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 Rv2740/ephG:

update plot	correlation	link to info on gene
Rv3165c/-	(cc=0.4995)	info on Rv3165c/-
Rv2060/-	(cc=0.4512)	info on Rv2060/-
Rv2308/-	(cc=0.4399)	info on Rv2308/-
Rv1218c/-	(cc=0.4285)	info on Rv1218c/-
Rv2040c/-	(cc=0.4014)	info on Rv2040c/-
Rv1954A/-	(cc=0.3991)	info on Rv1954A/-
Rv1353c/-	(cc=0.3983)	info on Rv1353c/-
Rv2408/PE24	(cc=0.3907)	info on Rv2408/PE24
Rv1496/-	(cc=0.3907)	info on Rv1496/-
Rv2252/-	(cc=0.3881)	info on Rv2252/-

Correlation of Rv2740/ephG with Rv1954A/-

Normalized LFCs for Rv2740/ephG:
(description and provenance of datasets)

	Rv2740/ephG	Rv1954A/-
Fe_supp_jason_reseq	0.23	-0.051
low_pH_jason_reseq	-0.579	-0.878
NO_jason_reseq	-0.735	0.795
B6_jason_reseq	-0.318	-1.023
MHCII_jason_reseq	0.109	-0.98
Isoniazid02	-0.389	0.162
Rifampicin4	-0.127	0.699
Ethambutol3	-0.264	-0.047
Meropenem3	-0.299	0.236
Vancomycin16	-0.631	0.034
Rv2680_day32	1.128	0.267
H37Rv_KO_MarP	-0.292	0.679
hypoxia_3wks	-0.67	-0.909
hypoxia_6wks	-0.238	-1.04
glycerol	-0.307	-1.412
cholesterol	-0.285	-1.382
AJ	-0.183	-0.906
Bibs02	-0.585	-0.631
Bibs02c	-0.77	-0.423
BL6	-0.372	1.662
BL6a	0.281	0.082
BXD01	-0.235	-0.17
BXD010	0.365	0.235
BXD011	0.709	0.376
BXD03	0.492	1.021
BXD04	-0.043	0.345
BXD05	0.429	1.009
BXD06	0.072	0.464
BXD07	0.409	0.734
BXD08	0.616	0.663
BXD09	0.427	0.683
CAST	0.327	-0.352
CCcont	-0.113	-0.105
DS01	-1.258	-0.441
DS02	-1.3	-0.199
DS04	0.066	0.049
DS0c	-0.757	-0.137
GP01	0.403	-0.69
GP02	0.014	0.515
GP0c	0.834	-0.193
NOD	-0.135	-0.351
NZO	0.428	-1.113
PWK	-0.675	-0.756
H37Rv_KO_CtpC	-0.598	-0.545
H37Rv_KO_CtpD	0.479	-0.004
H37Rv_KO_Rv1272	0.103	1.449
H37Rv_KO_SugABC	-2.096	-2.115
H37Rv_KO_MbtN	-0.306	-1.266
Trans05	0.053	0.628
macrophage_unactivated	-0.227	-0.174
IL1	0.448	-0.065
Rapamycin	0.672	0.7
Tcell	-0.635	0.414
GMCSF	0.734	0.121
IFNab	0.36	0.78
IFNg	0.222	0.123
IFNg_GMCSF1	-0.544	1.084
Rv1432_day32	-0.327	0.746
Rv1565c_day32	0.826	-0.839
secA2_input	-2.057	-1.506
delta_Rv3594	0.217	0.021
delta_Rv3717	1.121	0.461
delta_Rv3811	-0.311	-0.32
delta_Rv0954	-1.55	-0.605
PonA1	0.187	-0.433
EccD1_KO	1.217	0.135
EspI_KO	0.704	0.713
PE35_KO	0.933	0.12
PPE68_KO	1.094	0.32
glycerol2	0.404	-0.046
lignocerate	0.479	0.557
oleate	-0.713	-0.437
phosphatidylcholine	0.625	0.246
acetate	0.356	0.256
glucAc	0.869	0.797
Rv0950ko	0.241	-0.326
Rv1096ko	0.47	-0.745
Rv3684ko	-0.174	-1.896
delta_otsA_trehalose	0.404	-1.174