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 Rv1845c/blaR:

update plot	correlation	link to info on gene
Rv3645/-	(cc=0.5428)	info on Rv3645/-
Rv2207/cobT	(cc=0.5397)	info on Rv2207/cobT
Rv1458c/-	(cc=0.4975)	info on Rv1458c/-
Rv1349/irtB	(cc=0.4542)	info on Rv1349/irtB
Rv1081c/-	(cc=0.4414)	info on Rv1081c/-
Rv3446c/-	(cc=0.4167)	info on Rv3446c/-
Rv1692/-	(cc=0.4155)	info on Rv1692/-
Rv1308/atpA	(cc=0.4149)	info on Rv1308/atpA
Rv1534/-	(cc=0.4056)	info on Rv1534/-
Rv3776/-	(cc=0.4001)	info on Rv3776/-

Correlation of Rv1845c/blaR with Rv1692/-

Normalized LFCs for Rv1845c/blaR:
(description and provenance of datasets)

	Rv1845c/blaR	Rv1692/-
Fe_supp_jason_reseq	1.796	1.716
low_pH_jason_reseq	6.0	2.441
NO_jason_reseq	0.0	-1.25
B6_jason_reseq	0.0	-0.6
MHCII_jason_reseq	0.0	0.315
Isoniazid02	0.0	0.845
Rifampicin4	0.0	0.642
Ethambutol3	0.0	-0.232
Meropenem3	0.0	1.665
Vancomycin16	0.0	0.751
Rv2680_day32	0.0	-0.315
H37Rv_KO_MarP	0.961	-0.419
hypoxia_3wks	0.0	-0.227
hypoxia_6wks	0.0	0.28
glycerol	1.24	0.85
cholesterol	0.0	0.659
AJ	0.0	-0.188
Bibs02	0.0	-0.403
Bibs02c	0.0	0.174
BL6	0.0	-2.353
BL6a	0.0	-0.034
BXD01	0.13	-1.346
BXD010	0.0	-1.21
BXD011	0.0	-0.673
BXD03	0.0	-1.336
BXD04	0.0	-1.567
BXD05	0.0	-1.034
BXD06	0.254	-1.05
BXD07	0.0	-1.498
BXD08	0.0	-1.174
BXD09	0.0	-1.106
CAST	0.0	-1.942
CCcont	0.285	-0.039
DS01	0.0	-0.236
DS02	0.217	-0.411
DS04	0.37	0.628
DS0c	0.0	0.771
GP01	0.099	-0.69
GP02	0.0	2.275
GP0c	0.357	-0.343
NOD	0.0	0.727
NZO	0.0	-0.811
PWK	0.0	-1.064
H37Rv_KO_CtpC	0.162	-0.289
H37Rv_KO_CtpD	0.918	0.625
H37Rv_KO_Rv1272	0.0	0.226
H37Rv_KO_SugABC	0.099	0.136
H37Rv_KO_MbtN	0.943	-1.467
Trans05	0.0	-0.87
macrophage_unactivated	0.0	0.271
IL1	0.0	-0.813
Rapamycin	0.0	0.516
Tcell	0.0	-1.411
GMCSF	0.0	0.486
IFNab	0.0	1.336
IFNg	0.0	-0.909
IFNg_GMCSF1	0.0	-1.285
Rv1432_day32	0.0	-0.498
Rv1565c_day32	0.0	-0.747
secA2_input	3.034	0.751
delta_Rv3594	-1.319	-0.661
delta_Rv3717	-0.927	-2.164
delta_Rv3811	-1.096	-1.411
delta_Rv0954	-0.196	1.512
PonA1	2.086	1.132
EccD1_KO	0.77	1.075
EspI_KO	0.667	1.483
PE35_KO	-1.467	0.394
PPE68_KO	-0.579	0.256
glycerol2	0.0	-0.219
lignocerate	0.0	-0.045
oleate	0.0	0.269
phosphatidylcholine	0.0	-0.307
acetate	0.0	0.369
glucAc	0.0	0.34
Rv0950ko	-0.844	0.208
Rv1096ko	-0.546	0.139
Rv3684ko	2.184	-0.318
delta_otsA_trehalose	-4.196	-1.562