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 Rv2880c/-

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

	Rv3451/cut3	Rv2880c/-
Fe_supp_jason_reseq	0.147	-0.338
low_pH_jason_reseq	-0.683	-0.813
NO_jason_reseq	0.326	0.512
B6_jason_reseq	0.145	0.677
MHCII_jason_reseq	0.496	0.254
Isoniazid02	-0.822	0.058
Rifampicin4	0.13	0.791
Ethambutol3	-0.68	0.495
Meropenem3	-0.811	-0.01
Vancomycin16	-0.594	0.615
Rv2680_day32	0.388	-0.55
H37Rv_KO_MarP	0.433	0.065
hypoxia_3wks	0.159	-0.299
hypoxia_6wks	-0.76	-1.002
glycerol	0.451	-0.101
cholesterol	0.083	-0.136
AJ	0.37	0.168
Bibs02	0.997	0.87
Bibs02c	0.574	0.915
BL6	0.049	0.319
BL6a	-0.022	0.178
BXD01	-0.2	-0.144
BXD010	-0.432	0.043
BXD011	-0.35	-0.47
BXD03	0.015	0.121
BXD04	-0.316	-0.023
BXD05	-0.156	0.514
BXD06	-0.398	-0.332
BXD07	0.144	0.328
BXD08	-0.568	0.133
BXD09	-0.239	0.187
CAST	-0.017	0.11
CCcont	-0.945	-0.302
DS01	0.39	0.392
DS02	-0.361	0.469
DS04	0.344	0.937
DS0c	0.13	0.104
GP01	0.354	0.351
GP02	-0.031	-0.802
GP0c	-0.2	-0.251
NOD	0.547	-0.138
NZO	-0.022	0.279
PWK	0.318	0.418
H37Rv_KO_CtpC	-0.162	-0.062
H37Rv_KO_CtpD	0.53	0.341
H37Rv_KO_Rv1272	-0.793	-0.253
H37Rv_KO_SugABC	-0.052	0.362
H37Rv_KO_MbtN	-0.793	-0.839
Trans05	-0.58	0.25
macrophage_unactivated	-0.294	-0.17
IL1	-0.101	0.578
Rapamycin	0.509	0.16
Tcell	-0.89	-0.381
GMCSF	0.554	0.285
IFNab	-0.07	0.048
IFNg	-0.315	0.289
IFNg_GMCSF1	-0.273	0.867
Rv1432_day32	0.253	0.997
Rv1565c_day32	-1.115	0.27
secA2_input	-0.128	0.088
delta_Rv3594	-0.62	-1.169
delta_Rv3717	-0.526	-1.277
delta_Rv3811	-1.112	-1.097
delta_Rv0954	0.08	-1.151
PonA1	-0.075	-0.733
EccD1_KO	0.332	0.115
EspI_KO	0.511	0.753
PE35_KO	0.0	0.907
PPE68_KO	0.246	0.653
glycerol2	-0.254	0.179
lignocerate	-0.684	-0.018
oleate	0.5	0.252
phosphatidylcholine	-0.153	0.081
acetate	-0.72	-0.434
glucAc	-1.146	-0.54
Rv0950ko	0.087	0.757
Rv1096ko	0.069	0.072
Rv3684ko	-0.193	0.0
delta_otsA_trehalose	0.731	0.753