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 Rv0045c/-

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

	Rv1564c/treX	Rv0045c/-
Fe_supp_jason_reseq	0.115	0.309
low_pH_jason_reseq	0.877	-0.602
NO_jason_reseq	0.617	-0.394
B6_jason_reseq	1.042	1.451
MHCII_jason_reseq	0.449	1.068
Isoniazid02	0.048	-0.17
Rifampicin4	0.845	0.801
Ethambutol3	0.395	0.131
Meropenem3	1.053	0.323
Vancomycin16	0.417	0.459
Rv2680_day32	0.667	-0.091
H37Rv_KO_MarP	0.742	0.33
hypoxia_3wks	1.902	0.179
hypoxia_6wks	0.647	0.405
glycerol	-0.344	-0.521
cholesterol	-0.247	-0.524
AJ	0.166	0.558
Bibs02	0.409	0.513
Bibs02c	-0.039	-0.823
BL6	0.985	0.278
BL6a	0.29	0.093
BXD01	0.412	0.464
BXD010	0.482	1.14
BXD011	0.463	0.879
BXD03	0.544	0.524
BXD04	0.357	0.692
BXD05	0.607	1.081
BXD06	0.658	1.136
BXD07	0.931	0.646
BXD08	0.226	0.115
BXD09	0.356	0.526
CAST	0.697	-0.2
CCcont	-0.028	-1.136
DS01	-0.852	-0.727
DS02	-0.517	-0.534
DS04	-0.885	0.013
DS0c	-0.841	-0.905
GP01	0.969	-0.486
GP02	0.217	0.683
GP0c	0.464	-0.287
NOD	-0.241	0.906
NZO	0.851	-0.019
PWK	1.611	1.006
H37Rv_KO_CtpC	-0.586	-0.265
H37Rv_KO_CtpD	-0.346	0.358
H37Rv_KO_Rv1272	-0.319	-0.636
H37Rv_KO_SugABC	0.293	1.325
H37Rv_KO_MbtN	1.052	0.083
Trans05	0.222	0.116
macrophage_unactivated	0.0	-0.871
IL1	0.258	-0.561
Rapamycin	-0.08	-0.396
Tcell	-0.085	0.482
GMCSF	0.0	-0.66
IFNab	-0.039	-0.333
IFNg	0.102	0.011
IFNg_GMCSF1	0.352	-0.383
Rv1432_day32	0.997	0.228
Rv1565c_day32	0.103	0.275
secA2_input	-0.753	0.196
delta_Rv3594	-0.621	-0.095
delta_Rv3717	0.17	-0.635
delta_Rv3811	-0.631	0.59
delta_Rv0954	-0.255	-0.767
PonA1	-0.557	-1.421
EccD1_KO	-1.503	-0.046
EspI_KO	-1.101	-0.125
PE35_KO	-0.379	0.283
PPE68_KO	-0.806	0.288
glycerol2	-0.926	0.298
lignocerate	-0.788	-0.212
oleate	-0.917	0.357
phosphatidylcholine	-0.711	0.01
acetate	-0.404	-0.022
glucAc	-0.206	-0.591
Rv0950ko	-0.112	-0.021
Rv1096ko	-0.29	0.739
Rv3684ko	-0.445	0.088
delta_otsA_trehalose	3.876	2.269