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 Rv1564c/treX:

update plot	correlation	link to info on gene
Rv3363c/-	(cc=0.5751)	info on Rv3363c/-
Rv3168/-	(cc=0.5383)	info on Rv3168/-
Rv3218/-	(cc=0.479)	info on Rv3218/-
Rv0045c/-	(cc=0.4724)	info on Rv0045c/-
Rv1513/-	(cc=0.4578)	info on Rv1513/-
Rv2655c/-	(cc=0.4573)	info on Rv2655c/-
Rv0551c/fadD8	(cc=0.457)	info on Rv0551c/fadD8
Rv3320c/vapC44	(cc=0.4508)	info on Rv3320c/vapC44
Rv0592/mce2D	(cc=0.4396)	info on Rv0592/mce2D
Rv0112/gca	(cc=0.4356)	info on Rv0112/gca

Correlation of Rv1564c/treX with Rv3168/-

Normalized LFCs for Rv1564c/treX:
(description and provenance of datasets)

	Rv1564c/treX	Rv3168/-
Fe_supp_jason_reseq	0.115	0.789
low_pH_jason_reseq	0.877	0.383
NO_jason_reseq	0.617	0.711
B6_jason_reseq	1.042	0.903
MHCII_jason_reseq	0.449	0.85
Isoniazid02	0.048	0.383
Rifampicin4	0.845	-0.872
Ethambutol3	0.395	-0.06
Meropenem3	1.053	0.056
Vancomycin16	0.417	0.905
Rv2680_day32	0.667	0.465
H37Rv_KO_MarP	0.742	-0.209
hypoxia_3wks	1.902	2.121
hypoxia_6wks	0.647	2.397
glycerol	-0.344	-0.098
cholesterol	-0.247	0.338
AJ	0.166	0.309
Bibs02	0.409	1.142
Bibs02c	-0.039	-0.209
BL6	0.985	-1.322
BL6a	0.29	0.264
BXD01	0.412	0.422
BXD010	0.482	0.766
BXD011	0.463	0.655
BXD03	0.544	-0.245
BXD04	0.357	0.981
BXD05	0.607	0.975
BXD06	0.658	1.117
BXD07	0.931	0.97
BXD08	0.226	-0.204
BXD09	0.356	1.002
CAST	0.697	0.537
CCcont	-0.028	-1.578
DS01	-0.852	0.163
DS02	-0.517	-0.654
DS04	-0.885	-0.71
DS0c	-0.841	-0.793
GP01	0.969	-1.43
GP02	0.217	-0.996
GP0c	0.464	-1.292
NOD	-0.241	-0.109
NZO	0.851	0.348
PWK	1.611	0.769
H37Rv_KO_CtpC	-0.586	-0.039
H37Rv_KO_CtpD	-0.346	-0.229
H37Rv_KO_Rv1272	-0.319	-0.666
H37Rv_KO_SugABC	0.293	1.598
H37Rv_KO_MbtN	1.052	-0.487
Trans05	0.222	-0.063
macrophage_unactivated	0.0	-0.496
IL1	0.258	-0.128
Rapamycin	-0.08	0.19
Tcell	-0.085	0.645
GMCSF	0.0	-0.478
IFNab	-0.039	-0.13
IFNg	0.102	1.165
IFNg_GMCSF1	0.352	0.562
Rv1432_day32	0.997	-0.632
Rv1565c_day32	0.103	0.0
secA2_input	-0.753	-0.401
delta_Rv3594	-0.621	0.493
delta_Rv3717	0.17	0.555
delta_Rv3811	-0.631	-0.077
delta_Rv0954	-0.255	0.306
PonA1	-0.557	-0.328
EccD1_KO	-1.503	-1.273
EspI_KO	-1.101	-2.048
PE35_KO	-0.379	-0.169
PPE68_KO	-0.806	0.0
glycerol2	-0.926	-0.902
lignocerate	-0.788	-1.525
oleate	-0.917	-0.978
phosphatidylcholine	-0.711	-0.839
acetate	-0.404	-1.478
glucAc	-0.206	-2.128
Rv0950ko	-0.112	0.736
Rv1096ko	-0.29	1.016
Rv3684ko	-0.445	-1.277
delta_otsA_trehalose	3.876	2.697