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 Rv2584c/apt:

update plot	correlation	link to info on gene
Rv1059/-	(cc=0.6684)	info on Rv1059/-
Rv3150/nuoF	(cc=0.6665)	info on Rv3150/nuoF
Rv2430c/PPE41	(cc=0.6346)	info on Rv2430c/PPE41
Rv2569c/-	(cc=0.6256)	info on Rv2569c/-
Rv3864/espE	(cc=0.6219)	info on Rv3864/espE
Rv3152/nuoH	(cc=0.6182)	info on Rv3152/nuoH
Rv0059/-	(cc=0.6153)	info on Rv0059/-
Rv0260c/-	(cc=0.6146)	info on Rv0260c/-
Rv0502/-	(cc=0.6133)	info on Rv0502/-
Rv3153/nuoI	(cc=0.6126)	info on Rv3153/nuoI

Correlation of Rv2584c/apt with Rv3864/espE

Normalized LFCs for Rv2584c/apt:
(description and provenance of datasets)

	Rv2584c/apt	Rv3864/espE
Fe_supp_jason_reseq	-0.227	-0.532
low_pH_jason_reseq	0.565	3.42
NO_jason_reseq	0.404	-0.69
B6_jason_reseq	-0.929	-1.402
MHCII_jason_reseq	-1.215	-1.234
Isoniazid02	-0.808	-0.39
Rifampicin4	-0.146	-0.203
Ethambutol3	-0.59	0.142
Meropenem3	-0.443	0.768
Vancomycin16	-0.268	0.191
Rv2680_day32	0.892	-0.228
H37Rv_KO_MarP	-0.556	-2.191
hypoxia_3wks	0.738	-0.371
hypoxia_6wks	1.046	-0.263
glycerol	0.758	0.709
cholesterol	-0.069	0.614
AJ	0.81	0.0
Bibs02	1.106	0.0
Bibs02c	0.932	0.887
BL6	0.958	2.486
BL6a	1.499	2.131
BXD01	0.868	2.047
BXD010	1.16	1.598
BXD011	0.701	1.811
BXD03	1.101	0.664
BXD04	1.281	1.854
BXD05	1.845	1.878
BXD06	1.349	2.59
BXD07	1.389	1.003
BXD08	1.048	1.781
BXD09	1.278	2.036
CAST	0.576	0.0
CCcont	1.444	3.145
DS01	0.274	1.001
DS02	0.12	0.764
DS04	-0.471	1.689
DS0c	0.511	0.596
GP01	0.774	1.35
GP02	0.966	0.159
GP0c	1.337	1.072
NOD	-0.042	0.225
NZO	0.407	0.0
PWK	0.658	0.831
H37Rv_KO_CtpC	0.281	0.571
H37Rv_KO_CtpD	1.793	1.044
H37Rv_KO_Rv1272	1.014	2.149
H37Rv_KO_SugABC	1.26	3.545
H37Rv_KO_MbtN	0.707	2.695
Trans05	1.018	2.677
macrophage_unactivated	0.619	2.228
IL1	0.697	-0.736
Rapamycin	0.893	0.651
Tcell	0.228	2.3
GMCSF	2.017	0.89
IFNab	0.931	1.197
IFNg	-0.013	-0.663
IFNg_GMCSF1	0.264	1.059
Rv1432_day32	0.374	-0.664
Rv1565c_day32	0.041	0.182
secA2_input	-1.75	-1.387
delta_Rv3594	0.347	0.962
delta_Rv3717	-0.422	1.328
delta_Rv3811	-0.207	0.87
delta_Rv0954	-0.433	-0.615
PonA1	-0.406	-1.937
EccD1_KO	-0.977	-1.694
EspI_KO	-0.436	-2.718
PE35_KO	-0.688	0.0
PPE68_KO	-0.611	0.077
glycerol2	0.378	0.028
lignocerate	0.226	-0.296
oleate	0.55	-0.801
phosphatidylcholine	0.378	-0.515
acetate	0.484	-0.364
glucAc	-0.133	0.286
Rv0950ko	-0.703	-1.375
Rv1096ko	-0.401	-0.184
Rv3684ko	-1.117	-0.982
delta_otsA_trehalose	-0.167	0.366