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 Rv3887c/eccD2

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

	Rv1533/-	Rv3887c/eccD2
Fe_supp_jason_reseq	0.369	-0.952
low_pH_jason_reseq	-0.532	-0.554
NO_jason_reseq	-0.683	-0.501
B6_jason_reseq	0.119	0.097
MHCII_jason_reseq	0.458	-0.157
Isoniazid02	-0.212	0.32
Rifampicin4	-0.233	-0.764
Ethambutol3	0.114	0.765
Meropenem3	-0.612	-0.283
Vancomycin16	-0.512	-0.73
Rv2680_day32	0.272	-0.068
H37Rv_KO_MarP	0.068	0.267
hypoxia_3wks	0.63	0.215
hypoxia_6wks	1.253	0.766
glycerol	0.607	0.683
cholesterol	0.106	0.226
AJ	0.17	0.361
Bibs02	0.054	0.229
Bibs02c	0.605	0.364
BL6	0.797	0.521
BL6a	1.093	0.588
BXD01	0.944	0.287
BXD010	-0.21	1.072
BXD011	1.169	0.949
BXD03	0.647	0.451
BXD04	1.188	0.725
BXD05	1.156	0.682
BXD06	1.322	0.654
BXD07	0.537	0.504
BXD08	0.792	0.409
BXD09	0.658	0.559
CAST	-0.377	0.622
CCcont	1.47	0.42
DS01	0.303	0.222
DS02	0.249	0.6
DS04	0.0	0.734
DS0c	0.952	0.478
GP01	1.233	0.479
GP02	0.51	0.225
GP0c	0.218	-0.329
NOD	0.067	0.296
NZO	0.577	0.539
PWK	0.277	0.306
H37Rv_KO_CtpC	0.293	0.224
H37Rv_KO_CtpD	1.396	0.448
H37Rv_KO_Rv1272	0.674	0.739
H37Rv_KO_SugABC	1.739	0.718
H37Rv_KO_MbtN	1.062	1.228
Trans05	1.248	0.353
macrophage_unactivated	0.657	-0.047
IL1	0.252	0.279
Rapamycin	0.295	0.092
Tcell	0.782	-0.023
GMCSF	0.491	0.174
IFNab	-0.076	-0.07
IFNg	0.131	0.04
IFNg_GMCSF1	-0.16	-0.242
Rv1432_day32	-0.674	-0.448
Rv1565c_day32	0.174	0.422
secA2_input	1.207	0.794
delta_Rv3594	0.128	-0.171
delta_Rv3717	0.763	-0.659
delta_Rv3811	0.062	0.013
delta_Rv0954	0.671	0.09
PonA1	1.589	0.403
EccD1_KO	-1.125	-0.286
EspI_KO	-1.705	-0.459
PE35_KO	-0.948	0.023
PPE68_KO	-0.989	-0.099
glycerol2	0.31	0.53
lignocerate	0.395	0.245
oleate	0.143	0.69
phosphatidylcholine	0.637	0.27
acetate	0.284	-0.17
glucAc	0.212	-0.266
Rv0950ko	0.103	-0.078
Rv1096ko	0.305	0.051
Rv3684ko	0.832	0.223
delta_otsA_trehalose	-0.898	-0.049