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 Rv1111c/-:

update plot	correlation	link to info on gene
Rv3818/-	(cc=0.7343)	info on Rv3818/-
Rv3854c/ethA	(cc=0.69)	info on Rv3854c/ethA
Rv3267/-	(cc=0.6193)	info on Rv3267/-
Rv0497/-	(cc=0.6082)	info on Rv0497/-
Rv0050/ponA1	(cc=0.605)	info on Rv0050/ponA1
Rv1747/-	(cc=0.603)	info on Rv1747/-
Rv0309/-	(cc=0.5864)	info on Rv0309/-
Rv3794/embA	(cc=0.5803)	info on Rv3794/embA
Rv2190c/-	(cc=0.5646)	info on Rv2190c/-
Rv0397A/-	(cc=0.5632)	info on Rv0397A/-

Correlation of Rv1111c/- with Rv0309/-

Normalized LFCs for Rv1111c/-:
(description and provenance of datasets)

	Rv1111c/-	Rv0309/-
Fe_supp_jason_reseq	1.264	-1.236
low_pH_jason_reseq	-0.413	-1.338
NO_jason_reseq	1.945	-0.079
B6_jason_reseq	-0.818	-0.814
MHCII_jason_reseq	-0.503	-1.617
Isoniazid02	-0.885	-0.713
Rifampicin4	-2.32	-3.493
Ethambutol3	0.069	1.936
Meropenem3	0.183	1.336
Vancomycin16	-3.507	-0.698
Rv2680_day32	-1.668	1.423
H37Rv_KO_MarP	-2.198	-2.34
hypoxia_3wks	0.439	-0.682
hypoxia_6wks	1.685	-0.052
glycerol	-1.398	-0.889
cholesterol	0.952	0.734
AJ	-0.457	0.074
Bibs02	0.694	0.964
Bibs02c	0.317	0.696
BL6	1.483	1.436
BL6a	0.587	1.986
BXD01	0.552	1.759
BXD010	2.133	2.381
BXD011	0.913	1.917
BXD03	0.934	1.948
BXD04	1.083	2.591
BXD05	2.061	2.955
BXD06	1.355	2.962
BXD07	1.154	2.077
BXD08	0.549	1.625
BXD09	0.848	1.995
CAST	-0.903	1.026
CCcont	0.802	1.276
DS01	0.075	1.027
DS02	0.035	0.069
DS04	1.003	1.023
DS0c	0.478	0.748
GP01	0.83	1.221
GP02	0.0	-0.366
GP0c	1.352	1.074
NOD	-1.778	0.107
NZO	0.126	0.0
PWK	1.373	2.842
H37Rv_KO_CtpC	0.872	0.671
H37Rv_KO_CtpD	-0.437	0.1
H37Rv_KO_Rv1272	0.469	1.806
H37Rv_KO_SugABC	1.22	0.955
H37Rv_KO_MbtN	2.108	0.738
Trans05	1.251	1.373
macrophage_unactivated	0.988	0.129
IL1	0.131	0.0
Rapamycin	0.491	0.126
Tcell	0.456	0.541
GMCSF	1.299	0.438
IFNab	1.859	0.747
IFNg	0.663	0.267
IFNg_GMCSF1	-0.145	0.694
Rv1432_day32	0.082	1.09
Rv1565c_day32	0.619	0.603
secA2_input	0.199	-1.774
delta_Rv3594	1.103	0.375
delta_Rv3717	1.38	0.993
delta_Rv3811	1.06	0.479
delta_Rv0954	-1.398	-0.041
PonA1	-1.316	-0.826
EccD1_KO	-0.697	-0.562
EspI_KO	-0.231	-0.57
PE35_KO	-0.753	-0.379
PPE68_KO	-0.442	0.08
glycerol2	-0.398	0.149
lignocerate	-0.681	0.324
oleate	-0.403	0.75
phosphatidylcholine	-1.008	-0.426
acetate	-0.086	0.879
glucAc	-0.578	0.227
Rv0950ko	-0.142	-1.089
Rv1096ko	0.651	-0.109
Rv3684ko	-0.206	0.337
delta_otsA_trehalose	-0.474	-0.116