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 Rv3432c/gadB:

update plot	correlation	link to info on gene
Rv3772/hisC2	(cc=0.5061)	info on Rv3772/hisC2
Rv3736/-	(cc=0.4302)	info on Rv3736/-
Rv0834c/PE_PGRS14	(cc=0.4097)	info on Rv0834c/PE_PGRS14
Rv3523/ltp3	(cc=0.4093)	info on Rv3523/ltp3
Rv0110/-	(cc=0.4091)	info on Rv0110/-
Rv3171c/hpx	(cc=0.4049)	info on Rv3171c/hpx
Rv1177/fdxC	(cc=0.3936)	info on Rv1177/fdxC
Rv0597c/-	(cc=0.3918)	info on Rv0597c/-
Rv2571c/-	(cc=0.3898)	info on Rv2571c/-
Rv3785/-	(cc=0.3863)	info on Rv3785/-

Correlation of Rv3432c/gadB with Rv3171c/hpx

Normalized LFCs for Rv3432c/gadB:
(description and provenance of datasets)

	Rv3432c/gadB	Rv3171c/hpx
Fe_supp_jason_reseq	0.26	-0.45
low_pH_jason_reseq	0.156	-0.316
NO_jason_reseq	-0.541	0.037
B6_jason_reseq	-0.496	-0.735
MHCII_jason_reseq	0.08	-0.328
Isoniazid02	-0.102	-0.071
Rifampicin4	-0.068	-0.133
Ethambutol3	0.793	-0.045
Meropenem3	0.553	0.071
Vancomycin16	-0.05	0.218
Rv2680_day32	0.454	0.167
H37Rv_KO_MarP	0.243	-0.035
hypoxia_3wks	-0.171	0.056
hypoxia_6wks	-0.169	-0.867
glycerol	0.275	1.078
cholesterol	-0.12	0.718
AJ	-0.234	0.467
Bibs02	0.229	1.028
Bibs02c	0.39	0.0
BL6	0.42	0.955
BL6a	0.342	0.86
BXD01	-0.21	0.137
BXD010	0.278	0.258
BXD011	0.229	-0.172
BXD03	-0.093	-0.258
BXD04	-0.042	0.457
BXD05	0.754	0.667
BXD06	0.272	0.822
BXD07	0.169	0.686
BXD08	-0.171	0.735
BXD09	0.134	0.226
CAST	0.018	-0.818
CCcont	0.125	0.568
DS01	0.198	0.476
DS02	0.165	0.26
DS04	0.285	-0.298
DS0c	-0.393	0.228
GP01	-0.465	-0.491
GP02	0.996	0.111
GP0c	0.563	0.932
NOD	-0.43	-0.652
NZO	0.152	-0.497
PWK	-0.05	-1.186
H37Rv_KO_CtpC	-0.186	1.19
H37Rv_KO_CtpD	0.672	0.824
H37Rv_KO_Rv1272	-0.222	-0.565
H37Rv_KO_SugABC	0.39	0.903
H37Rv_KO_MbtN	0.148	0.334
Trans05	0.284	-0.352
macrophage_unactivated	-0.246	-0.609
IL1	0.19	0.62
Rapamycin	0.227	0.562
Tcell	-0.443	-0.463
GMCSF	-0.222	-0.694
IFNab	0.239	-0.184
IFNg	0.267	0.118
IFNg_GMCSF1	-0.119	-0.77
Rv1432_day32	0.46	0.88
Rv1565c_day32	0.201	0.0
secA2_input	0.894	2.558
delta_Rv3594	-0.153	0.312
delta_Rv3717	-0.062	-0.023
delta_Rv3811	-0.062	0.132
delta_Rv0954	0.31	-0.173
PonA1	1.094	0.18
EccD1_KO	0.168	-0.273
EspI_KO	0.066	0.987
PE35_KO	-0.187	0.155
PPE68_KO	-0.15	-0.502
glycerol2	0.171	-0.553
lignocerate	0.235	-0.386
oleate	0.233	-0.637
phosphatidylcholine	0.296	-0.462
acetate	-0.08	-0.384
glucAc	-0.239	-0.367
Rv0950ko	0.871	0.268
Rv1096ko	0.944	0.914
Rv3684ko	0.531	0.049
delta_otsA_trehalose	-0.909	0.086