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 Rv3166c/-:

update plot	correlation	link to info on gene
Rv2452c/-	(cc=0.6893)	info on Rv2452c/-
Rv0501/galE2	(cc=0.6028)	info on Rv0501/galE2
Rv0371c/-	(cc=0.589)	info on Rv0371c/-
Rv2548/vapC19	(cc=0.5851)	info on Rv2548/vapC19
Rv2584c/apt	(cc=0.562)	info on Rv2584c/apt
Rv1831/-	(cc=0.5606)	info on Rv1831/-
Rv1505c/-	(cc=0.5566)	info on Rv1505c/-
Rv1583c/-	(cc=0.5531)	info on Rv1583c/-
Rv2500c/fadE19	(cc=0.5521)	info on Rv2500c/fadE19
Rv2818c/-	(cc=0.5391)	info on Rv2818c/-

Correlation of Rv3166c/- with Rv2500c/fadE19

Normalized LFCs for Rv3166c/-:
(description and provenance of datasets)

	Rv3166c/-	Rv2500c/fadE19
Fe_supp_jason_reseq	1.028	0.0
low_pH_jason_reseq	0.482	-0.668
NO_jason_reseq	0.087	0.601
B6_jason_reseq	-1.11	0.0
MHCII_jason_reseq	-0.193	-0.05
Isoniazid02	0.412	0.201
Rifampicin4	-0.073	-0.2
Ethambutol3	0.501	0.0
Meropenem3	0.214	-0.28
Vancomycin16	0.21	0.186
Rv2680_day32	0.781	0.228
H37Rv_KO_MarP	0.183	-0.556
hypoxia_3wks	0.0	-0.566
hypoxia_6wks	-0.336	0.436
glycerol	0.803	0.813
cholesterol	0.497	0.246
AJ	0.861	-0.65
Bibs02	-0.621	-0.666
Bibs02c	1.303	-0.587
BL6	1.769	2.178
BL6a	2.045	1.969
BXD01	1.207	1.805
BXD010	0.811	1.178
BXD011	1.128	3.308
BXD03	1.462	1.136
BXD04	1.549	1.169
BXD05	1.91	1.599
BXD06	1.378	1.295
BXD07	1.851	1.309
BXD08	1.11	1.499
BXD09	1.744	1.67
CAST	-0.284	-0.467
CCcont	1.322	0.988
DS01	0.219	0.522
DS02	0.277	-0.285
DS04	0.28	-0.394
DS0c	0.082	1.435
GP01	-0.079	-0.2
GP02	1.205	-0.303
GP0c	0.694	0.077
NOD	1.009	1.695
NZO	-0.525	0.118
PWK	-1.138	-0.124
H37Rv_KO_CtpC	1.129	0.359
H37Rv_KO_CtpD	2.225	2.791
H37Rv_KO_Rv1272	0.296	1.261
H37Rv_KO_SugABC	0.159	0.984
H37Rv_KO_MbtN	-0.22	0.175
Trans05	0.097	1.628
macrophage_unactivated	0.71	0.953
IL1	0.86	0.647
Rapamycin	1.019	0.203
Tcell	0.248	0.417
GMCSF	0.158	-0.372
IFNab	1.128	0.387
IFNg	0.115	-0.184
IFNg_GMCSF1	1.439	0.305
Rv1432_day32	0.931	-0.833
Rv1565c_day32	0.035	-1.797
secA2_input	-0.233	0.266
delta_Rv3594	0.537	0.35
delta_Rv3717	-0.866	-0.586
delta_Rv3811	-0.235	-0.907
delta_Rv0954	-0.544	0.183
PonA1	-0.922	-0.386
EccD1_KO	0.533	1.151
EspI_KO	0.639	0.485
PE35_KO	0.359	0.767
PPE68_KO	0.266	1.299
glycerol2	-0.319	-0.82
lignocerate	0.222	-0.605
oleate	-0.323	0.829
phosphatidylcholine	0.088	-0.27
acetate	0.53	-0.826
glucAc	0.233	-0.348
Rv0950ko	-1.101	-1.224
Rv1096ko	-1.143	-0.253
Rv3684ko	-0.789	-0.468
delta_otsA_trehalose	-0.826	1.461