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 Rv3784/-:

update plot	correlation	link to info on gene
Rv3018c/PPE46	(cc=0.6375)	info on Rv3018c/PPE46
Rv0138/-	(cc=0.601)	info on Rv0138/-
Rv1917c/PPE34	(cc=0.5793)	info on Rv1917c/PPE34
Rv0686/-	(cc=0.5563)	info on Rv0686/-
Rv2958c/-	(cc=0.541)	info on Rv2958c/-
Rv3487c/lipF	(cc=0.5374)	info on Rv3487c/lipF
Rv2332/mez	(cc=0.5243)	info on Rv2332/mez
Rv0814c/sseC2	(cc=0.5213)	info on Rv0814c/sseC2
Rv2351c/plcA	(cc=0.5186)	info on Rv2351c/plcA
Rv1760/-	(cc=0.5178)	info on Rv1760/-

Correlation of Rv3784/- with Rv3018c/PPE46

Normalized LFCs for Rv3784/-:
(description and provenance of datasets)

	Rv3784/-	Rv3018c/PPE46
Fe_supp_jason_reseq	0.006	0.379
low_pH_jason_reseq	-0.898	-0.125
NO_jason_reseq	-0.21	0.391
B6_jason_reseq	0.092	0.618
MHCII_jason_reseq	0.297	0.516
Isoniazid02	0.688	0.911
Rifampicin4	-0.138	0.921
Ethambutol3	1.0	1.828
Meropenem3	0.948	0.552
Vancomycin16	0.066	0.446
Rv2680_day32	0.337	0.505
H37Rv_KO_MarP	0.03	0.274
hypoxia_3wks	-0.04	-0.471
hypoxia_6wks	0.092	-0.173
glycerol	0.522	0.181
cholesterol	0.186	0.214
AJ	0.546	0.706
Bibs02	0.0	0.576
Bibs02c	0.588	0.117
BL6	0.22	0.246
BL6a	0.455	0.304
BXD01	0.05	0.339
BXD010	0.168	0.369
BXD011	0.112	0.524
BXD03	-0.091	0.274
BXD04	0.291	-0.046
BXD05	-0.244	0.611
BXD06	0.22	0.556
BXD07	-0.032	0.281
BXD08	0.132	0.433
BXD09	0.236	0.208
CAST	0.506	0.676
CCcont	0.043	0.173
DS01	0.185	0.318
DS02	0.495	0.016
DS04	-0.07	0.287
DS0c	0.176	0.107
GP01	0.273	0.435
GP02	0.114	0.288
GP0c	-0.022	-0.339
NOD	1.71	1.173
NZO	0.363	0.331
PWK	0.482	0.628
H37Rv_KO_CtpC	0.437	0.613
H37Rv_KO_CtpD	0.656	0.758
H37Rv_KO_Rv1272	0.346	0.949
H37Rv_KO_SugABC	0.607	0.64
H37Rv_KO_MbtN	0.892	0.582
Trans05	0.842	0.563
macrophage_unactivated	0.413	-0.117
IL1	-0.51	-0.807
Rapamycin	0.077	-0.571
Tcell	-0.222	-1.062
GMCSF	-0.235	-0.536
IFNab	-0.187	-1.24
IFNg	0.094	-1.018
IFNg_GMCSF1	0.248	-0.613
Rv1432_day32	0.623	0.229
Rv1565c_day32	-0.316	0.55
secA2_input	-0.726	-0.706
delta_Rv3594	-0.494	-0.128
delta_Rv3717	-0.488	-0.837
delta_Rv3811	-0.175	-0.333
delta_Rv0954	-0.552	-0.335
PonA1	-0.545	-0.404
EccD1_KO	-0.135	-0.22
EspI_KO	0.225	0.163
PE35_KO	-0.152	-0.02
PPE68_KO	-0.33	0.138
glycerol2	0.737	0.807
lignocerate	0.811	1.119
oleate	0.777	0.055
phosphatidylcholine	0.817	0.961
acetate	0.243	0.987
glucAc	0.267	0.667
Rv0950ko	0.166	0.021
Rv1096ko	-0.621	-0.232
Rv3684ko	-0.606	-0.567
delta_otsA_trehalose	-0.267	-0.458