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 Rv3451/cut3:

update plot	correlation	link to info on gene
Rv2880c/-	(cc=0.4828)	info on Rv2880c/-
Rv3504/fadE26	(cc=0.4808)	info on Rv3504/fadE26
Rv2306A/-	(cc=0.4693)	info on Rv2306A/-
Rv2658c/-	(cc=0.4631)	info on Rv2658c/-
Rv2628/-	(cc=0.4501)	info on Rv2628/-
Rv2679/echA15	(cc=0.4496)	info on Rv2679/echA15
Rv0978c/PE_PGRS17	(cc=0.4427)	info on Rv0978c/PE_PGRS17
Rv1670/-	(cc=0.4423)	info on Rv1670/-
Rv0968/-	(cc=0.4364)	info on Rv0968/-
Rv0073/-	(cc=0.4339)	info on Rv0073/-

Correlation of Rv3451/cut3 with Rv2658c/-

Normalized LFCs for Rv3451/cut3:
(description and provenance of datasets)

	Rv3451/cut3	Rv2658c/-
Fe_supp_jason_reseq	0.147	0.387
low_pH_jason_reseq	-0.683	-0.974
NO_jason_reseq	0.326	0.0
B6_jason_reseq	0.145	0.034
MHCII_jason_reseq	0.496	0.572
Isoniazid02	-0.822	-0.778
Rifampicin4	0.13	0.311
Ethambutol3	-0.68	-0.143
Meropenem3	-0.811	-1.622
Vancomycin16	-0.594	-1.059
Rv2680_day32	0.388	-0.294
H37Rv_KO_MarP	0.433	0.78
hypoxia_3wks	0.159	0.279
hypoxia_6wks	-0.76	-0.186
glycerol	0.451	0.265
cholesterol	0.083	0.041
AJ	0.37	-0.655
Bibs02	0.997	0.229
Bibs02c	0.574	0.391
BL6	0.049	-0.702
BL6a	-0.022	0.564
BXD01	-0.2	-0.257
BXD010	-0.432	-0.135
BXD011	-0.35	-0.076
BXD03	0.015	0.005
BXD04	-0.316	-0.339
BXD05	-0.156	0.775
BXD06	-0.398	-0.034
BXD07	0.144	0.344
BXD08	-0.568	-0.109
BXD09	-0.239	0.098
CAST	-0.017	0.444
CCcont	-0.945	-0.182
DS01	0.39	0.05
DS02	-0.361	0.307
DS04	0.344	-0.197
DS0c	0.13	0.732
GP01	0.354	-0.697
GP02	-0.031	-0.467
GP0c	-0.2	-0.551
NOD	0.547	0.664
NZO	-0.022	0.118
PWK	0.318	0.448
H37Rv_KO_CtpC	-0.162	-0.272
H37Rv_KO_CtpD	0.53	0.798
H37Rv_KO_Rv1272	-0.793	0.35
H37Rv_KO_SugABC	-0.052	0.476
H37Rv_KO_MbtN	-0.793	0.685
Trans05	-0.58	0.346
macrophage_unactivated	-0.294	0.309
IL1	-0.101	0.653
Rapamycin	0.509	0.715
Tcell	-0.89	-0.101
GMCSF	0.554	0.512
IFNab	-0.07	0.435
IFNg	-0.315	0.446
IFNg_GMCSF1	-0.273	0.248
Rv1432_day32	0.253	0.037
Rv1565c_day32	-1.115	0.125
secA2_input	-0.128	-0.254
delta_Rv3594	-0.62	-0.052
delta_Rv3717	-0.526	-0.551
delta_Rv3811	-1.112	-0.425
delta_Rv0954	0.08	0.133
PonA1	-0.075	-0.97
EccD1_KO	0.332	0.089
EspI_KO	0.511	0.893
PE35_KO	0.0	0.939
PPE68_KO	0.246	0.189
glycerol2	-0.254	-0.472
lignocerate	-0.684	-0.756
oleate	0.5	0.191
phosphatidylcholine	-0.153	-0.282
acetate	-0.72	-0.233
glucAc	-1.146	-0.879
Rv0950ko	0.087	0.027
Rv1096ko	0.069	-0.784
Rv3684ko	-0.193	-0.802
delta_otsA_trehalose	0.731	1.711