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 Rv0778/cyp126:

update plot	correlation	link to info on gene
Rv0892/-	(cc=0.5985)	info on Rv0892/-
Rv0766c/cyp123	(cc=0.4897)	info on Rv0766c/cyp123
Rv0003/recF	(cc=0.486)	info on Rv0003/recF
Rv2537c/aroD	(cc=0.4777)	info on Rv2537c/aroD
Rv3116/moeB2	(cc=0.4552)	info on Rv3116/moeB2
Rv2530c/vapC39	(cc=0.4494)	info on Rv2530c/vapC39
Rv1298/rpmE	(cc=0.4475)	info on Rv1298/rpmE
Rv0781/ptrBa	(cc=0.4441)	info on Rv0781/ptrBa
Rv3104c/-	(cc=0.4422)	info on Rv3104c/-
Rv3125c/PPE49	(cc=0.4272)	info on Rv3125c/PPE49

Correlation of Rv0778/cyp126 with Rv1298/rpmE

Normalized LFCs for Rv0778/cyp126:
(description and provenance of datasets)

	Rv0778/cyp126	Rv1298/rpmE
Fe_supp_jason_reseq	2.014	0.766
low_pH_jason_reseq	-0.571	0.0
NO_jason_reseq	-0.651	0.0
B6_jason_reseq	0.523	0.0
MHCII_jason_reseq	0.706	0.0
Isoniazid02	-0.525	0.0
Rifampicin4	0.157	0.0
Ethambutol3	-0.403	0.0
Meropenem3	0.298	0.0
Vancomycin16	0.154	0.0
Rv2680_day32	0.508	0.0
H37Rv_KO_MarP	-0.423	-0.825
hypoxia_3wks	0.534	0.0
hypoxia_6wks	-0.021	0.0
glycerol	0.736	0.0
cholesterol	0.449	0.0
AJ	0.824	0.0
Bibs02	0.174	0.0
Bibs02c	0.246	0.0
BL6	-0.148	0.0
BL6a	0.756	0.0
BXD01	0.734	0.0
BXD010	0.959	0.0
BXD011	0.899	0.0
BXD03	0.561	0.0
BXD04	1.184	0.0
BXD05	0.862	0.0
BXD06	0.836	0.0
BXD07	0.79	0.0
BXD08	0.618	0.0
BXD09	0.696	0.0
CAST	0.756	0.0
CCcont	-0.056	0.0
DS01	0.921	0.0
DS02	1.078	0.0
DS04	0.207	0.0
DS0c	0.919	0.0
GP01	-0.265	0.0
GP02	-0.021	0.0
GP0c	0.665	0.0
NOD	1.642	0.0
NZO	0.581	0.0
PWK	0.715	0.0
H37Rv_KO_CtpC	0.916	0.0
H37Rv_KO_CtpD	1.194	0.127
H37Rv_KO_Rv1272	-0.269	0.0
H37Rv_KO_SugABC	1.345	0.0
H37Rv_KO_MbtN	0.918	0.0
Trans05	0.278	0.0
macrophage_unactivated	1.042	0.0
IL1	0.0	0.0
Rapamycin	0.341	0.0
Tcell	0.437	0.0
GMCSF	0.591	0.0
IFNab	0.0	0.0
IFNg	1.04	0.0
IFNg_GMCSF1	0.566	0.0
Rv1432_day32	-0.624	0.0
Rv1565c_day32	-0.347	0.0
secA2_input	0.23	0.0
delta_Rv3594	0.72	0.402
delta_Rv3717	-0.162	0.853
delta_Rv3811	0.744	0.564
delta_Rv0954	0.549	0.0
PonA1	0.753	0.0
EccD1_KO	0.52	0.414
EspI_KO	0.893	-0.394
PE35_KO	0.983	0.0
PPE68_KO	0.841	1.113
glycerol2	-0.13	-0.95
lignocerate	-0.614	-0.826
oleate	0.39	-0.961
phosphatidylcholine	0.088	-0.95
acetate	-0.748	-1.127
glucAc	-1.202	-0.701
Rv0950ko	0.329	-0.323
Rv1096ko	0.633	0.582
Rv3684ko	0.121	0.0
delta_otsA_trehalose	-1.184	-0.739