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 Rv2954c/-

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

	Rv2429/ahpD	Rv2954c/-
Fe_supp_jason_reseq	0.174	0.18
low_pH_jason_reseq	-0.867	-1.161
NO_jason_reseq	0.0	-0.412
B6_jason_reseq	0.363	-0.145
MHCII_jason_reseq	1.557	-0.033
Isoniazid02	-4.061	-0.723
Rifampicin4	0.171	0.241
Ethambutol3	0.32	-0.405
Meropenem3	-0.819	-0.68
Vancomycin16	0.167	-0.17
Rv2680_day32	-0.016	0.205
H37Rv_KO_MarP	0.567	-0.069
hypoxia_3wks	0.311	-0.104
hypoxia_6wks	0.464	0.052
glycerol	0.178	0.439
cholesterol	0.015	-0.029
AJ	0.513	-0.123
Bibs02	0.212	-0.449
Bibs02c	1.36	-0.631
BL6	0.58	0.216
BL6a	1.118	0.263
BXD01	0.56	0.268
BXD010	-0.448	0.447
BXD011	-0.123	0.468
BXD03	0.107	0.66
BXD04	0.418	0.546
BXD05	0.719	0.644
BXD06	0.053	0.056
BXD07	0.822	0.194
BXD08	0.04	-0.063
BXD09	-0.044	0.494
CAST	-0.072	-0.053
CCcont	0.816	0.171
DS01	0.0	-0.062
DS02	0.534	-0.169
DS04	-0.37	0.222
DS0c	0.718	0.368
GP01	0.509	1.056
GP02	-1.258	-0.374
GP0c	-1.082	-0.138
NOD	0.57	0.812
NZO	-0.481	0.012
PWK	0.155	0.347
H37Rv_KO_CtpC	-0.592	-0.465
H37Rv_KO_CtpD	0.751	0.501
H37Rv_KO_Rv1272	0.029	1.286
H37Rv_KO_SugABC	0.283	0.428
H37Rv_KO_MbtN	0.401	0.066
Trans05	1.134	0.423
macrophage_unactivated	0.294	-0.076
IL1	-1.006	-0.641
Rapamycin	0.083	0.055
Tcell	-0.228	-0.394
GMCSF	1.014	-0.05
IFNab	-0.085	-0.357
IFNg	0.732	0.206
IFNg_GMCSF1	0.17	1.178
Rv1432_day32	0.9	0.631
Rv1565c_day32	0.147	0.605
secA2_input	-2.016	-0.775
delta_Rv3594	1.462	0.083
delta_Rv3717	0.132	-0.186
delta_Rv3811	1.077	0.311
delta_Rv0954	1.145	0.075
PonA1	0.709	0.5
EccD1_KO	-0.756	0.234
EspI_KO	0.171	0.482
PE35_KO	0.502	0.846
PPE68_KO	0.963	0.419
glycerol2	0.943	1.092
lignocerate	0.839	0.822
oleate	0.818	1.143
phosphatidylcholine	0.796	1.049
acetate	0.519	0.007
glucAc	0.423	-0.026
Rv0950ko	-0.853	0.223
Rv1096ko	-1.668	-0.63
Rv3684ko	-1.723	-0.082
delta_otsA_trehalose	1.015	0.216