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 Rv1533/-:

update plot	correlation	link to info on gene
Rv3887c/eccD2	(cc=0.5504)	info on Rv3887c/eccD2
Rv3673c/-	(cc=0.5449)	info on Rv3673c/-
Rv0642c/mmaA4	(cc=0.5411)	info on Rv0642c/mmaA4
Rv3008/-	(cc=0.5388)	info on Rv3008/-
Rv0059/-	(cc=0.5306)	info on Rv0059/-
Rv0701/rplC	(cc=0.5207)	info on Rv0701/rplC
Rv3528c/-	(cc=0.5151)	info on Rv3528c/-
Rv3796/-	(cc=0.5085)	info on Rv3796/-
Rv0588/yrbE2B	(cc=0.4979)	info on Rv0588/yrbE2B
Rv2678c/hemE	(cc=0.4949)	info on Rv2678c/hemE

Correlation of Rv1533/- with Rv0588/yrbE2B

Normalized LFCs for Rv1533/-:
(description and provenance of datasets)

	Rv1533/-	Rv0588/yrbE2B
Fe_supp_jason_reseq	0.369	-0.254
low_pH_jason_reseq	-0.532	-0.761
NO_jason_reseq	-0.683	-0.137
B6_jason_reseq	0.119	-0.85
MHCII_jason_reseq	0.458	-0.215
Isoniazid02	-0.212	-1.806
Rifampicin4	-0.233	-0.127
Ethambutol3	0.114	-1.677
Meropenem3	-0.612	-1.681
Vancomycin16	-0.512	-0.639
Rv2680_day32	0.272	1.112
H37Rv_KO_MarP	0.068	0.102
hypoxia_3wks	0.63	-0.399
hypoxia_6wks	1.253	-0.209
glycerol	0.607	-0.645
cholesterol	0.106	-0.574
AJ	0.17	0.822
Bibs02	0.054	0.894
Bibs02c	0.605	-0.617
BL6	0.797	0.894
BL6a	1.093	0.512
BXD01	0.944	0.738
BXD010	-0.21	0.843
BXD011	1.169	1.88
BXD03	0.647	-0.272
BXD04	1.188	1.036
BXD05	1.156	0.348
BXD06	1.322	1.015
BXD07	0.537	0.595
BXD08	0.792	0.753
BXD09	0.658	0.81
CAST	-0.377	0.202
CCcont	1.47	0.73
DS01	0.303	-0.755
DS02	0.249	-0.748
DS04	0.0	0.07
DS0c	0.952	-0.165
GP01	1.233	0.882
GP02	0.51	-0.047
GP0c	0.218	0.24
NOD	0.067	-0.042
NZO	0.577	0.306
PWK	0.277	-0.578
H37Rv_KO_CtpC	0.293	0.348
H37Rv_KO_CtpD	1.396	1.415
H37Rv_KO_Rv1272	0.674	1.169
H37Rv_KO_SugABC	1.739	0.45
H37Rv_KO_MbtN	1.062	-0.656
Trans05	1.248	0.093
macrophage_unactivated	0.657	-0.057
IL1	0.252	0.05
Rapamycin	0.295	-0.055
Tcell	0.782	0.541
GMCSF	0.491	0.396
IFNab	-0.076	0.051
IFNg	0.131	0.315
IFNg_GMCSF1	-0.16	-0.654
Rv1432_day32	-0.674	0.169
Rv1565c_day32	0.174	0.621
secA2_input	1.207	0.25
delta_Rv3594	0.128	0.132
delta_Rv3717	0.763	0.541
delta_Rv3811	0.062	0.913
delta_Rv0954	0.671	0.842
PonA1	1.589	0.546
EccD1_KO	-1.125	-0.635
EspI_KO	-1.705	-0.927
PE35_KO	-0.948	-2.042
PPE68_KO	-0.989	-1.699
glycerol2	0.31	-0.029
lignocerate	0.395	0.421
oleate	0.143	0.274
phosphatidylcholine	0.637	0.112
acetate	0.284	0.0
glucAc	0.212	0.042
Rv0950ko	0.103	1.984
Rv1096ko	0.305	2.844
Rv3684ko	0.832	1.503
delta_otsA_trehalose	-0.898	-0.55