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 Rv0300/vapB2:

update plot	correlation	link to info on gene
Rv1976c/-	(cc=0.4675)	info on Rv1976c/-
Rv0633c/-	(cc=0.4561)	info on Rv0633c/-
Rv0435c/-	(cc=0.4317)	info on Rv0435c/-
Rv0778/cyp126	(cc=0.4231)	info on Rv0778/cyp126
Rv1358/-	(cc=0.4093)	info on Rv1358/-
Rv0936/pstA2	(cc=0.4087)	info on Rv0936/pstA2
Rv2320c/rocE	(cc=0.4081)	info on Rv2320c/rocE
Rv1541c/lprI	(cc=0.3939)	info on Rv1541c/lprI
Rv0388c/PPE9	(cc=0.3873)	info on Rv0388c/PPE9
Rv1363c/-	(cc=0.3835)	info on Rv1363c/-

Correlation of Rv0300/vapB2 with Rv0778/cyp126

Normalized LFCs for Rv0300/vapB2:
(description and provenance of datasets)

	Rv0300/vapB2	Rv0778/cyp126
Fe_supp_jason_reseq	0.464	2.014
low_pH_jason_reseq	-0.924	-0.571
NO_jason_reseq	-0.305	-0.651
B6_jason_reseq	0.449	0.523
MHCII_jason_reseq	0.094	0.706
Isoniazid02	-0.214	-0.525
Rifampicin4	-0.16	0.157
Ethambutol3	0.029	-0.403
Meropenem3	0.422	0.298
Vancomycin16	-0.098	0.154
Rv2680_day32	-0.998	0.508
H37Rv_KO_MarP	-0.378	-0.423
hypoxia_3wks	-0.682	0.534
hypoxia_6wks	-0.551	-0.021
glycerol	0.553	0.736
cholesterol	0.867	0.449
AJ	0.44	0.824
Bibs02	0.327	0.174
Bibs02c	0.026	0.246
BL6	-1.319	-0.148
BL6a	0.504	0.756
BXD01	-0.518	0.734
BXD010	-0.679	0.959
BXD011	-0.288	0.899
BXD03	-0.188	0.561
BXD04	-0.183	1.184
BXD05	0.488	0.862
BXD06	-0.314	0.836
BXD07	0.379	0.79
BXD08	-0.321	0.618
BXD09	-0.228	0.696
CAST	0.904	0.756
CCcont	-0.731	-0.056
DS01	0.053	0.921
DS02	0.884	1.078
DS04	-1.216	0.207
DS0c	0.107	0.919
GP01	-0.693	-0.265
GP02	-1.436	-0.021
GP0c	-0.722	0.665
NOD	0.477	1.642
NZO	0.168	0.581
PWK	0.219	0.715
H37Rv_KO_CtpC	0.0	0.916
H37Rv_KO_CtpD	0.2	1.194
H37Rv_KO_Rv1272	-0.461	-0.269
H37Rv_KO_SugABC	0.119	1.345
H37Rv_KO_MbtN	-0.46	0.918
Trans05	-0.193	0.278
macrophage_unactivated	-0.609	1.042
IL1	0.451	0.0
Rapamycin	0.479	0.341
Tcell	0.424	0.437
GMCSF	0.227	0.591
IFNab	0.599	0.0
IFNg	0.51	1.04
IFNg_GMCSF1	0.386	0.566
Rv1432_day32	-0.645	-0.624
Rv1565c_day32	1.42	-0.347
secA2_input	-0.908	0.23
delta_Rv3594	-0.434	0.72
delta_Rv3717	-0.888	-0.162
delta_Rv3811	0.813	0.744
delta_Rv0954	0.703	0.549
PonA1	0.935	0.753
EccD1_KO	0.559	0.52
EspI_KO	-0.194	0.893
PE35_KO	0.032	0.983
PPE68_KO	-0.278	0.841
glycerol2	-0.189	-0.13
lignocerate	-0.231	-0.614
oleate	-0.204	0.39
phosphatidylcholine	-0.59	0.088
acetate	-1.014	-0.748
glucAc	-0.841	-1.202
Rv0950ko	0.778	0.329
Rv1096ko	0.483	0.633
Rv3684ko	-0.183	0.121
delta_otsA_trehalose	-1.349	-1.184