_KO_CtpD	0.039	1.086
H37Rv_KO_Rv1272	1.84	0.988
H37Rv_KO_SugABC	-0.918	-0.565
H37Rv_KO_MbtN	-0.421	0.0
Trans05	1.52	1.093
macrophage_unactivated	0.325	0.764
IL1	0.089	0.667
Rapamycin	-0.046	0.509
Tcell	0.147	0.512
GMCSF	0.729	0.415
IFNab	0.091	0.366
IFNg	-0.385	0.128
IFNg_GMCSF1	0.826	0.352
Rv1432_day32	-0.415	0.216
Rv1565c_day32	-0.584	0.398
secA2_input	-2.616	-1.49
delta_Rv3594	0.352	0.324
delta_Rv3717	0.044	-0.503
delta_Rv3811	0.696	-0.265
delta_Rv0954	-0.439	0.512
PonA1	0.212	0.182
EccD1_KO	0.605	0.635
EspI_KO	0.727	1.035
PE35_KO	1.164	0.356
PPE68_KO	1.072	0.435
glycerol2	-0.273	0.163
lignocerate	0.012	-0.105
oleate	-0.597	0.79
phosphatidylcholine	0.193	0.38
acetate	-0.032	-0.16
glucAc	0.105	-0.879
Rv0950ko	-0.645	0.407
Rv1096ko	-1.23	0.446
Rv3684ko	-2.021	0.092
delta_otsA_trehalose	-0.103	-0.383