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 Rv3750c/-:

update plot	correlation	link to info on gene
Rv3232c/ppk2	(cc=0.6217)	info on Rv3232c/ppk2
Rv1504c/-	(cc=0.6116)	info on Rv1504c/-
Rv2430c/PPE41	(cc=0.5983)	info on Rv2430c/PPE41
Rv2519/PE26	(cc=0.5945)	info on Rv2519/PE26
Rv3152/nuoH	(cc=0.5911)	info on Rv3152/nuoH
Rv2513/-	(cc=0.5823)	info on Rv2513/-
Rv1059/-	(cc=0.5777)	info on Rv1059/-
Rv2735c/-	(cc=0.5705)	info on Rv2735c/-
Rv1500/-	(cc=0.5694)	info on Rv1500/-
Rv1664/pks9	(cc=0.5607)	info on Rv1664/pks9

Correlation of Rv3750c/- with Rv1504c/-

Normalized LFCs for Rv3750c/-:
(description and provenance of datasets)

	Rv3750c/-	Rv1504c/-
Fe_supp_jason_reseq	-0.723	0.161
low_pH_jason_reseq	-0.052	-0.294
NO_jason_reseq	-0.163	-0.11
B6_jason_reseq	-1.315	-0.505
MHCII_jason_reseq	-1.782	0.005
Isoniazid02	0.039	0.047
Rifampicin4	-0.758	-0.349
Ethambutol3	0.134	-0.06
Meropenem3	-0.492	-0.034
Vancomycin16	0.058	-0.218
Rv2680_day32	0.426	-0.607
H37Rv_KO_MarP	0.498	-0.364
hypoxia_3wks	-1.447	0.471
hypoxia_6wks	-0.679	0.255
glycerol	1.233	0.284
cholesterol	-0.765	0.316
AJ	-0.536	0.429
Bibs02	0.764	0.677
Bibs02c	1.075	0.218
BL6	0.798	1.455
BL6a	1.499	1.218
BXD01	1.087	0.632
BXD010	1.049	1.204
BXD011	0.801	1.111
BXD03	0.729	1.778
BXD04	0.932	1.499
BXD05	1.4	1.413
BXD06	1.206	0.825
BXD07	1.543	1.414
BXD08	1.697	1.164
BXD09	0.75	1.357
CAST	1.148	0.649
CCcont	1.338	0.778
DS01	0.811	1.304
DS02	1.257	1.23
DS04	0.032	1.085
DS0c	1.92	1.669
GP01	1.878	0.956
GP02	-0.042	1.205
GP0c	0.865	0.583
NOD	0.361	-0.586
NZO	0.685	0.787
PWK	-0.453	0.409
H37Rv_KO_CtpC	1.655	1.422
H37Rv_KO_CtpD	0.933	1.016
H37Rv_KO_Rv1272	1.322	2.168
H37Rv_KO_SugABC	0.409	0.981
H37Rv_KO_MbtN	1.622	1.97
Trans05	1.553	1.837
macrophage_unactivated	0.413	-0.524
IL1	-0.682	0.053
Rapamycin	0.095	0.068
Tcell	-0.062	0.43
GMCSF	0.224	0.198
IFNab	-0.435	-0.215
IFNg	0.545	0.441
IFNg_GMCSF1	0.936	0.352
Rv1432_day32	-0.563	0.068
Rv1565c_day32	1.265	0.687
secA2_input	-0.537	-0.479
delta_Rv3594	0.324	0.575
delta_Rv3717	-0.372	0.503
delta_Rv3811	-0.122	0.712
delta_Rv0954	-0.496	0.37
PonA1	-0.763	0.508
EccD1_KO	-0.023	-0.141
EspI_KO	0.294	0.488
PE35_KO	-1.041	0.543
PPE68_KO	-1.126	0.275
glycerol2	-0.261	0.433
lignocerate	0.226	-0.051
oleate	0.009	0.737
phosphatidylcholine	0.017	0.678
acetate	0.219	-0.389
glucAc	0.466	-0.673
Rv0950ko	-0.383	-0.567
Rv1096ko	-1.149	-1.378
Rv3684ko	-0.874	-0.796
delta_otsA_trehalose	2.322	0.464