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 Rv1040c/PE8:

update plot	correlation	link to info on gene
Rv2141c/-	(cc=0.5422)	info on Rv2141c/-
Rv3655c/-	(cc=0.5327)	info on Rv3655c/-
Rv3585/radA	(cc=0.5113)	info on Rv3585/radA
Rv2149c/yfiH	(cc=0.4961)	info on Rv2149c/yfiH
Rv2872/vapC43	(cc=0.4961)	info on Rv2872/vapC43
Rv3056/dinP	(cc=0.4883)	info on Rv3056/dinP
Rv1965/yrbE3B	(cc=0.4837)	info on Rv1965/yrbE3B
Rv0650/-	(cc=0.4687)	info on Rv0650/-
Rv3736/-	(cc=0.4636)	info on Rv3736/-
Rv3777/-	(cc=0.4604)	info on Rv3777/-

Correlation of Rv1040c/PE8 with Rv0650/-

Normalized LFCs for Rv1040c/PE8:
(description and provenance of datasets)

	Rv1040c/PE8	Rv0650/-
Fe_supp_jason_reseq	-0.418	-1.301
low_pH_jason_reseq	-1.323	-0.748
NO_jason_reseq	-0.995	-0.772
B6_jason_reseq	-0.239	-0.437
MHCII_jason_reseq	0.017	0.252
Isoniazid02	1.368	0.639
Rifampicin4	0.0	1.481
Ethambutol3	2.203	1.792
Meropenem3	0.519	0.304
Vancomycin16	-0.225	0.735
Rv2680_day32	-1.362	0.326
H37Rv_KO_MarP	0.178	0.446
hypoxia_3wks	-0.108	-0.235
hypoxia_6wks	-0.434	-1.503
glycerol	-0.377	2.342
cholesterol	-0.641	1.387
AJ	0.773	1.168
Bibs02	0.31	0.503
Bibs02c	0.882	1.44
BL6	-1.159	0.63
BL6a	0.768	0.684
BXD01	-0.214	-0.164
BXD010	-0.067	0.486
BXD011	-0.328	-0.383
BXD03	-0.722	-0.73
BXD04	-0.15	-0.692
BXD05	-0.57	-1.163
BXD06	-0.504	-0.37
BXD07	-0.312	-0.042
BXD08	-0.478	0.366
BXD09	0.044	-0.235
CAST	0.365	0.402
CCcont	-0.661	0.913
DS01	0.173	1.738
DS02	0.38	1.47
DS04	-0.564	-0.422
DS0c	0.234	1.466
GP01	0.084	0.919
GP02	-0.734	0.057
GP0c	0.469	0.669
NOD	0.332	0.805
NZO	-0.283	0.308
PWK	0.267	0.627
H37Rv_KO_CtpC	-0.267	-0.752
H37Rv_KO_CtpD	0.813	0.661
H37Rv_KO_Rv1272	0.939	-0.095
H37Rv_KO_SugABC	0.101	0.316
H37Rv_KO_MbtN	-1.64	-2.29
Trans05	-0.423	0.298
macrophage_unactivated	0.568	0.574
IL1	-1.014	2.058
Rapamycin	0.583	0.672
Tcell	-0.111	-0.368
GMCSF	-0.409	0.322
IFNab	0.36	0.846
IFNg	-0.184	0.668
IFNg_GMCSF1	0.405	0.927
Rv1432_day32	0.095	0.692
Rv1565c_day32	0.588	-0.415
secA2_input	1.41	1.669
delta_Rv3594	0.262	-0.463
delta_Rv3717	0.419	0.515
delta_Rv3811	-0.306	-0.076
delta_Rv0954	-0.114	1.26
PonA1	0.743	0.375
EccD1_KO	1.612	1.151
EspI_KO	0.844	0.325
PE35_KO	0.032	-0.814
PPE68_KO	0.544	-0.566
glycerol2	0.489	0.137
lignocerate	0.196	0.788
oleate	0.464	-0.544
phosphatidylcholine	0.576	0.416
acetate	-0.352	-0.115
glucAc	-0.451	0.453
Rv0950ko	0.1	1.493
Rv1096ko	1.056	3.088
Rv3684ko	1.176	3.76
delta_otsA_trehalose	-0.534	-0.197