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 Rv2593c/ruvA:

update plot	correlation	link to info on gene
Rv3274c/fadE25	(cc=0.4984)	info on Rv3274c/fadE25
Rv1157c/-	(cc=0.3966)	info on Rv1157c/-
Rv3593/lpqF	(cc=0.3871)	info on Rv3593/lpqF
Rv0495c/-	(cc=0.3836)	info on Rv0495c/-
Rv2522c/-	(cc=0.3582)	info on Rv2522c/-
Rv0324/-	(cc=0.3537)	info on Rv0324/-
Rv2198c/mmpS3	(cc=0.3531)	info on Rv2198c/mmpS3
Rv1423/whiA	(cc=0.3485)	info on Rv1423/whiA
Rv3243c/-	(cc=0.3458)	info on Rv3243c/-
Rv0859/fadA	(cc=0.337)	info on Rv0859/fadA

Correlation of Rv2593c/ruvA with Rv3243c/-

Normalized LFCs for Rv2593c/ruvA:
(description and provenance of datasets)

	Rv2593c/ruvA	Rv3243c/-
Fe_supp_jason_reseq	0.218	0.265
low_pH_jason_reseq	0.0	2.416
NO_jason_reseq	0.0	-0.777
B6_jason_reseq	0.0	0.186
MHCII_jason_reseq	0.0	-1.249
Isoniazid02	0.0	0.089
Rifampicin4	0.0	1.289
Ethambutol3	0.153	0.281
Meropenem3	0.151	0.277
Vancomycin16	0.0	0.753
Rv2680_day32	0.0	0.131
H37Rv_KO_MarP	-0.255	0.881
hypoxia_3wks	0.0	-0.542
hypoxia_6wks	0.0	-2.088
glycerol	1.355	1.217
cholesterol	0.145	0.639
AJ	0.0	-0.711
Bibs02	0.0	0.89
Bibs02c	0.0	-0.544
BL6	0.0	0.507
BL6a	0.0	0.804
BXD01	0.0	1.137
BXD010	0.0	0.679
BXD011	0.0	0.149
BXD03	0.0	-1.758
BXD04	0.0	0.221
BXD05	0.0	0.699
BXD06	0.0	0.693
BXD07	0.0	0.734
BXD08	0.0	-0.024
BXD09	0.0	1.042
CAST	0.0	-0.214
CCcont	0.0	1.337
DS01	0.0	0.041
DS02	0.0	-0.772
DS04	0.0	1.05
DS0c	0.0	-0.77
GP01	0.0	-1.832
GP02	0.0	-1.251
GP0c	0.0	-2.282
NOD	0.0	-0.913
NZO	0.0	-0.224
PWK	0.0	0.102
H37Rv_KO_CtpC	0.0	-1.599
H37Rv_KO_CtpD	0.0	-1.572
H37Rv_KO_Rv1272	0.0	-1.522
H37Rv_KO_SugABC	0.0	-0.634
H37Rv_KO_MbtN	0.0	-1.221
Trans05	0.0	0.761
macrophage_unactivated	0.0	-1.004
IL1	0.0	-1.631
Rapamycin	0.0	0.574
Tcell	0.0	-0.593
GMCSF	0.0	-2.915
IFNab	0.0	0.49
IFNg	0.0	0.567
IFNg_GMCSF1	0.0	-1.596
Rv1432_day32	0.0	-0.057
Rv1565c_day32	0.0	-2.578
secA2_input	-0.157	-0.662
delta_Rv3594	0.0	-0.662
delta_Rv3717	-0.331	-1.353
delta_Rv3811	-0.391	-3.637
delta_Rv0954	0.416	-0.266
PonA1	-0.304	-1.916
EccD1_KO	0.414	2.358
EspI_KO	-0.394	0.761
PE35_KO	0.0	0.534
PPE68_KO	-0.442	-0.16
glycerol2	0.0	4.126
lignocerate	0.0	4.86
oleate	0.0	0.196
phosphatidylcholine	0.0	3.989
acetate	1.662	5.617
glucAc	0.0	4.009
Rv0950ko	-0.727	1.815
Rv1096ko	-0.347	0.971
Rv3684ko	0.0	-0.93
delta_otsA_trehalose	0.35	1.715