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 Rv1059/-

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

	Rv2584c/apt	Rv1059/-
Fe_supp_jason_reseq	-0.227	0.182
low_pH_jason_reseq	0.565	0.371
NO_jason_reseq	0.404	0.302
B6_jason_reseq	-0.929	-1.402
MHCII_jason_reseq	-1.215	-1.842
Isoniazid02	-0.808	-0.509
Rifampicin4	-0.146	-0.582
Ethambutol3	-0.59	-0.685
Meropenem3	-0.443	0.94
Vancomycin16	-0.268	-0.639
Rv2680_day32	0.892	-2.147
H37Rv_KO_MarP	-0.556	0.178
hypoxia_3wks	0.738	0.642
hypoxia_6wks	1.046	0.639
glycerol	0.758	-1.121
cholesterol	-0.069	-0.294
AJ	0.81	-0.65
Bibs02	1.106	1.021
Bibs02c	0.932	-0.587
BL6	0.958	1.992
BL6a	1.499	2.468
BXD01	0.868	2.452
BXD010	1.16	2.106
BXD011	0.701	2.436
BXD03	1.101	3.572
BXD04	1.281	2.353
BXD05	1.845	2.247
BXD06	1.349	2.654
BXD07	1.389	2.607
BXD08	1.048	2.531
BXD09	1.278	2.688
CAST	0.576	1.023
CCcont	1.444	2.164
DS01	0.274	0.522
DS02	0.12	0.369
DS04	-0.471	0.225
DS0c	0.511	2.858
GP01	0.774	1.636
GP02	0.966	1.944
GP0c	1.337	0.981
NOD	-0.042	0.133
NZO	0.407	-1.107
PWK	0.658	0.433
H37Rv_KO_CtpC	0.281	2.426
H37Rv_KO_CtpD	1.793	2.855
H37Rv_KO_Rv1272	1.014	1.834
H37Rv_KO_SugABC	1.26	2.796
H37Rv_KO_MbtN	0.707	0.611
Trans05	1.018	3.009
macrophage_unactivated	0.619	2.197
IL1	0.697	0.635
Rapamycin	0.893	-0.043
Tcell	0.228	0.046
GMCSF	2.017	0.327
IFNab	0.931	-0.178
IFNg	-0.013	-0.238
IFNg_GMCSF1	0.264	-0.377
Rv1432_day32	0.374	-1.635
Rv1565c_day32	0.041	-0.218
secA2_input	-1.75	-2.481
delta_Rv3594	0.347	0.872
delta_Rv3717	-0.422	-0.365
delta_Rv3811	-0.207	1.246
delta_Rv0954	-0.433	0.952
PonA1	-0.406	0.0
EccD1_KO	-0.977	-0.069
EspI_KO	-0.436	0.394
PE35_KO	-0.688	-1.768
PPE68_KO	-0.611	-0.56
glycerol2	0.378	-0.37
lignocerate	0.226	-0.856
oleate	0.55	0.272
phosphatidylcholine	0.378	-0.204
acetate	0.484	-0.871
glucAc	-0.133	-1.382
Rv0950ko	-0.703	-1.393
Rv1096ko	-0.401	-1.915
Rv3684ko	-1.117	-1.883
delta_otsA_trehalose	-0.167	-0.675