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 Rv2275/-

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

	Rv3105c/prfB	Rv2275/-
Fe_supp_jason_reseq	1.76	0.827
low_pH_jason_reseq	-0.211	0.617
NO_jason_reseq	0.583	-0.244
B6_jason_reseq	-0.292	-0.7
MHCII_jason_reseq	0.0	0.61
Isoniazid02	0.135	0.153
Rifampicin4	0.49	0.975
Ethambutol3	0.22	0.188
Meropenem3	2.735	0.352
Vancomycin16	0.48	0.539
Rv2680_day32	-0.131	-0.471
H37Rv_KO_MarP	0.226	0.08
hypoxia_3wks	1.252	0.128
hypoxia_6wks	0.0	-0.288
glycerol	-0.202	-0.453
cholesterol	0.0	0.184
AJ	2.086	0.294
Bibs02	0.0	1.13
Bibs02c	-0.209	-0.47
BL6	2.658	0.864
BL6a	1.131	0.528
BXD01	1.222	1.203
BXD010	1.387	0.816
BXD011	0.923	1.745
BXD03	1.893	1.025
BXD04	0.896	0.0
BXD05	0.0	0.615
BXD06	1.252	0.39
BXD07	0.712	0.602
BXD08	1.686	0.871
BXD09	1.018	1.087
CAST	0.746	-1.054
CCcont	0.852	1.179
DS01	0.0	0.503
DS02	-0.217	0.142
DS04	0.0	0.929
DS0c	0.379	-0.231
GP01	0.847	-0.354
GP02	0.0	-0.523
GP0c	-0.13	-0.986
NOD	0.0	-0.239
NZO	2.021	1.306
PWK	1.009	-1.232
H37Rv_KO_CtpC	0.284	1.545
H37Rv_KO_CtpD	0.0	1.255
H37Rv_KO_Rv1272	3.081	2.719
H37Rv_KO_SugABC	0.321	2.705
H37Rv_KO_MbtN	0.884	1.924
Trans05	0.119	1.729
macrophage_unactivated	0.947	1.215
IL1	-0.341	-0.089
Rapamycin	0.328	1.114
Tcell	-0.186	0.873
GMCSF	-0.636	0.51
IFNab	0.163	0.088
IFNg	0.422	0.516
IFNg_GMCSF1	-0.556	-1.656
Rv1432_day32	0.0	-0.411
Rv1565c_day32	0.0	0.3
secA2_input	-0.412	-1.681
delta_Rv3594	-1.62	-0.725
delta_Rv3717	0.205	-0.927
delta_Rv3811	-1.761	-0.796
delta_Rv0954	0.0	-1.708
PonA1	-0.743	-0.936
EccD1_KO	0.793	2.111
EspI_KO	2.561	1.443
PE35_KO	0.0	1.17
PPE68_KO	0.0	1.872
glycerol2	0.332	0.0
lignocerate	-0.826	0.505
oleate	1.207	0.0
phosphatidylcholine	0.27	0.415
acetate	0.321	1.014
glucAc	-1.868	0.487
Rv0950ko	-0.395	-1.354
Rv1096ko	-0.832	-0.835
Rv3684ko	-1.428	-1.179
delta_otsA_trehalose	-0.675	-0.836