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 Rv3669/-:

update plot	correlation	link to info on gene
Rv1404/-	(cc=0.5149)	info on Rv1404/-
Rv2040c/-	(cc=0.4922)	info on Rv2040c/-
Rv1028A/kdpF	(cc=0.4505)	info on Rv1028A/kdpF
Rv1003/-	(cc=0.4431)	info on Rv1003/-
Rv3215/entC	(cc=0.4125)	info on Rv3215/entC
Rv1928c/-	(cc=0.4004)	info on Rv1928c/-
Rv1129c/-	(cc=0.3879)	info on Rv1129c/-
Rv2437/-	(cc=0.3711)	info on Rv2437/-
Rv2316/uspA	(cc=0.3669)	info on Rv2316/uspA
Rv0948c/-	(cc=0.3665)	info on Rv0948c/-

Correlation of Rv3669/- with Rv3215/entC

Normalized LFCs for Rv3669/-:
(description and provenance of datasets)

	Rv3669/-	Rv3215/entC
Fe_supp_jason_reseq	2.087	0.598
low_pH_jason_reseq	-0.811	0.0
NO_jason_reseq	-1.273	0.0
B6_jason_reseq	1.973	0.0
MHCII_jason_reseq	-0.474	0.0
Isoniazid02	0.21	0.0
Rifampicin4	0.912	0.0
Ethambutol3	0.617	0.0
Meropenem3	-0.409	0.0
Vancomycin16	0.0	0.0
Rv2680_day32	0.0	0.0
H37Rv_KO_MarP	-0.669	-0.535
hypoxia_3wks	0.267	0.0
hypoxia_6wks	2.362	0.0
glycerol	-1.463	0.0
cholesterol	0.528	0.0
AJ	-1.487	0.0
Bibs02	-1.673	0.0
Bibs02c	-1.914	0.0
BL6	0.053	0.0
BL6a	-0.088	0.0
BXD01	-0.64	0.0
BXD010	0.956	0.0
BXD011	1.714	0.0
BXD03	0.92	0.0
BXD04	-0.372	0.0
BXD05	0.682	0.0
BXD06	1.131	0.0
BXD07	1.2	0.0
BXD08	-0.4	0.0
BXD09	1.787	0.0
CAST	-0.21	0.0
CCcont	1.049	0.0
DS01	-0.216	0.0
DS02	-0.531	0.0
DS04	-1.775	0.0
DS0c	-1.985	0.0
GP01	-0.903	0.0
GP02	-0.761	0.083
GP0c	-1.19	0.0
NOD	-0.099	0.0
NZO	-0.38	0.0
PWK	0.388	0.0
H37Rv_KO_CtpC	2.166	0.0
H37Rv_KO_CtpD	-1.159	0.0
H37Rv_KO_Rv1272	-1.29	0.0
H37Rv_KO_SugABC	-0.906	0.0
H37Rv_KO_MbtN	-0.31	0.0
Trans05	-0.947	0.0
macrophage_unactivated	0.088	0.0
IL1	2.334	0.0
Rapamycin	0.252	0.0
Tcell	0.0	0.0
GMCSF	1.809	0.0
IFNab	2.228	0.0
IFNg	0.69	0.0
IFNg_GMCSF1	2.369	0.0
Rv1432_day32	0.0	0.0
Rv1565c_day32	0.0	0.0
secA2_input	-3.131	-2.237
delta_Rv3594	1.306	0.34
delta_Rv3717	2.017	0.145
delta_Rv3811	2.411	0.171
delta_Rv0954	-0.792	-0.34
PonA1	0.986	1.222
EccD1_KO	0.454	0.0
EspI_KO	2.852	0.0
PE35_KO	1.263	0.0
PPE68_KO	0.0	0.0
glycerol2	0.0	0.0
lignocerate	0.32	0.0
oleate	0.0	0.0
phosphatidylcholine	0.0	0.0
acetate	1.998	0.0
glucAc	1.306	0.0
Rv0950ko	-1.372	-1.143
Rv1096ko	-2.069	-0.347
Rv3684ko	-0.684	-1.241
delta_otsA_trehalose	-0.667	0.0