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 Rv3754/tyrA

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

	Rv0066c/icd2	Rv3754/tyrA
Fe_supp_jason_reseq	0.415	0.766
low_pH_jason_reseq	0.0	0.0
NO_jason_reseq	0.0	0.362
B6_jason_reseq	0.0	0.0
MHCII_jason_reseq	0.0	0.0
Isoniazid02	1.752	2.768
Rifampicin4	0.325	-0.923
Ethambutol3	2.251	0.175
Meropenem3	2.259	2.764
Vancomycin16	0.162	-0.424
Rv2680_day32	0.0	0.0
H37Rv_KO_MarP	0.957	-0.272
hypoxia_3wks	0.0	0.0
hypoxia_6wks	-0.288	-0.549
glycerol	0.0	-0.202
cholesterol	0.0	0.469
AJ	0.0	-0.232
Bibs02	0.0	-0.183
Bibs02c	0.0	1.194
BL6	0.0	-0.125
BL6a	0.198	-0.198
BXD01	0.0	0.0
BXD010	0.0	-0.128
BXD011	0.782	0.0
BXD03	0.0	0.0
BXD04	0.0	0.953
BXD05	0.256	0.235
BXD06	0.0	0.233
BXD07	0.0	0.126
BXD08	0.0	0.121
BXD09	0.0	0.128
CAST	0.0	0.402
CCcont	0.525	-0.149
DS01	0.0	-0.236
DS02	0.0	0.199
DS04	0.194	-0.194
DS0c	0.0	-0.217
GP01	0.0	-0.099
GP02	0.0	-0.083
GP0c	0.13	-0.13
NOD	0.0	0.0
NZO	0.0	-0.199
PWK	0.0	-0.196
H37Rv_KO_CtpC	0.162	0.0
H37Rv_KO_CtpD	0.127	-0.127
H37Rv_KO_Rv1272	0.0	-0.141
H37Rv_KO_SugABC	0.42	0.173
H37Rv_KO_MbtN	1.147	-0.103
Trans05	0.0	-0.131
macrophage_unactivated	-1.411	-0.65
IL1	-1.326	-0.955
Rapamycin	-1.372	-0.988
Tcell	-0.671	-0.326
GMCSF	-1.545	-0.544
IFNab	0.0	0.0
IFNg	-1.563	-1.195
IFNg_GMCSF1	-1.838	-1.405
Rv1432_day32	0.0	0.0
Rv1565c_day32	0.0	0.0
secA2_input	2.453	-0.412
delta_Rv3594	0.0	0.34
delta_Rv3717	1.067	0.279
delta_Rv3811	0.0	0.171
delta_Rv0954	0.627	1.512
PonA1	0.0	-0.304
EccD1_KO	-0.635	0.0
EspI_KO	-0.265	0.0
PE35_KO	-0.271	0.368
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	0.0
glucAc	0.0	0.0
Rv0950ko	-1.294	-0.582
Rv1096ko	-1.641	-1.252
Rv3684ko	-1.985	-1.772
delta_otsA_trehalose	0.468	0.254