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 Rv3152/nuoH

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

	Rv2584c/apt	Rv3152/nuoH
Fe_supp_jason_reseq	-0.227	-0.772
low_pH_jason_reseq	0.565	-0.092
NO_jason_reseq	0.404	-0.144
B6_jason_reseq	-0.929	-0.801
MHCII_jason_reseq	-1.215	-2.143
Isoniazid02	-0.808	0.444
Rifampicin4	-0.146	0.774
Ethambutol3	-0.59	0.069
Meropenem3	-0.443	-0.659
Vancomycin16	-0.268	-0.225
Rv2680_day32	0.892	-0.082
H37Rv_KO_MarP	-0.556	-0.697
hypoxia_3wks	0.738	1.009
hypoxia_6wks	1.046	0.979
glycerol	0.758	-0.992
cholesterol	-0.069	-0.54
AJ	0.81	0.232
Bibs02	1.106	1.123
Bibs02c	0.932	1.375
BL6	0.958	2.337
BL6a	1.499	2.946
BXD01	0.868	2.231
BXD010	1.16	2.447
BXD011	0.701	2.768
BXD03	1.101	2.634
BXD04	1.281	2.663
BXD05	1.845	2.747
BXD06	1.349	2.529
BXD07	1.389	2.629
BXD08	1.048	2.704
BXD09	1.278	2.869
CAST	0.576	0.117
CCcont	1.444	1.606
DS01	0.274	1.16
DS02	0.12	1.367
DS04	-0.471	1.528
DS0c	0.511	1.838
GP01	0.774	0.29
GP02	0.966	0.696
GP0c	1.337	1.218
NOD	-0.042	-0.06
NZO	0.407	0.465
PWK	0.658	-0.659
H37Rv_KO_CtpC	0.281	1.156
H37Rv_KO_CtpD	1.793	2.183
H37Rv_KO_Rv1272	1.014	2.115
H37Rv_KO_SugABC	1.26	2.463
H37Rv_KO_MbtN	0.707	1.452
Trans05	1.018	2.198
macrophage_unactivated	0.619	-0.205
IL1	0.697	-0.641
Rapamycin	0.893	-0.381
Tcell	0.228	0.261
GMCSF	2.017	0.256
IFNab	0.931	0.472
IFNg	-0.013	0.024
IFNg_GMCSF1	0.264	-0.295
Rv1432_day32	0.374	-0.481
Rv1565c_day32	0.041	1.035
secA2_input	-1.75	-0.382
delta_Rv3594	0.347	0.361
delta_Rv3717	-0.422	0.695
delta_Rv3811	-0.207	0.25
delta_Rv0954	-0.433	0.695
PonA1	-0.406	0.254
EccD1_KO	-0.977	-0.125
EspI_KO	-0.436	0.106
PE35_KO	-0.688	0.0
PPE68_KO	-0.611	0.643
glycerol2	0.378	1.645
lignocerate	0.226	-0.104
oleate	0.55	1.388
phosphatidylcholine	0.378	-0.38
acetate	0.484	0.707
glucAc	-0.133	1.157
Rv0950ko	-0.703	-0.217
Rv1096ko	-0.401	0.461
Rv3684ko	-1.117	-0.344
delta_otsA_trehalose	-0.167	0.69