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 Rv2284/lipM

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

	Rv2429/ahpD	Rv2284/lipM
Fe_supp_jason_reseq	0.174	0.701
low_pH_jason_reseq	-0.867	-0.629
NO_jason_reseq	0.0	-0.677
B6_jason_reseq	0.363	-0.318
MHCII_jason_reseq	1.557	1.182
Isoniazid02	-4.061	-1.531
Rifampicin4	0.171	-0.322
Ethambutol3	0.32	-1.711
Meropenem3	-0.819	-1.025
Vancomycin16	0.167	-1.427
Rv2680_day32	-0.016	-0.996
H37Rv_KO_MarP	0.567	-0.195
hypoxia_3wks	0.311	0.152
hypoxia_6wks	0.464	1.38
glycerol	0.178	-0.354
cholesterol	0.015	-0.472
AJ	0.513	-0.56
Bibs02	0.212	0.933
Bibs02c	1.36	-0.023
BL6	0.58	0.066
BL6a	1.118	-0.617
BXD01	0.56	-0.117
BXD010	-0.448	-0.578
BXD011	-0.123	0.203
BXD03	0.107	0.165
BXD04	0.418	-0.687
BXD05	0.719	-0.236
BXD06	0.053	-0.135
BXD07	0.822	-0.261
BXD08	0.04	0.042
BXD09	-0.044	-0.265
CAST	-0.072	-0.18
CCcont	0.816	-0.32
DS01	0.0	0.703
DS02	0.534	0.465
DS04	-0.37	0.7
DS0c	0.718	0.611
GP01	0.509	-1.682
GP02	-1.258	-0.63
GP0c	-1.082	-1.842
NOD	0.57	-0.482
NZO	-0.481	-1.647
PWK	0.155	-0.087
H37Rv_KO_CtpC	-0.592	-0.506
H37Rv_KO_CtpD	0.751	0.924
H37Rv_KO_Rv1272	0.029	0.476
H37Rv_KO_SugABC	0.283	-0.383
H37Rv_KO_MbtN	0.401	0.055
Trans05	1.134	-0.117
macrophage_unactivated	0.294	-0.104
IL1	-1.006	-0.145
Rapamycin	0.083	0.516
Tcell	-0.228	0.733
GMCSF	1.014	0.327
IFNab	-0.085	0.33
IFNg	0.732	-0.27
IFNg_GMCSF1	0.17	-1.153
Rv1432_day32	0.9	-1.008
Rv1565c_day32	0.147	-0.278
secA2_input	-2.016	-0.474
delta_Rv3594	1.462	0.821
delta_Rv3717	0.132	1.46
delta_Rv3811	1.077	1.707
delta_Rv0954	1.145	0.481
PonA1	0.709	0.215
EccD1_KO	-0.756	0.48
EspI_KO	0.171	0.108
PE35_KO	0.502	0.904
PPE68_KO	0.963	0.944
glycerol2	0.943	0.716
lignocerate	0.839	0.933
oleate	0.818	-1.045
phosphatidylcholine	0.796	0.786
acetate	0.519	0.763
glucAc	0.423	1.034
Rv0950ko	-0.853	-1.137
Rv1096ko	-1.668	-0.419
Rv3684ko	-1.723	-1.094
delta_otsA_trehalose	1.015	1.125