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 Rv3105c/prfB:

update plot	correlation	link to info on gene
Rv1616/-	(cc=0.5046)	info on Rv1616/-
Rv2492/-	(cc=0.4924)	info on Rv2492/-
Rv1083/-	(cc=0.4849)	info on Rv1083/-
Rv0149/-	(cc=0.4731)	info on Rv0149/-
Rv2275/-	(cc=0.4661)	info on Rv2275/-
Rv3796/-	(cc=0.4625)	info on Rv3796/-
Rv3278c/-	(cc=0.4563)	info on Rv3278c/-
Rv1215c/-	(cc=0.4555)	info on Rv1215c/-
Rv0728c/serA2	(cc=0.448)	info on Rv0728c/serA2
Rv3429/PPE59	(cc=0.4476)	info on Rv3429/PPE59

Correlation of Rv3105c/prfB with Rv1616/-

Normalized LFCs for Rv3105c/prfB:
(description and provenance of datasets)

	Rv3105c/prfB	Rv1616/-
Fe_supp_jason_reseq	1.76	-0.396
low_pH_jason_reseq	-0.211	-0.565
NO_jason_reseq	0.583	0.48
B6_jason_reseq	-0.292	-0.844
MHCII_jason_reseq	0.0	-0.966
Isoniazid02	0.135	1.371
Rifampicin4	0.49	1.162
Ethambutol3	0.22	1.67
Meropenem3	2.735	1.185
Vancomycin16	0.48	1.398
Rv2680_day32	-0.131	0.079
H37Rv_KO_MarP	0.226	-1.139
hypoxia_3wks	1.252	1.766
hypoxia_6wks	0.0	1.775
glycerol	-0.202	1.251
cholesterol	0.0	1.032
AJ	2.086	1.133
Bibs02	0.0	0.539
Bibs02c	-0.209	-0.621
BL6	2.658	1.823
BL6a	1.131	1.778
BXD01	1.222	1.536
BXD010	1.387	2.447
BXD011	0.923	1.72
BXD03	1.893	2.456
BXD04	0.896	1.862
BXD05	0.0	2.644
BXD06	1.252	2.342
BXD07	0.712	2.289
BXD08	1.686	2.089
BXD09	1.018	2.112
CAST	0.746	1.021
CCcont	0.852	1.046
DS01	0.0	0.524
DS02	-0.217	0.46
DS04	0.0	1.712
DS0c	0.379	1.043
GP01	0.847	1.749
GP02	0.0	1.063
GP0c	-0.13	1.472
NOD	0.0	-0.135
NZO	2.021	1.017
PWK	1.009	1.576
H37Rv_KO_CtpC	0.284	2.035
H37Rv_KO_CtpD	0.0	0.541
H37Rv_KO_Rv1272	3.081	1.932
H37Rv_KO_SugABC	0.321	1.821
H37Rv_KO_MbtN	0.884	1.227
Trans05	0.119	2.0
macrophage_unactivated	0.947	0.073
IL1	-0.341	0.217
Rapamycin	0.328	0.175
Tcell	-0.186	0.684
GMCSF	-0.636	0.697
IFNab	0.163	1.149
IFNg	0.422	0.783
IFNg_GMCSF1	-0.556	0.449
Rv1432_day32	0.0	0.46
Rv1565c_day32	0.0	-1.071
secA2_input	-0.412	-0.928
delta_Rv3594	-1.62	-0.578
delta_Rv3717	0.205	-0.642
delta_Rv3811	-1.761	-0.61
delta_Rv0954	0.0	-0.735
PonA1	-0.743	0.046
EccD1_KO	0.793	0.418
EspI_KO	2.561	-0.471
PE35_KO	0.0	0.528
PPE68_KO	0.0	0.224
glycerol2	0.332	-0.339
lignocerate	-0.826	-1.159
oleate	1.207	1.606
phosphatidylcholine	0.27	-0.305
acetate	0.321	-0.788
glucAc	-1.868	-0.999
Rv0950ko	-0.395	0.32
Rv1096ko	-0.832	-0.347
Rv3684ko	-1.428	0.314
delta_otsA_trehalose	-0.675	-1.703