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 Rv3854c/ethA:

update plot	correlation	link to info on gene
Rv1111c/-	(cc=0.69)	info on Rv1111c/-
Rv0049/-	(cc=0.6401)	info on Rv0049/-
Rv1633/uvrB	(cc=0.6285)	info on Rv1633/uvrB
Rv3818/-	(cc=0.6279)	info on Rv3818/-
Rv0497/-	(cc=0.6185)	info on Rv0497/-
Rv3050c/-	(cc=0.6182)	info on Rv3050c/-
Rv2735c/-	(cc=0.6143)	info on Rv2735c/-
Rv2190c/-	(cc=0.6139)	info on Rv2190c/-
Rv3218/-	(cc=0.6118)	info on Rv3218/-
Rv3125c/PPE49	(cc=0.6093)	info on Rv3125c/PPE49

Correlation of Rv3854c/ethA with Rv1111c/-

Normalized LFCs for Rv3854c/ethA:
(description and provenance of datasets)

	Rv3854c/ethA	Rv1111c/-
Fe_supp_jason_reseq	0.998	1.264
low_pH_jason_reseq	-0.467	-0.413
NO_jason_reseq	0.683	1.945
B6_jason_reseq	-0.283	-0.818
MHCII_jason_reseq	0.123	-0.503
Isoniazid02	-0.387	-0.885
Rifampicin4	-0.382	-2.32
Ethambutol3	-0.039	0.069
Meropenem3	-0.346	0.183
Vancomycin16	-0.767	-3.507
Rv2680_day32	0.22	-1.668
H37Rv_KO_MarP	-1.053	-2.198
hypoxia_3wks	-0.032	0.439
hypoxia_6wks	-0.033	1.685
glycerol	-0.385	-1.398
cholesterol	0.709	0.952
AJ	-0.788	-0.457
Bibs02	0.201	0.694
Bibs02c	-0.092	0.317
BL6	0.606	1.483
BL6a	0.933	0.587
BXD01	0.281	0.552
BXD010	0.77	2.133
BXD011	0.723	0.913
BXD03	1.176	0.934
BXD04	0.639	1.083
BXD05	1.269	2.061
BXD06	1.119	1.355
BXD07	0.804	1.154
BXD08	0.326	0.549
BXD09	0.918	0.848
CAST	-0.247	-0.903
CCcont	0.588	0.802
DS01	0.275	0.075
DS02	0.391	0.035
DS04	0.188	1.003
DS0c	0.016	0.478
GP01	0.561	0.83
GP02	0.572	0.0
GP0c	0.787	1.352
NOD	-0.428	-1.778
NZO	0.272	0.126
PWK	0.203	1.373
H37Rv_KO_CtpC	0.506	0.872
H37Rv_KO_CtpD	1.09	-0.437
H37Rv_KO_Rv1272	1.067	0.469
H37Rv_KO_SugABC	1.875	1.22
H37Rv_KO_MbtN	0.978	2.108
Trans05	0.77	1.251
macrophage_unactivated	0.492	0.988
IL1	0.169	0.131
Rapamycin	0.107	0.491
Tcell	0.277	0.456
GMCSF	0.298	1.299
IFNab	0.257	1.859
IFNg	0.673	0.663
IFNg_GMCSF1	0.355	-0.145
Rv1432_day32	0.454	0.082
Rv1565c_day32	-0.025	0.619
secA2_input	0.288	0.199
delta_Rv3594	0.649	1.103
delta_Rv3717	1.076	1.38
delta_Rv3811	1.147	1.06
delta_Rv0954	0.171	-1.398
PonA1	0.143	-1.316
EccD1_KO	0.253	-0.697
EspI_KO	-0.317	-0.231
PE35_KO	-0.615	-0.753
PPE68_KO	-0.109	-0.442
glycerol2	-0.493	-0.398
lignocerate	-0.235	-0.681
oleate	-0.179	-0.403
phosphatidylcholine	-0.43	-1.008
acetate	-0.321	-0.086
glucAc	-0.429	-0.578
Rv0950ko	0.639	-0.142
Rv1096ko	0.274	0.651
Rv3684ko	0.874	-0.206
delta_otsA_trehalose	-0.014	-0.474