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 Rv0066c/icd2:

update plot	correlation	link to info on gene
Rv3754/tyrA	(cc=0.6527)	info on Rv3754/tyrA
Rv0211/pckA	(cc=0.584)	info on Rv0211/pckA
Rv1610/-	(cc=0.5691)	info on Rv1610/-
Rv2524c/fas	(cc=0.569)	info on Rv2524c/fas
Rv1543/-	(cc=0.551)	info on Rv1543/-
Rv1457c/-	(cc=0.5495)	info on Rv1457c/-
Rv2202c/adoK	(cc=0.5306)	info on Rv2202c/adoK
Rv1120c/-	(cc=0.5241)	info on Rv1120c/-
Rv1872c/lldD2	(cc=0.5169)	info on Rv1872c/lldD2
Rv3410c/guaB3	(cc=0.5025)	info on Rv3410c/guaB3

Correlation of Rv0066c/icd2 with Rv1457c/-

Normalized LFCs for Rv0066c/icd2:
(description and provenance of datasets)

	Rv0066c/icd2	Rv1457c/-
Fe_supp_jason_reseq	0.415	0.415
low_pH_jason_reseq	0.0	0.44
NO_jason_reseq	0.0	0.0
B6_jason_reseq	0.0	0.0
MHCII_jason_reseq	0.0	0.0
Isoniazid02	1.752	0.0
Rifampicin4	0.325	0.374
Ethambutol3	2.251	0.931
Meropenem3	2.259	0.315
Vancomycin16	0.162	0.0
Rv2680_day32	0.0	-0.131
H37Rv_KO_MarP	0.957	1.249
hypoxia_3wks	0.0	0.0
hypoxia_6wks	-0.288	0.0
glycerol	0.0	0.0
cholesterol	0.0	0.0
AJ	0.0	0.0
Bibs02	0.0	0.0
Bibs02c	0.0	0.0
BL6	0.0	0.0
BL6a	0.198	0.0
BXD01	0.0	0.0
BXD010	0.0	0.0
BXD011	0.782	0.0
BXD03	0.0	0.0
BXD04	0.0	0.0
BXD05	0.256	0.0
BXD06	0.0	0.0
BXD07	0.0	0.0
BXD08	0.0	0.0
BXD09	0.0	0.0
CAST	0.0	0.0
CCcont	0.525	0.0
DS01	0.0	0.0
DS02	0.0	0.0
DS04	0.194	0.37
DS0c	0.0	0.0
GP01	0.0	0.0
GP02	0.0	0.0
GP0c	0.13	0.0
NOD	0.0	0.0
NZO	0.0	0.199
PWK	0.0	0.0
H37Rv_KO_CtpC	0.162	0.0
H37Rv_KO_CtpD	0.127	0.127
H37Rv_KO_Rv1272	0.0	0.0
H37Rv_KO_SugABC	0.42	0.0
H37Rv_KO_MbtN	1.147	0.0
Trans05	0.0	0.0
macrophage_unactivated	-1.411	0.0
IL1	-1.326	0.0
Rapamycin	-1.372	0.0
Tcell	-0.671	0.0
GMCSF	-1.545	0.0
IFNab	0.0	0.0
IFNg	-1.563	0.0
IFNg_GMCSF1	-1.838	0.0
Rv1432_day32	0.0	0.0
Rv1565c_day32	0.0	0.0
secA2_input	2.453	2.821
delta_Rv3594	0.0	-0.193
delta_Rv3717	1.067	-0.159
delta_Rv3811	0.0	0.0
delta_Rv0954	0.627	0.65
PonA1	0.0	-0.145
EccD1_KO	-0.635	-0.793
EspI_KO	-0.265	0.0
PE35_KO	-0.271	-0.703
PPE68_KO	0.278	0.0
glycerol2	0.193	0.0
lignocerate	0.0	0.0
oleate	0.0	0.0
phosphatidylcholine	0.0	0.0
acetate	0.229	0.806
glucAc	0.0	0.0
Rv0950ko	-1.294	0.0
Rv1096ko	-1.641	0.0
Rv3684ko	-1.985	-0.861
delta_otsA_trehalose	0.468	0.564