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 Rv3303c/lpdA:

update plot	correlation	link to info on gene
Rv0526/-	(cc=0.5704)	info on Rv0526/-
Rv3248c/sahH	(cc=0.5372)	info on Rv3248c/sahH
Rv0904c/accD3	(cc=0.4981)	info on Rv0904c/accD3
Rv2347c/esxP	(cc=0.4976)	info on Rv2347c/esxP
Rv2169c/-	(cc=0.4678)	info on Rv2169c/-
Rv3455c/truA	(cc=0.4675)	info on Rv3455c/truA
Rv2290/lppO	(cc=0.4633)	info on Rv2290/lppO
Rv3193c/-	(cc=0.4572)	info on Rv3193c/-
Rv1098c/fum	(cc=0.4498)	info on Rv1098c/fum
Rv1298/rpmE	(cc=0.4496)	info on Rv1298/rpmE

Correlation of Rv3303c/lpdA with Rv1298/rpmE

Normalized LFCs for Rv3303c/lpdA:
(description and provenance of datasets)

	Rv3303c/lpdA	Rv1298/rpmE
Fe_supp_jason_reseq	-1.274	0.766
low_pH_jason_reseq	0.811	0.0
NO_jason_reseq	4.284	0.0
B6_jason_reseq	0.752	0.0
MHCII_jason_reseq	0.446	0.0
Isoniazid02	-1.493	0.0
Rifampicin4	-0.699	0.0
Ethambutol3	-1.248	0.0
Meropenem3	-1.229	0.0
Vancomycin16	-1.414	0.0
Rv2680_day32	0.99	0.0
H37Rv_KO_MarP	0.535	-0.825
hypoxia_3wks	-1.244	0.0
hypoxia_6wks	-0.263	0.0
glycerol	1.24	0.0
cholesterol	0.325	0.0
AJ	-0.049	0.0
Bibs02	0.25	0.0
Bibs02c	-0.433	0.0
BL6	-0.393	0.0
BL6a	0.121	0.0
BXD01	-0.409	0.0
BXD010	-0.516	0.0
BXD011	-0.513	0.0
BXD03	0.573	0.0
BXD04	0.655	0.0
BXD05	-0.766	0.0
BXD06	0.107	0.0
BXD07	-0.475	0.0
BXD08	0.055	0.0
BXD09	-0.702	0.0
CAST	0.0	0.0
CCcont	-0.096	0.0
DS01	-0.881	0.0
DS02	-0.624	0.0
DS04	-1.036	0.0
DS0c	0.487	0.0
GP01	0.021	0.0
GP02	-1.047	0.0
GP0c	-0.65	0.0
NOD	0.308	0.0
NZO	0.042	0.0
PWK	1.272	0.0
H37Rv_KO_CtpC	-0.925	0.0
H37Rv_KO_CtpD	-0.473	0.127
H37Rv_KO_Rv1272	-1.279	0.0
H37Rv_KO_SugABC	-0.086	0.0
H37Rv_KO_MbtN	-0.354	0.0
Trans05	-0.947	0.0
macrophage_unactivated	-0.524	0.0
IL1	0.525	0.0
Rapamycin	0.457	0.0
Tcell	0.199	0.0
GMCSF	-0.438	0.0
IFNab	0.363	0.0
IFNg	-0.35	0.0
IFNg_GMCSF1	-1.647	0.0
Rv1432_day32	0.82	0.0
Rv1565c_day32	-1.02	0.0
secA2_input	-0.332	0.0
delta_Rv3594	0.958	0.402
delta_Rv3717	0.648	0.853
delta_Rv3811	-0.479	0.564
delta_Rv0954	0.426	0.0
PonA1	2.434	0.0
EccD1_KO	0.888	0.414
EspI_KO	0.12	-0.394
PE35_KO	0.788	0.0
PPE68_KO	1.779	1.113
glycerol2	-1.002	-0.95
lignocerate	-2.549	-0.826
oleate	-3.603	-0.961
phosphatidylcholine	-2.801	-0.95
acetate	-2.562	-1.127
glucAc	-1.463	-0.701
Rv0950ko	1.396	-0.323
Rv1096ko	1.879	0.582
Rv3684ko	1.326	0.0
delta_otsA_trehalose	0.0	-0.739