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 Rv3446c/-

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

	Rv1845c/blaR	Rv3446c/-
Fe_supp_jason_reseq	1.796	-0.393
low_pH_jason_reseq	6.0	3.503
NO_jason_reseq	0.0	-0.412
B6_jason_reseq	0.0	-0.747
MHCII_jason_reseq	0.0	-0.257
Isoniazid02	0.0	0.081
Rifampicin4	0.0	-0.157
Ethambutol3	0.0	0.0
Meropenem3	0.0	1.33
Vancomycin16	0.0	0.292
Rv2680_day32	0.0	-0.803
H37Rv_KO_MarP	0.961	0.45
hypoxia_3wks	0.0	-0.538
hypoxia_6wks	0.0	-0.816
glycerol	1.24	-0.123
cholesterol	0.0	-0.222
AJ	0.0	-0.771
Bibs02	0.0	-0.066
Bibs02c	0.0	0.488
BL6	0.0	0.014
BL6a	0.0	0.023
BXD01	0.13	-0.063
BXD010	0.0	-0.145
BXD011	0.0	-0.445
BXD03	0.0	1.195
BXD04	0.0	-0.06
BXD05	0.0	-0.049
BXD06	0.254	-0.048
BXD07	0.0	0.448
BXD08	0.0	-0.081
BXD09	0.0	-0.034
CAST	0.0	-0.385
CCcont	0.285	0.0
DS01	0.0	0.188
DS02	0.217	-0.189
DS04	0.37	0.112
DS0c	0.0	-1.193
GP01	0.099	0.0
GP02	0.0	-0.708
GP0c	0.357	0.398
NOD	0.0	0.155
NZO	0.0	-0.199
PWK	0.0	0.401
H37Rv_KO_CtpC	0.162	0.165
H37Rv_KO_CtpD	0.918	0.432
H37Rv_KO_Rv1272	0.0	-0.016
H37Rv_KO_SugABC	0.099	-1.114
H37Rv_KO_MbtN	0.943	-0.202
Trans05	0.0	-1.381
macrophage_unactivated	0.0	-0.054
IL1	0.0	-1.916
Rapamycin	0.0	-1.823
Tcell	0.0	0.72
GMCSF	0.0	-1.149
IFNab	0.0	-1.796
IFNg	0.0	-1.384
IFNg_GMCSF1	0.0	-1.904
Rv1432_day32	0.0	0.072
Rv1565c_day32	0.0	0.711
secA2_input	3.034	-0.7
delta_Rv3594	-1.319	0.133
delta_Rv3717	-0.927	0.312
delta_Rv3811	-1.096	0.906
delta_Rv0954	-0.196	0.49
PonA1	2.086	0.944
EccD1_KO	0.77	0.352
EspI_KO	0.667	-0.687
PE35_KO	-1.467	-0.948
PPE68_KO	-0.579	-0.669
glycerol2	0.0	0.057
lignocerate	0.0	0.362
oleate	0.0	-0.06
phosphatidylcholine	0.0	0.14
acetate	0.0	0.229
glucAc	0.0	0.289
Rv0950ko	-0.844	0.431
Rv1096ko	-0.546	0.727
Rv3684ko	2.184	0.684
delta_otsA_trehalose	-4.196	-1.129