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 Rv2819c/-

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

	Rv1948c/-	Rv2819c/-
Fe_supp_jason_reseq	-0.508	0.257
low_pH_jason_reseq	-0.206	-0.032
NO_jason_reseq	0.887	0.05
B6_jason_reseq	-2.506	0.083
MHCII_jason_reseq	-1.292	0.392
Isoniazid02	-0.185	-0.18
Rifampicin4	-0.791	0.406
Ethambutol3	1.612	1.216
Meropenem3	-0.38	-0.2
Vancomycin16	0.361	0.255
Rv2680_day32	0.915	0.526
H37Rv_KO_MarP	-0.123	-0.255
hypoxia_3wks	0.219	-0.506
hypoxia_6wks	-0.885	-0.196
glycerol	-0.348	0.149
cholesterol	0.064	0.49
AJ	1.086	1.397
Bibs02	-0.817	0.449
Bibs02c	1.984	1.205
BL6	1.445	0.652
BL6a	1.709	1.124
BXD01	0.512	0.761
BXD010	0.421	0.543
BXD011	0.163	0.591
BXD03	-0.513	0.755
BXD04	0.322	0.498
BXD05	0.991	0.611
BXD06	0.525	0.757
BXD07	0.707	0.642
BXD08	0.437	0.294
BXD09	0.152	0.652
CAST	-0.277	0.48
CCcont	1.509	0.938
DS01	0.571	1.025
DS02	0.321	0.312
DS04	1.292	-0.122
DS0c	1.31	1.152
GP01	1.547	0.958
GP02	0.019	1.04
GP0c	1.727	0.714
NOD	-0.576	0.858
NZO	0.483	0.653
PWK	0.74	2.593
H37Rv_KO_CtpC	0.981	0.992
H37Rv_KO_CtpD	1.213	-0.144
H37Rv_KO_Rv1272	1.702	0.774
H37Rv_KO_SugABC	0.706	0.194
H37Rv_KO_MbtN	1.766	1.627
Trans05	1.32	1.227
macrophage_unactivated	-0.521	-0.205
IL1	0.0	-0.193
Rapamycin	-0.856	0.374
Tcell	-0.831	0.202
GMCSF	-0.053	0.164
IFNab	-0.121	0.0
IFNg	0.0	-0.219
IFNg_GMCSF1	-0.126	0.148
Rv1432_day32	0.117	0.87
Rv1565c_day32	-0.839	-0.935
secA2_input	-0.87	-1.116
delta_Rv3594	0.193	0.0
delta_Rv3717	0.06	-0.292
delta_Rv3811	0.419	0.085
delta_Rv0954	0.041	-1.056
PonA1	-0.058	-0.464
EccD1_KO	-0.493	0.378
EspI_KO	-0.687	0.516
PE35_KO	0.312	2.106
PPE68_KO	0.294	1.769
glycerol2	-0.233	1.002
lignocerate	0.216	1.189
oleate	0.211	0.438
phosphatidylcholine	0.127	1.028
acetate	0.514	1.107
glucAc	0.319	0.709
Rv0950ko	0.217	-1.013
Rv1096ko	-1.342	-0.805
Rv3684ko	-2.319	-1.336
delta_otsA_trehalose	-0.785	-0.851