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 Rv1917c/PPE34

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

	Rv3784/-	Rv1917c/PPE34
Fe_supp_jason_reseq	0.006	0.756
low_pH_jason_reseq	-0.898	-0.311
NO_jason_reseq	-0.21	0.15
B6_jason_reseq	0.092	0.621
MHCII_jason_reseq	0.297	0.641
Isoniazid02	0.688	0.063
Rifampicin4	-0.138	0.173
Ethambutol3	1.0	0.472
Meropenem3	0.948	0.435
Vancomycin16	0.066	0.0
Rv2680_day32	0.337	0.08
H37Rv_KO_MarP	0.03	-0.09
hypoxia_3wks	-0.04	-0.327
hypoxia_6wks	0.092	-0.048
glycerol	0.522	-0.107
cholesterol	0.186	0.128
AJ	0.546	0.57
Bibs02	0.0	0.162
Bibs02c	0.588	0.318
BL6	0.22	-0.053
BL6a	0.455	0.471
BXD01	0.05	0.587
BXD010	0.168	0.534
BXD011	0.112	0.557
BXD03	-0.091	-0.042
BXD04	0.291	0.582
BXD05	-0.244	0.634
BXD06	0.22	0.566
BXD07	-0.032	0.283
BXD08	0.132	0.237
BXD09	0.236	0.465
CAST	0.506	0.489
CCcont	0.043	0.059
DS01	0.185	0.71
DS02	0.495	0.517
DS04	-0.07	0.492
DS0c	0.176	0.368
GP01	0.273	0.503
GP02	0.114	0.523
GP0c	-0.022	0.496
NOD	1.71	0.657
NZO	0.363	0.522
PWK	0.482	0.281
H37Rv_KO_CtpC	0.437	0.743
H37Rv_KO_CtpD	0.656	1.346
H37Rv_KO_Rv1272	0.346	1.285
H37Rv_KO_SugABC	0.607	1.237
H37Rv_KO_MbtN	0.892	0.899
Trans05	0.842	1.105
macrophage_unactivated	0.413	0.275
IL1	-0.51	-0.116
Rapamycin	0.077	-0.203
Tcell	-0.222	0.44
GMCSF	-0.235	0.325
IFNab	-0.187	-0.366
IFNg	0.094	0.035
IFNg_GMCSF1	0.248	-0.082
Rv1432_day32	0.623	0.139
Rv1565c_day32	-0.316	0.366
secA2_input	-0.726	-0.675
delta_Rv3594	-0.494	0.503
delta_Rv3717	-0.488	0.072
delta_Rv3811	-0.175	0.363
delta_Rv0954	-0.552	-0.36
PonA1	-0.545	-0.493
EccD1_KO	-0.135	-0.138
EspI_KO	0.225	-0.12
PE35_KO	-0.152	-0.123
PPE68_KO	-0.33	-0.067
glycerol2	0.737	0.303
lignocerate	0.811	0.424
oleate	0.777	0.289
phosphatidylcholine	0.817	0.641
acetate	0.243	0.209
glucAc	0.267	0.274
Rv0950ko	0.166	-0.187
Rv1096ko	-0.621	-0.841
Rv3684ko	-0.606	-0.796
delta_otsA_trehalose	-0.267	-0.262