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 Rv1245c/-:

update plot	correlation	link to info on gene
Rv2088/pknJ	(cc=0.4545)	info on Rv2088/pknJ
Rv0731c/-	(cc=0.4479)	info on Rv0731c/-
Rv1831/-	(cc=0.4248)	info on Rv1831/-
Rv2770c/PPE44	(cc=0.4242)	info on Rv2770c/PPE44
Rv2695/-	(cc=0.418)	info on Rv2695/-
Rv0576/-	(cc=0.4057)	info on Rv0576/-
Rv2495c/bkdC	(cc=0.4046)	info on Rv2495c/bkdC
Rv3521/-	(cc=0.4045)	info on Rv3521/-
Rv2618/-	(cc=0.3913)	info on Rv2618/-
Rv3268/-	(cc=0.3895)	info on Rv3268/-

Correlation of Rv1245c/- with Rv2618/-

Normalized LFCs for Rv1245c/-:
(description and provenance of datasets)

	Rv1245c/-	Rv2618/-
Fe_supp_jason_reseq	-0.677	-1.361
low_pH_jason_reseq	-0.534	0.0
NO_jason_reseq	-0.084	-1.097
B6_jason_reseq	-1.086	-1.279
MHCII_jason_reseq	-0.021	0.397
Isoniazid02	-0.386	0.934
Rifampicin4	0.314	0.401
Ethambutol3	0.241	0.67
Meropenem3	0.183	0.791
Vancomycin16	-0.082	0.143
Rv2680_day32	-0.198	0.701
H37Rv_KO_MarP	-0.056	0.128
hypoxia_3wks	0.12	2.277
hypoxia_6wks	0.585	3.328
glycerol	-0.051	-0.379
cholesterol	-0.101	0.331
AJ	-0.203	-0.308
Bibs02	-0.886	0.784
Bibs02c	0.53	0.388
BL6	-0.478	0.68
BL6a	0.352	0.626
BXD01	-0.253	1.019
BXD010	-0.414	0.567
BXD011	-0.369	1.197
BXD03	-0.501	0.402
BXD04	0.764	1.162
BXD05	-0.012	1.236
BXD06	-0.081	1.161
BXD07	-0.401	0.948
BXD08	1.002	0.939
BXD09	-0.36	0.737
CAST	-0.245	-0.187
CCcont	-0.305	0.534
DS01	0.453	0.364
DS02	-0.211	1.078
DS04	1.19	1.072
DS0c	0.141	0.877
GP01	0.677	0.874
GP02	1.268	-0.237
GP0c	0.388	0.624
NOD	-0.303	-0.285
NZO	-0.533	-0.639
PWK	-0.421	0.185
H37Rv_KO_CtpC	0.368	-0.285
H37Rv_KO_CtpD	0.321	0.535
H37Rv_KO_Rv1272	0.179	-0.412
H37Rv_KO_SugABC	0.017	-0.723
H37Rv_KO_MbtN	-0.179	0.293
Trans05	0.777	-0.158
macrophage_unactivated	0.218	0.59
IL1	0.178	0.543
Rapamycin	0.184	-0.448
Tcell	-0.453	0.472
GMCSF	0.235	0.18
IFNab	0.121	1.515
IFNg	0.08	-0.013
IFNg_GMCSF1	0.707	0.145
Rv1432_day32	0.155	1.461
Rv1565c_day32	-1.632	-1.109
secA2_input	-0.798	0.013
delta_Rv3594	0.106	0.684
delta_Rv3717	0.273	0.987
delta_Rv3811	0.0	0.58
delta_Rv0954	-0.047	0.752
PonA1	0.285	0.713
EccD1_KO	0.668	0.48
EspI_KO	-0.068	0.288
PE35_KO	0.306	-0.02
PPE68_KO	-0.32	-0.23
glycerol2	0.06	1.9
lignocerate	-0.457	-1.29
oleate	0.411	1.418
phosphatidylcholine	-0.139	-1.172
acetate	-0.426	0.0
glucAc	-0.459	-0.333
Rv0950ko	0.063	0.308
Rv1096ko	0.0	0.0
Rv3684ko	0.233	-0.406
delta_otsA_trehalose	-1.386	-1.145