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 Rv3770B/-:

update plot	correlation	link to info on gene
Rv1831/-	(cc=0.5911)	info on Rv1831/-
Rv0222/echA1	(cc=0.5824)	info on Rv0222/echA1
Rv1616/-	(cc=0.5693)	info on Rv1616/-
Rv3146/nuoB	(cc=0.5674)	info on Rv3146/nuoB
Rv0309/-	(cc=0.5335)	info on Rv0309/-
Rv1505c/-	(cc=0.5273)	info on Rv1505c/-
Rv2825c/-	(cc=0.5243)	info on Rv2825c/-
Rv2495c/bkdC	(cc=0.5208)	info on Rv2495c/bkdC
Rv2456c/-	(cc=0.5148)	info on Rv2456c/-
Rv3470c/ilvB2	(cc=0.514)	info on Rv3470c/ilvB2

Correlation of Rv3770B/- with Rv2825c/-

Normalized LFCs for Rv3770B/-:
(description and provenance of datasets)

	Rv3770B/-	Rv2825c/-
Fe_supp_jason_reseq	-1.675	0.169
low_pH_jason_reseq	-1.302	0.741
NO_jason_reseq	-0.16	-1.121
B6_jason_reseq	-2.219	-1.759
MHCII_jason_reseq	-3.504	-1.171
Isoniazid02	0.819	0.281
Rifampicin4	-0.842	1.394
Ethambutol3	0.026	0.34
Meropenem3	-0.31	1.792
Vancomycin16	1.173	0.629
Rv2680_day32	0.368	0.0
H37Rv_KO_MarP	-0.346	0.279
hypoxia_3wks	-0.211	0.961
hypoxia_6wks	-0.342	0.384
glycerol	1.542	-0.184
cholesterol	2.008	0.696
AJ	0.18	-0.212
Bibs02	-0.319	0.294
Bibs02c	0.681	-0.399
BL6	2.153	2.513
BL6a	2.365	1.6
BXD01	1.88	1.292
BXD010	1.015	0.385
BXD011	1.725	0.68
BXD03	1.77	0.856
BXD04	3.099	1.792
BXD05	2.054	2.578
BXD06	2.271	1.963
BXD07	2.047	2.353
BXD08	2.3	1.837
BXD09	2.524	1.941
CAST	2.865	1.346
CCcont	1.557	1.146
DS01	-1.619	-0.45
DS02	0.128	0.792
DS04	2.781	3.195
DS0c	1.114	0.506
GP01	1.543	-0.188
GP02	-1.205	-0.159
GP0c	0.404	0.391
NOD	2.257	0.361
NZO	-1.793	0.465
PWK	1.361	0.315
H37Rv_KO_CtpC	-0.033	1.957
H37Rv_KO_CtpD	0.121	-0.241
H37Rv_KO_Rv1272	0.918	1.195
H37Rv_KO_SugABC	1.782	4.445
H37Rv_KO_MbtN	2.066	1.122
Trans05	2.42	0.764
macrophage_unactivated	0.331	-1.253
IL1	0.211	0.922
Rapamycin	0.028	1.086
Tcell	1.219	-0.267
GMCSF	-0.145	0.987
IFNab	1.533	0.387
IFNg	0.457	0.275
IFNg_GMCSF1	1.389	-0.534
Rv1432_day32	0.0	0.0
Rv1565c_day32	1.204	0.0
secA2_input	-0.266	-1.327
delta_Rv3594	1.747	1.53
delta_Rv3717	0.292	1.403
delta_Rv3811	0.836	3.557
delta_Rv0954	-0.942	2.149
PonA1	1.377	1.526
EccD1_KO	0.664	1.108
EspI_KO	0.693	0.0
PE35_KO	0.825	3.436
PPE68_KO	-0.358	4.278
glycerol2	0.464	-0.413
lignocerate	-0.884	-0.812
oleate	0.224	-0.077
phosphatidylcholine	0.231	-0.266
acetate	-1.584	-0.928
glucAc	-2.417	-2.419
Rv0950ko	1.098	0.0
Rv1096ko	1.794	2.135
Rv3684ko	1.677	2.414
delta_otsA_trehalose	-2.395	-2.372