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 Rv3199c/nudC:

update plot	correlation	link to info on gene
Rv1533/-	(cc=0.4843)	info on Rv1533/-
Rv3787c/-	(cc=0.4667)	info on Rv3787c/-
Rv0701/rplC	(cc=0.4364)	info on Rv0701/rplC
Rv1726/-	(cc=0.4303)	info on Rv1726/-
Rv0342/iniA	(cc=0.4279)	info on Rv0342/iniA
Rv0968/-	(cc=0.4104)	info on Rv0968/-
Rv2164c/-	(cc=0.4031)	info on Rv2164c/-
Rv2719c/-	(cc=0.3943)	info on Rv2719c/-
Rv0145/-	(cc=0.3907)	info on Rv0145/-
Rv0588/yrbE2B	(cc=0.3858)	info on Rv0588/yrbE2B

Correlation of Rv3199c/nudC with Rv1533/-

Normalized LFCs for Rv3199c/nudC:
(description and provenance of datasets)

	Rv3199c/nudC	Rv1533/-
Fe_supp_jason_reseq	-0.95	0.369
low_pH_jason_reseq	-0.795	-0.532
NO_jason_reseq	-0.47	-0.683
B6_jason_reseq	0.17	0.119
MHCII_jason_reseq	-1.222	0.458
Isoniazid02	-1.491	-0.212
Rifampicin4	0.682	-0.233
Ethambutol3	-1.409	0.114
Meropenem3	-1.422	-0.612
Vancomycin16	-0.57	-0.512
Rv2680_day32	-0.374	0.272
H37Rv_KO_MarP	0.365	0.068
hypoxia_3wks	-0.786	0.63
hypoxia_6wks	-0.393	1.253
glycerol	0.584	0.607
cholesterol	-0.992	0.106
AJ	0.41	0.17
Bibs02	-0.021	0.054
Bibs02c	0.441	0.605
BL6	-0.913	0.797
BL6a	-0.131	1.093
BXD01	0.497	0.944
BXD010	-0.524	-0.21
BXD011	-0.83	1.169
BXD03	-0.159	0.647
BXD04	0.949	1.188
BXD05	-0.335	1.156
BXD06	-0.294	1.322
BXD07	-0.497	0.537
BXD08	-0.715	0.792
BXD09	-0.663	0.658
CAST	-0.864	-0.377
CCcont	-0.372	1.47
DS01	-0.293	0.303
DS02	-0.038	0.249
DS04	-0.082	0.0
DS0c	0.811	0.952
GP01	0.25	1.233
GP02	0.127	0.51
GP0c	-0.25	0.218
NOD	-0.415	0.067
NZO	-0.497	0.577
PWK	-0.217	0.277
H37Rv_KO_CtpC	-0.873	0.293
H37Rv_KO_CtpD	0.701	1.396
H37Rv_KO_Rv1272	1.622	0.674
H37Rv_KO_SugABC	1.681	1.739
H37Rv_KO_MbtN	0.307	1.062
Trans05	-0.924	1.248
macrophage_unactivated	-0.133	0.657
IL1	-0.955	0.252
Rapamycin	0.979	0.295
Tcell	0.508	0.782
GMCSF	-0.264	0.491
IFNab	-1.185	-0.076
IFNg	-0.954	0.131
IFNg_GMCSF1	0.129	-0.16
Rv1432_day32	-0.395	-0.674
Rv1565c_day32	-0.406	0.174
secA2_input	0.697	1.207
delta_Rv3594	-0.214	0.128
delta_Rv3717	0.196	0.763
delta_Rv3811	-0.036	0.062
delta_Rv0954	-0.062	0.671
PonA1	0.305	1.589
EccD1_KO	-0.648	-1.125
EspI_KO	-1.871	-1.705
PE35_KO	-1.018	-0.948
PPE68_KO	-2.48	-0.989
glycerol2	-0.102	0.31
lignocerate	-0.247	0.395
oleate	0.05	0.143
phosphatidylcholine	-0.137	0.637
acetate	-0.304	0.284
glucAc	-0.85	0.212
Rv0950ko	-0.859	0.103
Rv1096ko	0.642	0.305
Rv3684ko	-0.458	0.832
delta_otsA_trehalose	0.221	-0.898