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 Rv3150/nuoF:

update plot	correlation	link to info on gene
Rv3146/nuoB	(cc=0.8695)	info on Rv3146/nuoB
Rv3152/nuoH	(cc=0.8676)	info on Rv3152/nuoH
Rv3153/nuoI	(cc=0.8414)	info on Rv3153/nuoI
Rv3148/nuoD	(cc=0.8182)	info on Rv3148/nuoD
Rv3151/nuoG	(cc=0.7969)	info on Rv3151/nuoG
Rv3145/nuoA	(cc=0.7635)	info on Rv3145/nuoA
Rv3158/nuoN	(cc=0.7516)	info on Rv3158/nuoN
Rv3156/nuoL	(cc=0.7338)	info on Rv3156/nuoL
Rv3818/-	(cc=0.6963)	info on Rv3818/-
Rv1059/-	(cc=0.6944)	info on Rv1059/-

Correlation of Rv3150/nuoF with Rv3145/nuoA

Normalized LFCs for Rv3150/nuoF:
(description and provenance of datasets)

	Rv3150/nuoF	Rv3145/nuoA
Fe_supp_jason_reseq	-1.514	-1.179
low_pH_jason_reseq	-0.313	-1.959
NO_jason_reseq	-0.252	-0.357
B6_jason_reseq	-1.087	-0.294
MHCII_jason_reseq	-1.509	-1.336
Isoniazid02	0.611	0.054
Rifampicin4	0.282	0.295
Ethambutol3	-0.595	0.832
Meropenem3	-0.847	-0.646
Vancomycin16	-0.196	-0.931
Rv2680_day32	0.266	-0.768
H37Rv_KO_MarP	-0.246	-1.171
hypoxia_3wks	1.097	1.284
hypoxia_6wks	0.754	1.059
glycerol	-0.471	-0.831
cholesterol	-0.216	-1.031
AJ	-0.983	0.013
Bibs02	0.55	0.738
Bibs02c	-0.23	-0.256
BL6	1.845	1.561
BL6a	2.251	1.574
BXD01	1.864	1.616
BXD010	2.266	1.38
BXD011	2.05	1.62
BXD03	2.177	1.234
BXD04	2.337	1.514
BXD05	2.126	1.456
BXD06	2.045	1.549
BXD07	2.3	1.562
BXD08	2.274	1.655
BXD09	2.374	1.726
CAST	0.506	0.782
CCcont	1.451	0.596
DS01	0.583	0.79
DS02	0.147	0.432
DS04	0.426	1.039
DS0c	0.969	1.2
GP01	0.715	0.549
GP02	0.875	0.709
GP0c	1.092	0.633
NOD	-0.838	-0.07
NZO	0.38	-0.584
PWK	-0.142	0.236
H37Rv_KO_CtpC	1.463	0.621
H37Rv_KO_CtpD	2.661	0.822
H37Rv_KO_Rv1272	1.929	1.298
H37Rv_KO_SugABC	1.426	1.78
H37Rv_KO_MbtN	1.537	0.813
Trans05	1.798	2.421
macrophage_unactivated	0.284	-0.322
IL1	0.267	-0.54
Rapamycin	0.365	-0.915
Tcell	0.746	0.31
GMCSF	0.388	0.108
IFNab	1.69	0.502
IFNg	-0.302	0.056
IFNg_GMCSF1	0.145	-0.016
Rv1432_day32	0.568	-0.641
Rv1565c_day32	-0.208	-0.605
secA2_input	-0.116	-0.421
delta_Rv3594	0.392	0.769
delta_Rv3717	0.299	0.594
delta_Rv3811	0.094	0.504
delta_Rv0954	-0.057	0.81
PonA1	-0.39	0.312
EccD1_KO	-0.474	0.086
EspI_KO	-0.177	0.334
PE35_KO	-0.467	0.776
PPE68_KO	0.0	1.043
glycerol2	1.866	2.566
lignocerate	-0.192	-0.301
oleate	2.076	2.451
phosphatidylcholine	-0.221	-0.38
acetate	-0.263	0.198
glucAc	0.587	1.023
Rv0950ko	0.311	1.022
Rv1096ko	0.639	0.685
Rv3684ko	0.098	0.115
delta_otsA_trehalose	0.965	0.229