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 Rv1948c/-:

update plot	correlation	link to info on gene
Rv3429/PPE59	(cc=0.5502)	info on Rv3429/PPE59
Rv1504c/-	(cc=0.5446)	info on Rv1504c/-
Rv3142c/-	(cc=0.5371)	info on Rv3142c/-
Rv2107/PE22	(cc=0.5334)	info on Rv2107/PE22
Rv2735c/-	(cc=0.5311)	info on Rv2735c/-
Rv2519/PE26	(cc=0.5278)	info on Rv2519/PE26
Rv2666/-	(cc=0.5261)	info on Rv2666/-
Rv2819c/-	(cc=0.5251)	info on Rv2819c/-
Rv2929/-	(cc=0.5198)	info on Rv2929/-
Rv2134c/-	(cc=0.5166)	info on Rv2134c/-

Correlation of Rv1948c/- with Rv1504c/-

Normalized LFCs for Rv1948c/-:
(description and provenance of datasets)

	Rv1948c/-	Rv1504c/-
Fe_supp_jason_reseq	-0.508	0.161
low_pH_jason_reseq	-0.206	-0.294
NO_jason_reseq	0.887	-0.11
B6_jason_reseq	-2.506	-0.505
MHCII_jason_reseq	-1.292	0.005
Isoniazid02	-0.185	0.047
Rifampicin4	-0.791	-0.349
Ethambutol3	1.612	-0.06
Meropenem3	-0.38	-0.034
Vancomycin16	0.361	-0.218
Rv2680_day32	0.915	-0.607
H37Rv_KO_MarP	-0.123	-0.364
hypoxia_3wks	0.219	0.471
hypoxia_6wks	-0.885	0.255
glycerol	-0.348	0.284
cholesterol	0.064	0.316
AJ	1.086	0.429
Bibs02	-0.817	0.677
Bibs02c	1.984	0.218
BL6	1.445	1.455
BL6a	1.709	1.218
BXD01	0.512	0.632
BXD010	0.421	1.204
BXD011	0.163	1.111
BXD03	-0.513	1.778
BXD04	0.322	1.499
BXD05	0.991	1.413
BXD06	0.525	0.825
BXD07	0.707	1.414
BXD08	0.437	1.164
BXD09	0.152	1.357
CAST	-0.277	0.649
CCcont	1.509	0.778
DS01	0.571	1.304
DS02	0.321	1.23
DS04	1.292	1.085
DS0c	1.31	1.669
GP01	1.547	0.956
GP02	0.019	1.205
GP0c	1.727	0.583
NOD	-0.576	-0.586
NZO	0.483	0.787
PWK	0.74	0.409
H37Rv_KO_CtpC	0.981	1.422
H37Rv_KO_CtpD	1.213	1.016
H37Rv_KO_Rv1272	1.702	2.168
H37Rv_KO_SugABC	0.706	0.981
H37Rv_KO_MbtN	1.766	1.97
Trans05	1.32	1.837
macrophage_unactivated	-0.521	-0.524
IL1	0.0	0.053
Rapamycin	-0.856	0.068
Tcell	-0.831	0.43
GMCSF	-0.053	0.198
IFNab	-0.121	-0.215
IFNg	0.0	0.441
IFNg_GMCSF1	-0.126	0.352
Rv1432_day32	0.117	0.068
Rv1565c_day32	-0.839	0.687
secA2_input	-0.87	-0.479
delta_Rv3594	0.193	0.575
delta_Rv3717	0.06	0.503
delta_Rv3811	0.419	0.712
delta_Rv0954	0.041	0.37
PonA1	-0.058	0.508
EccD1_KO	-0.493	-0.141
EspI_KO	-0.687	0.488
PE35_KO	0.312	0.543
PPE68_KO	0.294	0.275
glycerol2	-0.233	0.433
lignocerate	0.216	-0.051
oleate	0.211	0.737
phosphatidylcholine	0.127	0.678
acetate	0.514	-0.389
glucAc	0.319	-0.673
Rv0950ko	0.217	-0.567
Rv1096ko	-1.342	-1.378
Rv3684ko	-2.319	-0.796
delta_otsA_trehalose	-0.785	0.464