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 Rv3388/PE_PGRS52:

update plot	correlation	link to info on gene
Rv0336/-	(cc=0.6014)	info on Rv0336/-
Rv1087/PE_PGRS21	(cc=0.6002)	info on Rv1087/PE_PGRS21
Rv0515/-	(cc=0.5868)	info on Rv0515/-
Rv0747/PE_PGRS10	(cc=0.585)	info on Rv0747/PE_PGRS10
Rv3512/PE_PGRS56	(cc=0.5508)	info on Rv3512/PE_PGRS56
Rv1818c/PE_PGRS33	(cc=0.5484)	info on Rv1818c/PE_PGRS33
Rv2487c/PE_PGRS42	(cc=0.5445)	info on Rv2487c/PE_PGRS42
Rv3345c/PE_PGRS50	(cc=0.5322)	info on Rv3345c/PE_PGRS50
Rv1091/PE_PGRS22	(cc=0.5307)	info on Rv1091/PE_PGRS22
Rv3508/PE_PGRS54	(cc=0.5111)	info on Rv3508/PE_PGRS54

Correlation of Rv3388/PE_PGRS52 with Rv0336/-

Normalized LFCs for Rv3388/PE_PGRS52:
(description and provenance of datasets)

	Rv3388/PE_PGRS52	Rv0336/-
Fe_supp_jason_reseq	0.06	0.0
low_pH_jason_reseq	-1.486	-1.445
NO_jason_reseq	-0.433	0.221
B6_jason_reseq	0.124	-0.394
MHCII_jason_reseq	1.471	0.203
Isoniazid02	-0.784	0.074
Rifampicin4	1.137	0.685
Ethambutol3	0.368	0.111
Meropenem3	-0.678	0.601
Vancomycin16	-0.31	0.207
Rv2680_day32	-0.095	-0.097
H37Rv_KO_MarP	-0.347	-0.025
hypoxia_3wks	-0.132	0.267
hypoxia_6wks	-1.155	-0.361
glycerol	1.021	-0.079
cholesterol	0.034	0.043
AJ	1.627	0.553
Bibs02	0.844	0.562
Bibs02c	0.77	0.934
BL6	-0.768	-0.042
BL6a	0.09	0.4
BXD01	-0.422	0.064
BXD010	-0.375	0.131
BXD011	0.03	-0.161
BXD03	-0.276	0.355
BXD04	-0.568	0.501
BXD05	-0.031	0.286
BXD06	-1.064	-0.07
BXD07	-0.207	0.103
BXD08	-0.817	0.146
BXD09	-0.805	0.008
CAST	0.205	0.532
CCcont	-0.305	-0.184
DS01	-0.055	0.662
DS02	-0.158	0.233
DS04	0.617	0.49
DS0c	-0.845	0.149
GP01	-0.89	0.475
GP02	0.142	0.591
GP0c	-0.23	0.068
NOD	1.988	0.472
NZO	0.493	0.485
PWK	1.047	0.821
H37Rv_KO_CtpC	-0.038	0.905
H37Rv_KO_CtpD	0.81	0.604
H37Rv_KO_Rv1272	2.051	0.296
H37Rv_KO_SugABC	1.024	0.205
H37Rv_KO_MbtN	0.273	0.534
Trans05	-0.698	0.455
macrophage_unactivated	-0.625	-0.603
IL1	-0.715	-0.581
Rapamycin	-1.163	-0.503
Tcell	-1.391	-1.098
GMCSF	0.792	-0.164
IFNab	-2.116	-1.037
IFNg	-0.762	-0.246
IFNg_GMCSF1	0.116	-0.242
Rv1432_day32	0.585	0.269
Rv1565c_day32	-0.599	0.028
secA2_input	0.238	-0.034
delta_Rv3594	-0.623	-0.785
delta_Rv3717	-0.384	-0.686
delta_Rv3811	-0.895	-0.781
delta_Rv0954	-1.614	-0.853
PonA1	-0.886	-0.488
EccD1_KO	-0.089	-0.181
EspI_KO	-0.157	0.06
PE35_KO	-0.289	0.093
PPE68_KO	-0.131	-0.022
glycerol2	0.283	0.0
lignocerate	0.392	0.116
oleate	-0.105	-0.136
phosphatidylcholine	0.193	0.014
acetate	0.0	-0.043
glucAc	1.306	0.308
Rv0950ko	-0.136	0.398
Rv1096ko	-0.045	0.012
Rv3684ko	0.714	0.354
delta_otsA_trehalose	0.378	0.144