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 Rv2958c/-

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

	Rv3784/-	Rv2958c/-
Fe_supp_jason_reseq	0.006	0.218
low_pH_jason_reseq	-0.898	-0.591
NO_jason_reseq	-0.21	-0.412
B6_jason_reseq	0.092	-0.317
MHCII_jason_reseq	0.297	0.082
Isoniazid02	0.688	0.674
Rifampicin4	-0.138	0.103
Ethambutol3	1.0	0.818
Meropenem3	0.948	0.367
Vancomycin16	0.066	0.257
Rv2680_day32	0.337	0.459
H37Rv_KO_MarP	0.03	0.464
hypoxia_3wks	-0.04	0.016
hypoxia_6wks	0.092	-0.495
glycerol	0.522	-1.678
cholesterol	0.186	-0.524
AJ	0.546	0.212
Bibs02	0.0	0.257
Bibs02c	0.588	0.382
BL6	0.22	-0.448
BL6a	0.455	0.211
BXD01	0.05	-0.022
BXD010	0.168	0.164
BXD011	0.112	0.071
BXD03	-0.091	-0.041
BXD04	0.291	0.179
BXD05	-0.244	0.198
BXD06	0.22	-0.162
BXD07	-0.032	-0.105
BXD08	0.132	0.008
BXD09	0.236	-0.21
CAST	0.506	0.092
CCcont	0.043	-0.071
DS01	0.185	0.269
DS02	0.495	0.263
DS04	-0.07	0.548
DS0c	0.176	0.225
GP01	0.273	0.408
GP02	0.114	0.959
GP0c	-0.022	-0.35
NOD	1.71	0.937
NZO	0.363	0.475
PWK	0.482	0.485
H37Rv_KO_CtpC	0.437	0.377
H37Rv_KO_CtpD	0.656	0.694
H37Rv_KO_Rv1272	0.346	0.96
H37Rv_KO_SugABC	0.607	0.495
H37Rv_KO_MbtN	0.892	0.425
Trans05	0.842	1.058
macrophage_unactivated	0.413	0.136
IL1	-0.51	-0.744
Rapamycin	0.077	-0.276
Tcell	-0.222	-0.306
GMCSF	-0.235	-0.177
IFNab	-0.187	-0.414
IFNg	0.094	-0.179
IFNg_GMCSF1	0.248	0.277
Rv1432_day32	0.623	0.365
Rv1565c_day32	-0.316	0.303
secA2_input	-0.726	-0.524
delta_Rv3594	-0.494	0.366
delta_Rv3717	-0.488	-0.198
delta_Rv3811	-0.175	0.26
delta_Rv0954	-0.552	-0.059
PonA1	-0.545	-0.108
EccD1_KO	-0.135	0.28
EspI_KO	0.225	0.342
PE35_KO	-0.152	0.586
PPE68_KO	-0.33	0.394
glycerol2	0.737	0.509
lignocerate	0.811	0.6
oleate	0.777	0.509
phosphatidylcholine	0.817	0.71
acetate	0.243	0.166
glucAc	0.267	0.194
Rv0950ko	0.166	0.066
Rv1096ko	-0.621	-0.682
Rv3684ko	-0.606	-0.465
delta_otsA_trehalose	-0.267	0.014