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 Rv2524c/fas

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

	Rv0066c/icd2	Rv2524c/fas
Fe_supp_jason_reseq	0.415	0.218
low_pH_jason_reseq	0.0	0.0
NO_jason_reseq	0.0	0.0
B6_jason_reseq	0.0	0.0
MHCII_jason_reseq	0.0	0.0
Isoniazid02	1.752	-0.201
Rifampicin4	0.325	-0.374
Ethambutol3	2.251	1.701
Meropenem3	2.259	-0.165
Vancomycin16	0.162	-0.366
Rv2680_day32	0.0	0.0
H37Rv_KO_MarP	0.957	1.51
hypoxia_3wks	0.0	0.0
hypoxia_6wks	-0.288	-0.209
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	0.633
DS01	0.0	0.236
DS02	0.0	0.0
DS04	0.194	0.0
DS0c	0.0	0.596
GP01	0.0	0.0
GP02	0.0	0.0
GP0c	0.13	0.0
NOD	0.0	0.0
NZO	0.0	0.0
PWK	0.0	0.0
H37Rv_KO_CtpC	0.162	0.0
H37Rv_KO_CtpD	0.127	0.0
H37Rv_KO_Rv1272	0.0	0.0
H37Rv_KO_SugABC	0.42	0.0
H37Rv_KO_MbtN	1.147	0.103
Trans05	0.0	0.0
macrophage_unactivated	-1.411	0.0
IL1	-1.326	-0.409
Rapamycin	-1.372	0.0
Tcell	-0.671	-0.45
GMCSF	-1.545	-0.364
IFNab	0.0	0.381
IFNg	-1.563	-0.369
IFNg_GMCSF1	-1.838	-0.434
Rv1432_day32	0.0	0.0
Rv1565c_day32	0.0	0.0
secA2_input	2.453	0.136
delta_Rv3594	0.0	1.037
delta_Rv3717	1.067	1.432
delta_Rv3811	0.0	0.87
delta_Rv0954	0.627	0.178
PonA1	0.0	0.437
EccD1_KO	-0.635	-1.121
EspI_KO	-0.265	-0.707
PE35_KO	-0.271	-0.228
PPE68_KO	0.278	-0.25
glycerol2	0.193	0.369
lignocerate	0.0	0.168
oleate	0.0	0.0
phosphatidylcholine	0.0	0.679
acetate	0.229	0.0
glucAc	0.0	0.143
Rv0950ko	-1.294	-1.764
Rv1096ko	-1.641	-1.463
Rv3684ko	-1.985	-1.588
delta_otsA_trehalose	0.468	-0.133