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 Rv1513/-:

update plot	correlation	link to info on gene
Rv0404/fadD30	(cc=0.607)	info on Rv0404/fadD30
Rv0913c/-	(cc=0.5375)	info on Rv0913c/-
Rv3504/fadE26	(cc=0.4764)	info on Rv3504/fadE26
Rv0477/-	(cc=0.4679)	info on Rv0477/-
Rv2892c/PPE45	(cc=0.4592)	info on Rv2892c/PPE45
Rv1564c/treX	(cc=0.4578)	info on Rv1564c/treX
Rv0045c/-	(cc=0.4543)	info on Rv0045c/-
Rv3218/-	(cc=0.45)	info on Rv3218/-
Rv2683/-	(cc=0.4426)	info on Rv2683/-
Rv3378c/-	(cc=0.4367)	info on Rv3378c/-

Correlation of Rv1513/- with Rv2892c/PPE45

Normalized LFCs for Rv1513/-:
(description and provenance of datasets)

	Rv1513/-	Rv2892c/PPE45
Fe_supp_jason_reseq	1.725	-0.267
low_pH_jason_reseq	-0.539	-0.482
NO_jason_reseq	1.62	-0.192
B6_jason_reseq	0.052	-0.296
MHCII_jason_reseq	-0.72	0.057
Isoniazid02	-0.39	0.501
Rifampicin4	-0.726	0.644
Ethambutol3	-0.326	0.241
Meropenem3	-0.531	0.478
Vancomycin16	-0.072	0.592
Rv2680_day32	0.881	0.499
H37Rv_KO_MarP	1.051	-0.277
hypoxia_3wks	1.061	0.73
hypoxia_6wks	-0.731	0.94
glycerol	-0.992	-0.506
cholesterol	-0.568	-0.862
AJ	0.417	0.182
Bibs02	0.694	0.221
Bibs02c	-1.808	-0.186
BL6	-1.52	0.487
BL6a	1.083	0.42
BXD01	0.9	0.656
BXD010	0.041	0.4
BXD011	1.169	0.248
BXD03	0.74	0.348
BXD04	0.993	0.005
BXD05	1.324	0.253
BXD06	0.9	0.672
BXD07	1.112	0.551
BXD08	1.006	0.863
BXD09	0.822	0.674
CAST	1.26	0.01
CCcont	-0.988	0.129
DS01	-0.419	0.157
DS02	0.449	-0.246
DS04	-1.677	1.483
DS0c	-0.652	0.431
GP01	-0.138	0.387
GP02	1.734	0.964
GP0c	-0.86	0.263
NOD	-1.351	0.314
NZO	0.845	-0.15
PWK	-1.695	-0.502
H37Rv_KO_CtpC	-1.53	-0.199
H37Rv_KO_CtpD	1.586	0.351
H37Rv_KO_Rv1272	0.877	0.386
H37Rv_KO_SugABC	-0.933	0.38
H37Rv_KO_MbtN	-0.183	-0.27
Trans05	1.088	0.282
macrophage_unactivated	-1.474	0.092
IL1	-1.622	0.039
Rapamycin	-1.197	-0.147
Tcell	-0.189	0.124
GMCSF	-0.367	-0.011
IFNab	0.333	-0.266
IFNg	-2.106	0.166
IFNg_GMCSF1	-1.549	-0.317
Rv1432_day32	0.0	-0.613
Rv1565c_day32	-1.82	0.659
secA2_input	-1.398	0.02
delta_Rv3594	-1.741	0.0
delta_Rv3717	-1.601	-0.322
delta_Rv3811	-2.787	-0.595
delta_Rv0954	-0.7	0.155
PonA1	-3.817	-0.182
EccD1_KO	-1.171	0.71
EspI_KO	-0.776	0.63
PE35_KO	0.0	-0.038
PPE68_KO	-0.374	0.102
glycerol2	-0.388	0.509
lignocerate	-1.431	0.349
oleate	0.352	0.885
phosphatidylcholine	-0.506	0.798
acetate	-1.553	-0.776
glucAc	-4.028	-0.792
Rv0950ko	1.885	1.2
Rv1096ko	0.682	1.14
Rv3684ko	2.047	0.495
delta_otsA_trehalose	5.088	2.157