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 Rv1511/gmdA

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

	Rv2429/ahpD	Rv1511/gmdA
Fe_supp_jason_reseq	0.174	-0.218
low_pH_jason_reseq	-0.867	0.435
NO_jason_reseq	0.0	-0.614
B6_jason_reseq	0.363	0.411
MHCII_jason_reseq	1.557	0.579
Isoniazid02	-4.061	-1.493
Rifampicin4	0.171	0.436
Ethambutol3	0.32	-0.48
Meropenem3	-0.819	-0.871
Vancomycin16	0.167	-0.74
Rv2680_day32	-0.016	-0.333
H37Rv_KO_MarP	0.567	-0.11
hypoxia_3wks	0.311	-0.132
hypoxia_6wks	0.464	0.194
glycerol	0.178	0.075
cholesterol	0.015	0.355
AJ	0.513	0.229
Bibs02	0.212	0.14
Bibs02c	1.36	0.365
BL6	0.58	0.108
BL6a	1.118	-0.156
BXD01	0.56	-0.142
BXD010	-0.448	0.177
BXD011	-0.123	0.008
BXD03	0.107	0.339
BXD04	0.418	-0.188
BXD05	0.719	-0.299
BXD06	0.053	0.089
BXD07	0.822	-0.267
BXD08	0.04	0.097
BXD09	-0.044	-0.069
CAST	-0.072	0.36
CCcont	0.816	-0.113
DS01	0.0	0.597
DS02	0.534	0.591
DS04	-0.37	0.921
DS0c	0.718	0.995
GP01	0.509	0.813
GP02	-1.258	0.608
GP0c	-1.082	-0.088
NOD	0.57	0.727
NZO	-0.481	-0.477
PWK	0.155	0.382
H37Rv_KO_CtpC	-0.592	-0.313
H37Rv_KO_CtpD	0.751	0.515
H37Rv_KO_Rv1272	0.029	1.062
H37Rv_KO_SugABC	0.283	0.113
H37Rv_KO_MbtN	0.401	0.192
Trans05	1.134	0.273
macrophage_unactivated	0.294	-0.243
IL1	-1.006	0.03
Rapamycin	0.083	-0.285
Tcell	-0.228	-0.016
GMCSF	1.014	-0.388
IFNab	-0.085	-0.248
IFNg	0.732	0.321
IFNg_GMCSF1	0.17	-0.063
Rv1432_day32	0.9	0.532
Rv1565c_day32	0.147	0.049
secA2_input	-2.016	-0.479
delta_Rv3594	1.462	0.479
delta_Rv3717	0.132	0.415
delta_Rv3811	1.077	0.278
delta_Rv0954	1.145	-0.066
PonA1	0.709	0.568
EccD1_KO	-0.756	0.039
EspI_KO	0.171	-0.436
PE35_KO	0.502	0.615
PPE68_KO	0.963	0.426
glycerol2	0.943	0.392
lignocerate	0.839	0.621
oleate	0.818	0.452
phosphatidylcholine	0.796	0.76
acetate	0.519	0.186
glucAc	0.423	0.09
Rv0950ko	-0.853	-0.223
Rv1096ko	-1.668	-0.425
Rv3684ko	-1.723	-0.242
delta_otsA_trehalose	1.015	0.924