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 Rv0149/-

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

	Rv3105c/prfB	Rv0149/-
Fe_supp_jason_reseq	1.76	0.456
low_pH_jason_reseq	-0.211	-0.174
NO_jason_reseq	0.583	0.344
B6_jason_reseq	-0.292	-0.072
MHCII_jason_reseq	0.0	-0.111
Isoniazid02	0.135	0.46
Rifampicin4	0.49	0.463
Ethambutol3	0.22	1.317
Meropenem3	2.735	2.06
Vancomycin16	0.48	0.406
Rv2680_day32	-0.131	0.49
H37Rv_KO_MarP	0.226	0.593
hypoxia_3wks	1.252	0.152
hypoxia_6wks	0.0	-0.027
glycerol	-0.202	-0.278
cholesterol	0.0	-0.034
AJ	2.086	0.576
Bibs02	0.0	0.282
Bibs02c	-0.209	0.323
BL6	2.658	1.501
BL6a	1.131	0.651
BXD01	1.222	0.846
BXD010	1.387	0.984
BXD011	0.923	1.073
BXD03	1.893	0.429
BXD04	0.896	0.999
BXD05	0.0	1.11
BXD06	1.252	1.007
BXD07	0.712	0.966
BXD08	1.686	0.815
BXD09	1.018	0.913
CAST	0.746	0.2
CCcont	0.852	0.804
DS01	0.0	-0.017
DS02	-0.217	0.065
DS04	0.0	0.458
DS0c	0.379	0.512
GP01	0.847	0.708
GP02	0.0	0.843
GP0c	-0.13	0.413
NOD	0.0	-0.877
NZO	2.021	0.422
PWK	1.009	0.072
H37Rv_KO_CtpC	0.284	0.96
H37Rv_KO_CtpD	0.0	0.992
H37Rv_KO_Rv1272	3.081	0.772
H37Rv_KO_SugABC	0.321	0.68
H37Rv_KO_MbtN	0.884	0.467
Trans05	0.119	0.547
macrophage_unactivated	0.947	0.413
IL1	-0.341	0.181
Rapamycin	0.328	0.144
Tcell	-0.186	0.218
GMCSF	-0.636	0.665
IFNab	0.163	0.846
IFNg	0.422	0.5
IFNg_GMCSF1	-0.556	0.663
Rv1432_day32	0.0	1.199
Rv1565c_day32	0.0	-0.464
secA2_input	-0.412	-0.587
delta_Rv3594	-1.62	0.06
delta_Rv3717	0.205	0.296
delta_Rv3811	-1.761	-0.152
delta_Rv0954	0.0	0.388
PonA1	-0.743	0.067
EccD1_KO	0.793	-0.388
EspI_KO	2.561	0.26
PE35_KO	0.0	0.283
PPE68_KO	0.0	-0.022
glycerol2	0.332	-0.66
lignocerate	-0.826	-0.524
oleate	1.207	-0.24
phosphatidylcholine	0.27	-1.006
acetate	0.321	-1.112
glucAc	-1.868	-0.999
Rv0950ko	-0.395	-0.024
Rv1096ko	-0.832	-0.268
Rv3684ko	-1.428	-0.265
delta_otsA_trehalose	-0.675	0.749