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 Rv1308/atpA

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

	Rv1845c/blaR	Rv1308/atpA
Fe_supp_jason_reseq	1.796	0.655
low_pH_jason_reseq	6.0	4.256
NO_jason_reseq	0.0	3.208
B6_jason_reseq	0.0	1.57
MHCII_jason_reseq	0.0	-0.257
Isoniazid02	0.0	0.0
Rifampicin4	0.0	0.0
Ethambutol3	0.0	0.168
Meropenem3	0.0	0.0
Vancomycin16	0.0	0.0
Rv2680_day32	0.0	0.0
H37Rv_KO_MarP	0.961	1.782
hypoxia_3wks	0.0	-0.961
hypoxia_6wks	0.0	0.0
glycerol	1.24	0.531
cholesterol	0.0	-0.509
AJ	0.0	-0.18
Bibs02	0.0	1.031
Bibs02c	0.0	0.293
BL6	0.0	-0.439
BL6a	0.0	-0.499
BXD01	0.13	1.167
BXD010	0.0	-0.45
BXD011	0.0	0.407
BXD03	0.0	-0.475
BXD04	0.0	-0.312
BXD05	0.0	0.636
BXD06	0.254	0.351
BXD07	0.0	0.718
BXD08	0.0	-0.214
BXD09	0.0	0.285
CAST	0.0	0.859
CCcont	0.285	-0.525
DS01	0.0	-0.38
DS02	0.217	0.158
DS04	0.37	1.093
DS0c	0.0	0.44
GP01	0.099	-0.347
GP02	0.0	-0.21
GP0c	0.357	-0.457
NOD	0.0	0.0
NZO	0.0	1.849
PWK	0.0	0.274
H37Rv_KO_CtpC	0.162	0.0
H37Rv_KO_CtpD	0.918	1.135
H37Rv_KO_Rv1272	0.0	-0.495
H37Rv_KO_SugABC	0.099	-0.348
H37Rv_KO_MbtN	0.943	0.821
Trans05	0.0	0.265
macrophage_unactivated	0.0	-0.436
IL1	0.0	-0.409
Rapamycin	0.0	-0.424
Tcell	0.0	0.411
GMCSF	0.0	-0.364
IFNab	0.0	-0.417
IFNg	0.0	-0.369
IFNg_GMCSF1	0.0	-0.434
Rv1432_day32	0.0	0.0
Rv1565c_day32	0.0	0.0
secA2_input	3.034	0.302
delta_Rv3594	-1.319	-0.119
delta_Rv3717	-0.927	0.424
delta_Rv3811	-1.096	-1.377
delta_Rv0954	-0.196	-1.196
PonA1	2.086	-1.069
EccD1_KO	0.77	0.414
EspI_KO	0.667	-0.394
PE35_KO	-1.467	0.0
PPE68_KO	-0.579	0.0
glycerol2	0.0	-1.153
lignocerate	0.0	-1.296
oleate	0.0	-0.391
phosphatidylcholine	0.0	-0.864
acetate	0.0	-1.026
glucAc	0.0	-1.1
Rv0950ko	-0.844	0.416
Rv1096ko	-0.546	1.463
Rv3684ko	2.184	1.241
delta_otsA_trehalose	-4.196	0.133