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 Rv3701c/-:

update plot	correlation	link to info on gene
Rv0348/-	(cc=0.5023)	info on Rv0348/-
Rv2529/-	(cc=0.445)	info on Rv2529/-
Rv1540/-	(cc=0.4204)	info on Rv1540/-
Rv3223c/sigH	(cc=0.4133)	info on Rv3223c/sigH
Rv2239c/-	(cc=0.4052)	info on Rv2239c/-
Rv3208A/TB9.4	(cc=0.4027)	info on Rv3208A/TB9.4
Rv0686/-	(cc=0.4003)	info on Rv0686/-
Rv3407/vapB47	(cc=0.4002)	info on Rv3407/vapB47
Rv2119/-	(cc=0.3984)	info on Rv2119/-
Rv1441c/PE_PGRS26	(cc=0.3977)	info on Rv1441c/PE_PGRS26

Correlation of Rv3701c/- with Rv1540/-

Normalized LFCs for Rv3701c/-:
(description and provenance of datasets)

	Rv3701c/-	Rv1540/-
Fe_supp_jason_reseq	0.391	0.415
low_pH_jason_reseq	0.0	0.0
NO_jason_reseq	-0.244	0.0
B6_jason_reseq	0.0	0.0
MHCII_jason_reseq	-0.293	0.0
Isoniazid02	0.156	0.0
Rifampicin4	1.048	-0.374
Ethambutol3	2.178	0.658
Meropenem3	0.829	1.418
Vancomycin16	0.419	0.0
Rv2680_day32	-0.359	0.0
H37Rv_KO_MarP	0.401	0.123
hypoxia_3wks	0.0	0.0
hypoxia_6wks	-1.222	0.0
glycerol	1.537	0.0
cholesterol	0.203	0.0
AJ	-0.373	0.0
Bibs02	-0.294	0.0
Bibs02c	-0.735	0.0
BL6	-0.439	0.0
BL6a	0.277	0.0
BXD01	0.0	0.0
BXD010	-0.45	0.0
BXD011	0.475	0.0
BXD03	0.701	0.0
BXD04	0.325	0.0
BXD05	0.924	0.0
BXD06	0.498	0.0
BXD07	-0.107	0.0
BXD08	0.913	0.0
BXD09	0.37	0.0
CAST	-0.809	0.0
CCcont	0.477	0.285
DS01	0.479	0.0
DS02	-0.35	0.0
DS04	-0.489	0.0
DS0c	0.809	0.0
GP01	-0.347	0.0
GP02	-0.21	0.0
GP0c	0.182	0.0
NOD	0.314	0.0
NZO	-0.503	0.0
PWK	-0.152	0.0
H37Rv_KO_CtpC	-0.126	0.0
H37Rv_KO_CtpD	0.333	0.0
H37Rv_KO_Rv1272	1.264	0.0
H37Rv_KO_SugABC	-0.348	0.0
H37Rv_KO_MbtN	1.209	0.362
Trans05	0.554	0.0
macrophage_unactivated	0.0	0.0
IL1	0.0	0.0
Rapamycin	-1.488	0.0
Tcell	-0.228	0.0
GMCSF	-0.38	0.0
IFNab	0.762	0.0
IFNg	-0.385	0.0
IFNg_GMCSF1	-0.698	0.0
Rv1432_day32	0.0	0.0
Rv1565c_day32	0.0	0.0
secA2_input	-1.299	-2.215
delta_Rv3594	0.61	0.0
delta_Rv3717	0.944	0.0
delta_Rv3811	-0.1	0.0
delta_Rv0954	-0.715	0.34
PonA1	-0.753	0.783
EccD1_KO	1.273	0.0
EspI_KO	-0.163	0.0
PE35_KO	2.018	1.978
PPE68_KO	1.501	0.442
glycerol2	0.161	0.0
lignocerate	0.27	0.0
oleate	-0.179	0.0
phosphatidylcholine	-0.176	0.0
acetate	1.561	0.437
glucAc	1.415	0.0
Rv0950ko	-0.817	-0.38
Rv1096ko	0.688	0.0
Rv3684ko	-0.573	0.377
delta_otsA_trehalose	0.133	-0.111