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 Rv0049/-

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

	Rv3854c/ethA	Rv0049/-
Fe_supp_jason_reseq	0.998	0.404
low_pH_jason_reseq	-0.467	-0.361
NO_jason_reseq	0.683	2.237
B6_jason_reseq	-0.283	2.761
MHCII_jason_reseq	0.123	1.686
Isoniazid02	-0.387	-4.265
Rifampicin4	-0.382	-2.889
Ethambutol3	-0.039	-4.182
Meropenem3	-0.346	-1.01
Vancomycin16	-0.767	-6.0
Rv2680_day32	0.22	-1.252
H37Rv_KO_MarP	-1.053	-5.444
hypoxia_3wks	-0.032	-0.546
hypoxia_6wks	-0.033	-1.334
glycerol	-0.385	0.774
cholesterol	0.709	1.774
AJ	-0.788	0.889
Bibs02	0.201	-2.229
Bibs02c	-0.092	-0.308
BL6	0.606	1.028
BL6a	0.933	2.627
BXD01	0.281	2.217
BXD010	0.77	2.728
BXD011	0.723	4.652
BXD03	1.176	3.087
BXD04	0.639	2.028
BXD05	1.269	3.906
BXD06	1.119	4.436
BXD07	0.804	4.021
BXD08	0.326	2.172
BXD09	0.918	2.471
CAST	-0.247	-1.203
CCcont	0.588	2.649
DS01	0.275	-1.921
DS02	0.391	-2.774
DS04	0.188	0.575
DS0c	0.016	-2.211
GP01	0.561	1.773
GP02	0.572	2.935
GP0c	0.787	3.495
NOD	-0.428	-1.515
NZO	0.272	1.376
PWK	0.203	3.436
H37Rv_KO_CtpC	0.506	1.75
H37Rv_KO_CtpD	1.09	-1.411
H37Rv_KO_Rv1272	1.067	2.554
H37Rv_KO_SugABC	1.875	2.361
H37Rv_KO_MbtN	0.978	4.289
Trans05	0.77	1.424
macrophage_unactivated	0.492	0.268
IL1	0.169	1.092
Rapamycin	0.107	-0.42
Tcell	0.277	2.9
GMCSF	0.298	-2.044
IFNab	0.257	-1.811
IFNg	0.673	0.043
IFNg_GMCSF1	0.355	-0.949
Rv1432_day32	0.454	4.133
Rv1565c_day32	-0.025	0.218
secA2_input	0.288	2.224
delta_Rv3594	0.649	6.0
delta_Rv3717	1.076	6.0
delta_Rv3811	1.147	5.737
delta_Rv0954	0.171	4.229
PonA1	0.143	1.526
EccD1_KO	0.253	-0.763
EspI_KO	-0.317	-0.257
PE35_KO	-0.615	-1.062
PPE68_KO	-0.109	0.47
glycerol2	-0.493	0.227
lignocerate	-0.235	-1.453
oleate	-0.179	-1.11
phosphatidylcholine	-0.43	-1.426
acetate	-0.321	0.347
glucAc	-0.429	0.216
Rv0950ko	0.639	-0.461
Rv1096ko	0.274	0.308
Rv3684ko	0.874	1.618
delta_otsA_trehalose	-0.014	-0.75