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 Rv1534/-

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

	Rv1845c/blaR	Rv1534/-
Fe_supp_jason_reseq	1.796	0.834
low_pH_jason_reseq	6.0	1.186
NO_jason_reseq	0.0	0.347
B6_jason_reseq	0.0	-0.421
MHCII_jason_reseq	0.0	0.676
Isoniazid02	0.0	-1.31
Rifampicin4	0.0	0.035
Ethambutol3	0.0	0.179
Meropenem3	0.0	0.562
Vancomycin16	0.0	-0.629
Rv2680_day32	0.0	-0.24
H37Rv_KO_MarP	0.961	0.492
hypoxia_3wks	0.0	-0.65
hypoxia_6wks	0.0	-0.223
glycerol	1.24	1.325
cholesterol	0.0	0.844
AJ	0.0	0.521
Bibs02	0.0	-0.42
Bibs02c	0.0	0.206
BL6	0.0	-1.264
BL6a	0.0	-0.383
BXD01	0.13	-1.002
BXD010	0.0	-1.63
BXD011	0.0	-0.637
BXD03	0.0	-0.811
BXD04	0.0	-1.349
BXD05	0.0	-0.493
BXD06	0.254	-1.349
BXD07	0.0	-1.065
BXD08	0.0	-1.023
BXD09	0.0	-0.806
CAST	0.0	-0.796
CCcont	0.285	-0.137
DS01	0.0	0.416
DS02	0.217	-0.309
DS04	0.37	-0.836
DS0c	0.0	0.512
GP01	0.099	0.233
GP02	0.0	0.104
GP0c	0.357	0.519
NOD	0.0	0.366
NZO	0.0	-0.029
PWK	0.0	0.597
H37Rv_KO_CtpC	0.162	-0.073
H37Rv_KO_CtpD	0.918	-0.138
H37Rv_KO_Rv1272	0.0	0.061
H37Rv_KO_SugABC	0.099	-0.174
H37Rv_KO_MbtN	0.943	-0.762
Trans05	0.0	-1.27
macrophage_unactivated	0.0	1.215
IL1	0.0	-0.78
Rapamycin	0.0	-0.522
Tcell	0.0	0.495
GMCSF	0.0	-0.108
IFNab	0.0	0.671
IFNg	0.0	0.0
IFNg_GMCSF1	0.0	-0.396
Rv1432_day32	0.0	-1.212
Rv1565c_day32	0.0	0.831
secA2_input	3.034	0.388
delta_Rv3594	-1.319	-1.144
delta_Rv3717	-0.927	-0.466
delta_Rv3811	-1.096	-0.025
delta_Rv0954	-0.196	0.553
PonA1	2.086	0.223
EccD1_KO	0.77	0.441
EspI_KO	0.667	0.0
PE35_KO	-1.467	0.283
PPE68_KO	-0.579	0.429
glycerol2	0.0	-0.426
lignocerate	0.0	-0.636
oleate	0.0	-0.936
phosphatidylcholine	0.0	-0.244
acetate	0.0	0.565
glucAc	0.0	0.161
Rv0950ko	-0.844	0.691
Rv1096ko	-0.546	0.971
Rv3684ko	2.184	0.933
delta_otsA_trehalose	-4.196	-2.406