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 Rv3406/-:

update plot	correlation	link to info on gene
Rv2679/echA15	(cc=0.5782)	info on Rv2679/echA15
Rv0342/iniA	(cc=0.5703)	info on Rv0342/iniA
Rv3504/fadE26	(cc=0.5238)	info on Rv3504/fadE26
Rv3329/-	(cc=0.5224)	info on Rv3329/-
Rv0443/-	(cc=0.5187)	info on Rv0443/-
Rv3397c/phyA	(cc=0.5177)	info on Rv3397c/phyA
Rv3191c/-	(cc=0.505)	info on Rv3191c/-
Rv0399c/lpqK	(cc=0.5021)	info on Rv0399c/lpqK
Rv0968/-	(cc=0.4967)	info on Rv0968/-
Rv0104/-	(cc=0.4936)	info on Rv0104/-

Correlation of Rv3406/- with Rv3397c/phyA

Normalized LFCs for Rv3406/-:
(description and provenance of datasets)

	Rv3406/-	Rv3397c/phyA
Fe_supp_jason_reseq	-0.343	-0.665
low_pH_jason_reseq	-0.477	-0.343
NO_jason_reseq	-0.347	0.512
B6_jason_reseq	-0.298	-0.843
MHCII_jason_reseq	0.298	-1.389
Isoniazid02	-1.986	-2.929
Rifampicin4	0.368	-1.449
Ethambutol3	-1.893	-2.479
Meropenem3	-0.167	-1.773
Vancomycin16	-0.748	-1.273
Rv2680_day32	-0.062	-0.341
H37Rv_KO_MarP	0.524	0.313
hypoxia_3wks	-0.032	0.068
hypoxia_6wks	-0.386	0.591
glycerol	0.023	0.856
cholesterol	-0.246	0.676
AJ	0.531	-0.8
Bibs02	0.201	0.564
Bibs02c	-0.662	0.132
BL6	1.034	2.198
BL6a	0.145	1.301
BXD01	-0.008	1.656
BXD010	0.811	1.652
BXD011	0.153	1.667
BXD03	-0.158	1.82
BXD04	0.425	1.101
BXD05	0.565	1.455
BXD06	0.274	1.683
BXD07	0.336	1.289
BXD08	0.023	1.938
BXD09	0.494	1.629
CAST	0.46	0.766
CCcont	0.043	2.127
DS01	0.31	0.729
DS02	-0.05	0.564
DS04	0.077	-0.131
DS0c	-0.239	0.0
GP01	0.288	0.919
GP02	1.221	0.937
GP0c	-0.528	0.432
NOD	0.809	0.903
NZO	-0.194	0.517
PWK	0.512	0.124
H37Rv_KO_CtpC	-0.067	1.067
H37Rv_KO_CtpD	0.795	1.56
H37Rv_KO_Rv1272	-0.911	0.744
H37Rv_KO_SugABC	0.155	1.18
H37Rv_KO_MbtN	-0.211	0.523
Trans05	-0.565	0.082
macrophage_unactivated	-0.331	0.369
IL1	0.039	0.742
Rapamycin	-0.04	0.961
Tcell	0.124	0.427
GMCSF	0.195	0.417
IFNab	-0.218	0.0
IFNg	0.449	0.901
IFNg_GMCSF1	0.251	0.233
Rv1432_day32	0.252	0.176
Rv1565c_day32	-0.24	0.861
secA2_input	-0.016	-1.363
delta_Rv3594	-0.465	-0.052
delta_Rv3717	-0.262	0.447
delta_Rv3811	-0.149	0.678
delta_Rv0954	0.419	-0.044
PonA1	0.259	0.076
EccD1_KO	0.691	0.743
EspI_KO	0.046	0.819
PE35_KO	-0.047	1.28
PPE68_KO	-0.211	0.374
glycerol2	0.553	0.328
lignocerate	0.225	0.677
oleate	0.527	0.604
phosphatidylcholine	0.5	0.71
acetate	0.219	0.181
glucAc	0.06	0.483
Rv0950ko	0.573	0.326
Rv1096ko	0.694	0.582
Rv3684ko	0.151	0.354
delta_otsA_trehalose	1.329	0.481