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 Rv3854c/ethA:

update plot	correlation	link to info on gene
Rv1111c/-	(cc=0.69)	info on Rv1111c/-
Rv0049/-	(cc=0.6401)	info on Rv0049/-
Rv1633/uvrB	(cc=0.6285)	info on Rv1633/uvrB
Rv3818/-	(cc=0.6279)	info on Rv3818/-
Rv0497/-	(cc=0.6185)	info on Rv0497/-
Rv3050c/-	(cc=0.6182)	info on Rv3050c/-
Rv2735c/-	(cc=0.6143)	info on Rv2735c/-
Rv2190c/-	(cc=0.6139)	info on Rv2190c/-
Rv3218/-	(cc=0.6118)	info on Rv3218/-
Rv3125c/PPE49	(cc=0.6093)	info on Rv3125c/PPE49

Correlation of Rv3854c/ethA with Rv2190c/-

Normalized LFCs for Rv3854c/ethA:
(description and provenance of datasets)

	Rv3854c/ethA	Rv2190c/-
Fe_supp_jason_reseq	0.998	2.516
low_pH_jason_reseq	-0.467	-0.221
NO_jason_reseq	0.683	-3.877
B6_jason_reseq	-0.283	-0.596
MHCII_jason_reseq	0.123	-0.565
Isoniazid02	-0.387	0.563
Rifampicin4	-0.382	-3.541
Ethambutol3	-0.039	-2.182
Meropenem3	-0.346	-0.786
Vancomycin16	-0.767	-4.51
Rv2680_day32	0.22	2.417
H37Rv_KO_MarP	-1.053	-6.0
hypoxia_3wks	-0.032	-2.767
hypoxia_6wks	-0.033	-0.228
glycerol	-0.385	-0.098
cholesterol	0.709	2.214
AJ	-0.788	-1.276
Bibs02	0.201	0.993
Bibs02c	-0.092	1.306
BL6	0.606	3.063
BL6a	0.933	2.749
BXD01	0.281	2.595
BXD010	0.77	2.438
BXD011	0.723	2.323
BXD03	1.176	2.42
BXD04	0.639	2.446
BXD05	1.269	3.337
BXD06	1.119	3.167
BXD07	0.804	2.933
BXD08	0.326	2.286
BXD09	0.918	3.087
CAST	-0.247	-1.088
CCcont	0.588	3.364
DS01	0.275	1.001
DS02	0.391	0.0
DS04	0.188	1.359
DS0c	0.016	1.298
GP01	0.561	1.498
GP02	0.572	-0.128
GP0c	0.787	1.031
NOD	-0.428	-1.061
NZO	0.272	-1.263
PWK	0.203	-0.786
H37Rv_KO_CtpC	0.506	2.295
H37Rv_KO_CtpD	1.09	1.805
H37Rv_KO_Rv1272	1.067	2.512
H37Rv_KO_SugABC	1.875	1.815
H37Rv_KO_MbtN	0.978	4.046
Trans05	0.77	2.172
macrophage_unactivated	0.492	0.076
IL1	0.169	0.575
Rapamycin	0.107	-0.23
Tcell	0.277	-0.329
GMCSF	0.298	0.568
IFNab	0.257	1.103
IFNg	0.673	1.563
IFNg_GMCSF1	0.355	0.575
Rv1432_day32	0.454	2.996
Rv1565c_day32	-0.025	0.0
secA2_input	0.288	-4.612
delta_Rv3594	0.649	2.299
delta_Rv3717	1.076	2.896
delta_Rv3811	1.147	2.019
delta_Rv0954	0.171	0.358
PonA1	0.143	-0.825
EccD1_KO	0.253	-1.766
EspI_KO	-0.317	-1.634
PE35_KO	-0.615	-3.246
PPE68_KO	-0.109	-1.411
glycerol2	-0.493	-0.531
lignocerate	-0.235	-0.462
oleate	-0.179	-0.537
phosphatidylcholine	-0.43	-0.531
acetate	-0.321	1.15
glucAc	-0.429	0.213
Rv0950ko	0.639	-6.0
Rv1096ko	0.274	-1.176
Rv3684ko	0.874	-0.364
delta_otsA_trehalose	-0.014	1.066