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 Rv3617/ephA:

update plot	correlation	link to info on gene
Rv0338c/-	(cc=0.4594)	info on Rv0338c/-
Rv0433/-	(cc=0.4583)	info on Rv0433/-
Rv0196/-	(cc=0.4392)	info on Rv0196/-
Rv3618/-	(cc=0.4377)	info on Rv3618/-
Rv1181/pks4	(cc=0.4361)	info on Rv1181/pks4
Rv2095c/pafC	(cc=0.4348)	info on Rv2095c/pafC
Rv2636/-	(cc=0.4295)	info on Rv2636/-
Rv3276c/purK	(cc=0.428)	info on Rv3276c/purK
Rv0263c/-	(cc=0.428)	info on Rv0263c/-
Rv0942/-	(cc=0.4278)	info on Rv0942/-

Correlation of Rv3617/ephA with Rv0338c/-

Normalized LFCs for Rv3617/ephA:
(description and provenance of datasets)

	Rv3617/ephA	Rv0338c/-
Fe_supp_jason_reseq	0.096	0.0
low_pH_jason_reseq	0.614	0.0
NO_jason_reseq	-0.265	0.0
B6_jason_reseq	0.315	0.0
MHCII_jason_reseq	1.159	0.0
Isoniazid02	0.685	0.0
Rifampicin4	-0.057	0.0
Ethambutol3	0.535	0.0
Meropenem3	-1.017	0.0
Vancomycin16	-0.814	0.0
Rv2680_day32	-0.319	0.0
H37Rv_KO_MarP	-0.216	0.0
hypoxia_3wks	-0.698	0.0
hypoxia_6wks	-0.505	0.0
glycerol	0.578	0.385
cholesterol	2.126	3.545
AJ	0.371	0.0
Bibs02	-0.044	0.0
Bibs02c	-0.944	0.0
BL6	0.125	0.0
BL6a	-0.894	0.0
BXD01	-0.415	0.0
BXD010	-0.572	0.0
BXD011	-0.412	0.0
BXD03	0.072	0.0
BXD04	-0.546	0.0
BXD05	-0.06	0.0
BXD06	-0.535	0.0
BXD07	-0.596	0.0
BXD08	-0.257	0.0
BXD09	-0.627	0.0
CAST	0.622	0.0
CCcont	-0.883	0.0
DS01	-0.409	0.0
DS02	0.484	0.0
DS04	-0.947	0.0
DS0c	-0.492	0.0
GP01	-0.136	0.0
GP02	-0.411	0.0
GP0c	-0.333	0.0
NOD	1.046	0.0
NZO	-0.048	0.0
PWK	0.51	0.0
H37Rv_KO_CtpC	-0.488	0.0
H37Rv_KO_CtpD	0.514	0.0
H37Rv_KO_Rv1272	-0.578	0.0
H37Rv_KO_SugABC	0.564	0.0
H37Rv_KO_MbtN	-0.154	0.0
Trans05	0.287	0.0
macrophage_unactivated	-0.461	0.0
IL1	-0.409	0.0
Rapamycin	-0.546	0.0
Tcell	0.0	0.0
GMCSF	-0.077	0.0
IFNab	-0.296	0.0
IFNg	0.19	0.0
IFNg_GMCSF1	0.396	0.0
Rv1432_day32	0.102	0.0
Rv1565c_day32	0.613	0.0
secA2_input	0.587	0.847
delta_Rv3594	-0.239	0.0
delta_Rv3717	0.125	0.0
delta_Rv3811	0.183	0.0
delta_Rv0954	-0.315	0.0
PonA1	-0.045	0.0
EccD1_KO	0.016	0.0
EspI_KO	-0.086	0.0
PE35_KO	0.058	0.0
PPE68_KO	0.157	0.0
glycerol2	0.977	0.0
lignocerate	0.558	0.0
oleate	-0.422	0.0
phosphatidylcholine	0.471	0.0
acetate	0.071	0.0
glucAc	-0.337	0.0
Rv0950ko	-0.036	0.0
Rv1096ko	0.344	0.0
Rv3684ko	1.251	0.0
delta_otsA_trehalose	0.257	0.133