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 Rv3223c/sigH

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

	Rv3701c/-	Rv3223c/sigH
Fe_supp_jason_reseq	0.391	1.377
low_pH_jason_reseq	0.0	-1.166
NO_jason_reseq	-0.244	-1.011
B6_jason_reseq	0.0	-1.144
MHCII_jason_reseq	-0.293	-0.3
Isoniazid02	0.156	-0.799
Rifampicin4	1.048	-0.333
Ethambutol3	2.178	1.049
Meropenem3	0.829	-0.879
Vancomycin16	0.419	-0.432
Rv2680_day32	-0.359	-1.414
H37Rv_KO_MarP	0.401	-0.024
hypoxia_3wks	0.0	-1.782
hypoxia_6wks	-1.222	-2.817
glycerol	1.537	1.612
cholesterol	0.203	2.7
AJ	-0.373	0.432
Bibs02	-0.294	1.605
Bibs02c	-0.735	1.106
BL6	-0.439	0.969
BL6a	0.277	1.435
BXD01	0.0	0.96
BXD010	-0.45	0.554
BXD011	0.475	0.712
BXD03	0.701	1.014
BXD04	0.325	0.426
BXD05	0.924	1.074
BXD06	0.498	0.554
BXD07	-0.107	0.316
BXD08	0.913	0.857
BXD09	0.37	0.677
CAST	-0.809	0.707
CCcont	0.477	2.402
DS01	0.479	1.021
DS02	-0.35	0.055
DS04	-0.489	0.52
DS0c	0.809	2.11
GP01	-0.347	1.964
GP02	-0.21	0.301
GP0c	0.182	0.297
NOD	0.314	0.418
NZO	-0.503	1.202
PWK	-0.152	-0.509
H37Rv_KO_CtpC	-0.126	1.047
H37Rv_KO_CtpD	0.333	1.055
H37Rv_KO_Rv1272	1.264	2.343
H37Rv_KO_SugABC	-0.348	1.068
H37Rv_KO_MbtN	1.209	2.627
Trans05	0.554	2.3
macrophage_unactivated	0.0	0.237
IL1	0.0	-3.45
Rapamycin	-1.488	-1.715
Tcell	-0.228	-1.352
GMCSF	-0.38	-0.51
IFNab	0.762	0.65
IFNg	-0.385	-2.405
IFNg_GMCSF1	-0.698	-1.197
Rv1432_day32	0.0	-0.645
Rv1565c_day32	0.0	0.317
secA2_input	-1.299	-1.633
delta_Rv3594	0.61	1.975
delta_Rv3717	0.944	0.896
delta_Rv3811	-0.1	1.619
delta_Rv0954	-0.715	0.833
PonA1	-0.753	-0.444
EccD1_KO	1.273	0.444
EspI_KO	-0.163	0.197
PE35_KO	2.018	0.925
PPE68_KO	1.501	1.075
glycerol2	0.161	0.68
lignocerate	0.27	0.983
oleate	-0.179	0.822
phosphatidylcholine	-0.176	1.21
acetate	1.561	0.457
glucAc	1.415	0.374
Rv0950ko	-0.817	-0.06
Rv1096ko	0.688	-0.516
Rv3684ko	-0.573	-0.711
delta_otsA_trehalose	0.133	2.183