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 Rv2429/ahpD:

update plot	correlation	link to info on gene
Rv0713/-	(cc=0.5404)	info on Rv0713/-
Rv1511/gmdA	(cc=0.4924)	info on Rv1511/gmdA
Rv2289/cdh	(cc=0.4917)	info on Rv2289/cdh
Rv2953/-	(cc=0.4832)	info on Rv2953/-
Rv0873/fadE10	(cc=0.4783)	info on Rv0873/fadE10
Rv2954c/-	(cc=0.4693)	info on Rv2954c/-
Rv2399c/cysT	(cc=0.4632)	info on Rv2399c/cysT
Rv3680/-	(cc=0.4458)	info on Rv3680/-
Rv3490/otsA	(cc=0.443)	info on Rv3490/otsA
Rv2284/lipM	(cc=0.4402)	info on Rv2284/lipM

Correlation of Rv2429/ahpD with Rv3680/-

Normalized LFCs for Rv2429/ahpD:
(description and provenance of datasets)

	Rv2429/ahpD	Rv3680/-
Fe_supp_jason_reseq	0.174	1.689
low_pH_jason_reseq	-0.867	1.673
NO_jason_reseq	0.0	0.0
B6_jason_reseq	0.363	0.0
MHCII_jason_reseq	1.557	0.0
Isoniazid02	-4.061	-1.072
Rifampicin4	0.171	-0.474
Ethambutol3	0.32	-0.59
Meropenem3	-0.819	-0.21
Vancomycin16	0.167	-0.464
Rv2680_day32	-0.016	0.0
H37Rv_KO_MarP	0.567	-0.766
hypoxia_3wks	0.311	-0.55
hypoxia_6wks	0.464	-0.288
glycerol	0.178	2.455
cholesterol	0.015	1.612
AJ	0.513	0.0
Bibs02	0.212	1.015
Bibs02c	1.36	1.822
BL6	0.58	0.0
BL6a	1.118	1.812
BXD01	0.56	0.358
BXD010	-0.448	0.128
BXD011	-0.123	1.109
BXD03	0.107	0.75
BXD04	0.418	0.34
BXD05	0.719	0.369
BXD06	0.053	1.035
BXD07	0.822	0.38
BXD08	0.04	0.253
BXD09	-0.044	0.69
CAST	-0.072	0.0
CCcont	0.816	1.765
DS01	0.0	0.83
DS02	0.534	0.217
DS04	-0.37	1.301
DS0c	0.718	0.413
GP01	0.509	0.0
GP02	-1.258	0.0
GP0c	-1.082	0.0
NOD	0.57	0.0
NZO	-0.481	0.0
PWK	0.155	0.0
H37Rv_KO_CtpC	-0.592	0.162
H37Rv_KO_CtpD	0.751	0.445
H37Rv_KO_Rv1272	0.029	0.0
H37Rv_KO_SugABC	0.283	0.768
H37Rv_KO_MbtN	0.401	0.691
Trans05	1.134	0.0
macrophage_unactivated	0.294	0.436
IL1	-1.006	0.0
Rapamycin	0.083	0.0
Tcell	-0.228	0.857
GMCSF	1.014	0.0
IFNab	-0.085	0.0
IFNg	0.732	0.0
IFNg_GMCSF1	0.17	0.0
Rv1432_day32	0.9	0.0
Rv1565c_day32	0.147	0.0
secA2_input	-2.016	-2.069
delta_Rv3594	1.462	1.895
delta_Rv3717	0.132	3.237
delta_Rv3811	1.077	2.787
delta_Rv0954	1.145	0.375
PonA1	0.709	1.599
EccD1_KO	-0.756	0.635
EspI_KO	0.171	0.878
PE35_KO	0.502	0.735
PPE68_KO	0.963	1.245
glycerol2	0.943	-0.193
lignocerate	0.839	-0.168
oleate	0.818	-0.196
phosphatidylcholine	0.796	-0.193
acetate	0.519	0.743
glucAc	0.423	0.462
Rv0950ko	-0.853	-1.9
Rv1096ko	-1.668	-2.111
Rv3684ko	-1.723	-2.663
delta_otsA_trehalose	1.015	0.895