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 Rv2991/-:

update plot	correlation	link to info on gene
Rv2723/-	(cc=0.4636)	info on Rv2723/-
Rv0499/-	(cc=0.4526)	info on Rv0499/-
Rv1874/-	(cc=0.4023)	info on Rv1874/-
Rv3064c/-	(cc=0.3878)	info on Rv3064c/-
Rv1583c/-	(cc=0.38)	info on Rv1583c/-
Rv1524/-	(cc=0.38)	info on Rv1524/-
Rv2775/-	(cc=0.3789)	info on Rv2775/-
Rv1585c/-	(cc=0.3729)	info on Rv1585c/-
Rv1530/adh	(cc=0.3559)	info on Rv1530/adh
Rv0345/-	(cc=0.3489)	info on Rv0345/-

Correlation of Rv2991/- with Rv0499/-

Normalized LFCs for Rv2991/-:
(description and provenance of datasets)

	Rv2991/-	Rv0499/-
Fe_supp_jason_reseq	0.101	0.152
low_pH_jason_reseq	1.258	0.209
NO_jason_reseq	0.2	0.06
B6_jason_reseq	-0.183	-0.542
MHCII_jason_reseq	-1.269	-1.733
Isoniazid02	-0.028	0.319
Rifampicin4	0.152	0.609
Ethambutol3	-0.235	0.331
Meropenem3	0.11	0.152
Vancomycin16	0.05	0.435
Rv2680_day32	-0.256	-0.46
H37Rv_KO_MarP	0.679	1.35
hypoxia_3wks	-0.327	0.032
hypoxia_6wks	-0.424	0.451
glycerol	-0.262	0.579
cholesterol	-0.402	-0.994
AJ	1.573	0.449
Bibs02	-0.97	-0.832
Bibs02c	0.032	-0.746
BL6	1.067	0.127
BL6a	-0.28	-0.362
BXD01	-0.082	-0.747
BXD010	0.471	-0.168
BXD011	0.404	0.816
BXD03	0.582	-0.135
BXD04	-0.327	-0.108
BXD05	1.426	1.044
BXD06	1.383	0.161
BXD07	0.505	0.255
BXD08	1.122	-0.053
BXD09	1.091	0.534
CAST	0.447	-0.105
CCcont	0.206	0.453
DS01	-0.474	-2.19
DS02	0.17	-0.775
DS04	-0.252	-1.249
DS0c	0.431	-0.896
GP01	-0.051	0.998
GP02	0.82	-0.608
GP0c	0.213	0.499
NOD	2.182	0.465
NZO	0.579	-0.273
PWK	0.554	0.406
H37Rv_KO_CtpC	0.368	-0.753
H37Rv_KO_CtpD	1.816	0.014
H37Rv_KO_Rv1272	0.063	-0.998
H37Rv_KO_SugABC	-0.275	-1.522
H37Rv_KO_MbtN	-0.342	0.816
Trans05	0.27	-0.319
macrophage_unactivated	0.417	0.96
IL1	-0.332	0.65
Rapamycin	0.559	1.096
Tcell	-0.808	-0.137
GMCSF	0.055	0.869
IFNab	0.063	0.819
IFNg	0.526	1.676
IFNg_GMCSF1	1.194	0.918
Rv1432_day32	-0.454	-0.343
Rv1565c_day32	2.042	-0.321
secA2_input	1.794	0.0
delta_Rv3594	-0.5	-0.899
delta_Rv3717	-1.112	-0.008
delta_Rv3811	0.167	0.248
delta_Rv0954	-0.047	0.844
PonA1	0.379	0.589
EccD1_KO	0.266	0.434
EspI_KO	-0.445	-0.414
PE35_KO	0.341	0.184
PPE68_KO	0.339	0.278
glycerol2	0.041	1.145
lignocerate	1.369	2.056
oleate	-0.672	-3.077
phosphatidylcholine	0.665	0.431
acetate	1.564	2.519
glucAc	1.275	1.7
Rv0950ko	0.247	-0.597
Rv1096ko	0.736	0.0
Rv3684ko	0.111	-1.539
delta_otsA_trehalose	1.428	0.999