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 Rv0497/-

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

	Rv1111c/-	Rv0497/-
Fe_supp_jason_reseq	1.264	2.155
low_pH_jason_reseq	-0.413	-1.887
NO_jason_reseq	1.945	0.858
B6_jason_reseq	-0.818	-1.375
MHCII_jason_reseq	-0.503	-1.155
Isoniazid02	-0.885	-1.622
Rifampicin4	-2.32	-1.66
Ethambutol3	0.069	-0.19
Meropenem3	0.183	-1.154
Vancomycin16	-3.507	-2.555
Rv2680_day32	-1.668	1.148
H37Rv_KO_MarP	-2.198	-3.88
hypoxia_3wks	0.439	-1.244
hypoxia_6wks	1.685	-1.038
glycerol	-1.398	-1.24
cholesterol	0.952	0.748
AJ	-0.457	0.487
Bibs02	0.694	-0.697
Bibs02c	0.317	-1.773
BL6	1.483	0.731
BL6a	0.587	-0.755
BXD01	0.552	0.209
BXD010	2.133	0.518
BXD011	0.913	0.54
BXD03	0.934	0.377
BXD04	1.083	0.524
BXD05	2.061	-0.354
BXD06	1.355	0.248
BXD07	1.154	0.786
BXD08	0.549	-0.4
BXD09	0.848	0.622
CAST	-0.903	-2.853
CCcont	0.802	1.016
DS01	0.075	-1.001
DS02	0.035	-0.129
DS04	1.003	-0.115
DS0c	0.478	-0.826
GP01	0.83	1.52
GP02	0.0	-0.025
GP0c	1.352	1.579
NOD	-1.778	-2.39
NZO	0.126	0.727
PWK	1.373	2.552
H37Rv_KO_CtpC	0.872	0.092
H37Rv_KO_CtpD	-0.437	0.235
H37Rv_KO_Rv1272	0.469	0.824
H37Rv_KO_SugABC	1.22	2.212
H37Rv_KO_MbtN	2.108	3.528
Trans05	1.251	1.205
macrophage_unactivated	0.988	-0.514
IL1	0.131	0.703
Rapamycin	0.491	0.157
Tcell	0.456	-2.346
GMCSF	1.299	1.31
IFNab	1.859	2.53
IFNg	0.663	0.136
IFNg_GMCSF1	-0.145	1.618
Rv1432_day32	0.082	2.092
Rv1565c_day32	0.619	-1.93
secA2_input	0.199	-2.038
delta_Rv3594	1.103	1.086
delta_Rv3717	1.38	2.536
delta_Rv3811	1.06	0.828
delta_Rv0954	-1.398	-0.282
PonA1	-1.316	-0.912
EccD1_KO	-0.697	-0.109
EspI_KO	-0.231	-0.719
PE35_KO	-0.753	-1.485
PPE68_KO	-0.442	-0.806
glycerol2	-0.398	-0.177
lignocerate	-0.681	-0.32
oleate	-0.403	0.457
phosphatidylcholine	-1.008	-0.176
acetate	-0.086	0.0
glucAc	-0.578	0.119
Rv0950ko	-0.142	-0.615
Rv1096ko	0.651	0.305
Rv3684ko	-0.206	-0.157
delta_otsA_trehalose	-0.474	-0.118