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 Rv3528c/-

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

	Rv1533/-	Rv3528c/-
Fe_supp_jason_reseq	0.369	0.838
low_pH_jason_reseq	-0.532	-0.607
NO_jason_reseq	-0.683	0.137
B6_jason_reseq	0.119	0.547
MHCII_jason_reseq	0.458	0.445
Isoniazid02	-0.212	-0.068
Rifampicin4	-0.233	0.0
Ethambutol3	0.114	-0.449
Meropenem3	-0.612	-0.442
Vancomycin16	-0.512	0.353
Rv2680_day32	0.272	-0.186
H37Rv_KO_MarP	0.068	-0.054
hypoxia_3wks	0.63	-0.833
hypoxia_6wks	1.253	0.967
glycerol	0.607	0.102
cholesterol	0.106	-0.652
AJ	0.17	1.356
Bibs02	0.054	0.956
Bibs02c	0.605	0.812
BL6	0.797	0.97
BL6a	1.093	2.408
BXD01	0.944	1.562
BXD010	-0.21	1.676
BXD011	1.169	1.705
BXD03	0.647	2.078
BXD04	1.188	1.619
BXD05	1.156	2.306
BXD06	1.322	1.881
BXD07	0.537	2.076
BXD08	0.792	1.617
BXD09	0.658	1.922
CAST	-0.377	0.117
CCcont	1.47	1.492
DS01	0.303	0.551
DS02	0.249	1.459
DS04	0.0	1.248
DS0c	0.952	-0.809
GP01	1.233	1.216
GP02	0.51	-0.141
GP0c	0.218	0.0
NOD	0.067	-0.12
NZO	0.577	-0.465
PWK	0.277	0.615
H37Rv_KO_CtpC	0.293	2.026
H37Rv_KO_CtpD	1.396	0.662
H37Rv_KO_Rv1272	0.674	2.217
H37Rv_KO_SugABC	1.739	1.188
H37Rv_KO_MbtN	1.062	1.632
Trans05	1.248	0.725
macrophage_unactivated	0.657	0.89
IL1	0.252	0.243
Rapamycin	0.295	0.0
Tcell	0.782	0.762
GMCSF	0.491	0.145
IFNab	-0.076	-0.088
IFNg	0.131	0.754
IFNg_GMCSF1	-0.16	-0.273
Rv1432_day32	-0.674	-0.168
Rv1565c_day32	0.174	-0.357
secA2_input	1.207	0.377
delta_Rv3594	0.128	0.731
delta_Rv3717	0.763	-0.135
delta_Rv3811	0.062	0.219
delta_Rv0954	0.671	-0.211
PonA1	1.589	-0.645
EccD1_KO	-1.125	-1.085
EspI_KO	-1.705	-0.713
PE35_KO	-0.948	-0.403
PPE68_KO	-0.989	-0.326
glycerol2	0.31	0.598
lignocerate	0.395	1.391
oleate	0.143	0.136
phosphatidylcholine	0.637	0.933
acetate	0.284	0.999
glucAc	0.212	1.377
Rv0950ko	0.103	0.742
Rv1096ko	0.305	0.48
Rv3684ko	0.832	0.318
delta_otsA_trehalose	-0.898	-1.179