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 Rv1190/-:

update plot	correlation	link to info on gene
Rv2208/cobS	(cc=0.5103)	info on Rv2208/cobS
Rv0590A/-	(cc=0.4855)	info on Rv0590A/-
Rv3353c/-	(cc=0.4852)	info on Rv3353c/-
Rv2281/pitB	(cc=0.4847)	info on Rv2281/pitB
Rv0906/-	(cc=0.4783)	info on Rv0906/-
Rv0376c/-	(cc=0.4777)	info on Rv0376c/-
Rv2237/-	(cc=0.4768)	info on Rv2237/-
Rv0278c/PE_PGRS3	(cc=0.4717)	info on Rv0278c/PE_PGRS3
Rv3335c/-	(cc=0.4683)	info on Rv3335c/-
Rv0488/-	(cc=0.4605)	info on Rv0488/-

Correlation of Rv1190/- with Rv2237/-

Normalized LFCs for Rv1190/-:
(description and provenance of datasets)

	Rv1190/-	Rv2237/-
Fe_supp_jason_reseq	-0.126	0.23
low_pH_jason_reseq	0.037	-0.676
NO_jason_reseq	1.105	-0.302
B6_jason_reseq	0.834	-0.548
MHCII_jason_reseq	-0.149	0.053
Isoniazid02	-1.247	0.397
Rifampicin4	-0.29	-0.674
Ethambutol3	-1.002	-0.32
Meropenem3	-0.712	-0.231
Vancomycin16	-0.679	-0.064
Rv2680_day32	0.752	0.594
H37Rv_KO_MarP	-0.317	0.254
hypoxia_3wks	-0.881	-0.762
hypoxia_6wks	0.461	-0.814
glycerol	1.062	0.12
cholesterol	0.753	0.447
AJ	0.376	0.235
Bibs02	1.127	0.013
Bibs02c	1.664	-0.52
BL6	-0.075	0.847
BL6a	1.167	0.201
BXD01	-0.025	-0.443
BXD010	0.768	0.241
BXD011	0.037	0.53
BXD03	0.429	-0.725
BXD04	0.428	-0.369
BXD05	0.942	0.165
BXD06	0.543	0.284
BXD07	0.336	-0.399
BXD08	0.281	-0.084
BXD09	0.581	0.228
CAST	0.152	-0.464
CCcont	0.029	1.023
DS01	0.833	0.399
DS02	0.706	1.096
DS04	0.559	0.45
DS0c	0.476	0.129
GP01	0.855	0.95
GP02	-0.595	-0.93
GP0c	0.285	0.356
NOD	0.439	-0.371
NZO	-0.315	0.35
PWK	-0.223	-0.625
H37Rv_KO_CtpC	0.806	-0.013
H37Rv_KO_CtpD	-0.32	-0.315
H37Rv_KO_Rv1272	0.156	-0.297
H37Rv_KO_SugABC	-1.388	0.422
H37Rv_KO_MbtN	0.087	0.656
Trans05	1.051	0.02
macrophage_unactivated	0.824	0.076
IL1	-0.845	0.24
Rapamycin	0.328	-0.11
Tcell	-1.196	0.339
GMCSF	0.731	-0.261
IFNab	-0.862	0.0
IFNg	-0.099	0.644
IFNg_GMCSF1	-0.179	0.628
Rv1432_day32	0.627	-0.01
Rv1565c_day32	-1.022	-0.479
secA2_input	0.719	0.252
delta_Rv3594	0.13	1.153
delta_Rv3717	1.62	1.364
delta_Rv3811	1.096	0.772
delta_Rv0954	1.052	0.16
PonA1	1.545	0.84
EccD1_KO	-0.214	0.53
EspI_KO	0.211	0.91
PE35_KO	0.388	0.858
PPE68_KO	-0.793	0.733
glycerol2	1.618	1.88
lignocerate	2.3	2.527
oleate	0.091	-1.276
phosphatidylcholine	1.795	2.426
acetate	2.241	2.72
glucAc	1.897	2.503
Rv0950ko	-0.401	0.0
Rv1096ko	1.65	-0.078
Rv3684ko	0.4	-0.819
delta_otsA_trehalose	-1.378	-0.569