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 Rv1400c/lipI:

update plot	correlation	link to info on gene
Rv3702c/-	(cc=0.49)	info on Rv3702c/-
Rv3016/lpqA	(cc=0.4824)	info on Rv3016/lpqA
Rv1106c/-	(cc=0.4154)	info on Rv1106c/-
Rv1358/-	(cc=0.4148)	info on Rv1358/-
Rv1946c/lppG	(cc=0.4121)	info on Rv1946c/lppG
Rv1436/gap	(cc=0.4039)	info on Rv1436/gap
Rv2537c/aroD	(cc=0.4031)	info on Rv2537c/aroD
Rv1875/-	(cc=0.4003)	info on Rv1875/-
Rv2734/-	(cc=0.3977)	info on Rv2734/-
Rv1424c/-	(cc=0.3948)	info on Rv1424c/-

Correlation of Rv1400c/lipI with Rv1436/gap

Normalized LFCs for Rv1400c/lipI:
(description and provenance of datasets)

	Rv1400c/lipI	Rv1436/gap
Fe_supp_jason_reseq	0.276	0.218
low_pH_jason_reseq	0.427	0.0
NO_jason_reseq	0.772	0.0
B6_jason_reseq	0.326	0.0
MHCII_jason_reseq	-0.932	0.0
Isoniazid02	0.163	0.0
Rifampicin4	0.588	0.0
Ethambutol3	0.18	0.0
Meropenem3	0.892	0.0
Vancomycin16	0.393	0.0
Rv2680_day32	-1.139	0.0
H37Rv_KO_MarP	-1.204	-1.307
hypoxia_3wks	-0.132	0.0
hypoxia_6wks	0.779	0.0
glycerol	-0.363	0.0
cholesterol	-0.898	0.0
AJ	-1.114	0.0
Bibs02	-0.212	0.0
Bibs02c	0.218	0.0
BL6	0.53	0.0
BL6a	0.35	0.0
BXD01	0.73	0.0
BXD010	-0.072	0.0
BXD011	0.869	0.0
BXD03	-0.076	0.0
BXD04	-0.034	0.0
BXD05	0.0	0.0
BXD06	0.236	0.0
BXD07	0.144	0.0
BXD08	0.106	0.0
BXD09	-0.208	0.0
CAST	-0.34	0.0
CCcont	-0.173	0.0
DS01	-0.065	0.0
DS02	-0.391	0.0
DS04	0.557	0.0
DS0c	-0.123	0.0
GP01	0.127	0.0
GP02	-0.023	0.0
GP0c	-0.112	0.0
NOD	-0.332	0.0
NZO	-0.295	0.0
PWK	0.521	0.0
H37Rv_KO_CtpC	-1.365	0.0
H37Rv_KO_CtpD	-0.405	0.0
H37Rv_KO_Rv1272	2.418	0.0
H37Rv_KO_SugABC	1.65	0.0
H37Rv_KO_MbtN	-1.001	0.0
Trans05	2.361	0.0
macrophage_unactivated	0.751	0.0
IL1	-0.11	0.0
Rapamycin	0.221	0.0
Tcell	0.978	0.0
GMCSF	0.372	0.0
IFNab	1.339	0.0
IFNg	1.184	0.0
IFNg_GMCSF1	0.336	0.0
Rv1432_day32	0.0	0.0
Rv1565c_day32	-0.137	0.0
secA2_input	0.0	-0.7
delta_Rv3594	0.125	0.0
delta_Rv3717	-0.148	0.0
delta_Rv3811	-0.269	0.0
delta_Rv0954	0.394	0.34
PonA1	0.063	0.0
EccD1_KO	0.888	0.0
EspI_KO	0.12	0.0
PE35_KO	1.706	1.978
PPE68_KO	1.395	2.169
glycerol2	-0.835	-0.369
lignocerate	-0.532	-0.32
oleate	-0.096	-0.373
phosphatidylcholine	-0.374	-0.368
acetate	-0.535	-0.437
glucAc	-0.724	-0.272
Rv0950ko	-0.181	0.347
Rv1096ko	0.0	-0.793
Rv3684ko	0.282	0.727
delta_otsA_trehalose	0.139	0.0