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 Rv2332/mez:

update plot	correlation	link to info on gene
Rv3018c/PPE46	(cc=0.6556)	info on Rv3018c/PPE46
Rv2958c/-	(cc=0.6158)	info on Rv2958c/-
Rv3136A/-	(cc=0.5801)	info on Rv3136A/-
Rv1056/-	(cc=0.5729)	info on Rv1056/-
Rv1614/lgt	(cc=0.5638)	info on Rv1614/lgt
Rv0846c/-	(cc=0.551)	info on Rv0846c/-
Rv1182/papA3	(cc=0.5508)	info on Rv1182/papA3
Rv0686/-	(cc=0.5378)	info on Rv0686/-
Rv2517c/-	(cc=0.5354)	info on Rv2517c/-
Rv3784/-	(cc=0.5243)	info on Rv3784/-

Correlation of Rv2332/mez with Rv2958c/-

Normalized LFCs for Rv2332/mez:
(description and provenance of datasets)

	Rv2332/mez	Rv2958c/-
Fe_supp_jason_reseq	0.751	0.218
low_pH_jason_reseq	-0.437	-0.591
NO_jason_reseq	-0.076	-0.412
B6_jason_reseq	0.227	-0.317
MHCII_jason_reseq	0.472	0.082
Isoniazid02	1.672	0.674
Rifampicin4	0.181	0.103
Ethambutol3	0.955	0.818
Meropenem3	0.319	0.367
Vancomycin16	0.424	0.257
Rv2680_day32	0.305	0.459
H37Rv_KO_MarP	0.356	0.464
hypoxia_3wks	0.363	0.016
hypoxia_6wks	0.0	-0.495
glycerol	-0.806	-1.678
cholesterol	-0.336	-0.524
AJ	0.534	0.212
Bibs02	0.246	0.257
Bibs02c	0.091	0.382
BL6	-0.165	-0.448
BL6a	-0.06	0.211
BXD01	-0.059	-0.022
BXD010	-0.243	0.164
BXD011	0.103	0.071
BXD03	-0.4	-0.041
BXD04	0.25	0.179
BXD05	-0.103	0.198
BXD06	-0.041	-0.162
BXD07	0.08	-0.105
BXD08	-0.276	0.008
BXD09	0.225	-0.21
CAST	0.557	0.092
CCcont	-0.365	-0.071
DS01	0.046	0.269
DS02	-0.099	0.263
DS04	0.423	0.548
DS0c	-0.179	0.225
GP01	-0.279	0.408
GP02	-0.658	0.959
GP0c	-1.335	-0.35
NOD	0.747	0.937
NZO	0.552	0.475
PWK	0.364	0.485
H37Rv_KO_CtpC	-0.16	0.377
H37Rv_KO_CtpD	0.103	0.694
H37Rv_KO_Rv1272	0.208	0.96
H37Rv_KO_SugABC	0.444	0.495
H37Rv_KO_MbtN	0.074	0.425
Trans05	0.874	1.058
macrophage_unactivated	-0.3	0.136
IL1	-0.362	-0.744
Rapamycin	-0.752	-0.276
Tcell	-0.609	-0.306
GMCSF	-0.752	-0.177
IFNab	-0.396	-0.414
IFNg	-1.101	-0.179
IFNg_GMCSF1	-0.927	0.277
Rv1432_day32	0.81	0.365
Rv1565c_day32	0.376	0.303
secA2_input	-0.794	-0.524
delta_Rv3594	-0.257	0.366
delta_Rv3717	-0.614	-0.198
delta_Rv3811	-0.228	0.26
delta_Rv0954	-0.497	-0.059
PonA1	0.433	-0.108
EccD1_KO	0.464	0.28
EspI_KO	0.707	0.342
PE35_KO	0.368	0.586
PPE68_KO	0.477	0.394
glycerol2	0.67	0.509
lignocerate	0.664	0.6
oleate	0.543	0.509
phosphatidylcholine	0.647	0.71
acetate	0.221	0.166
glucAc	0.187	0.194
Rv0950ko	-0.555	0.066
Rv1096ko	-0.79	-0.682
Rv3684ko	-1.294	-0.465
delta_otsA_trehalose	-0.092	0.014