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 Rv1254/-:

update plot	correlation	link to info on gene
Rv2195/qcrA	(cc=0.5168)	info on Rv2195/qcrA
Rv2004c/-	(cc=0.4678)	info on Rv2004c/-
Rv0479c/-	(cc=0.4554)	info on Rv0479c/-
Rv2176/pknL	(cc=0.4476)	info on Rv2176/pknL
Rv0016c/pbpA	(cc=0.4144)	info on Rv0016c/pbpA
Rv0260c/-	(cc=0.3995)	info on Rv0260c/-
Rv3593/lpqF	(cc=0.3839)	info on Rv3593/lpqF
Rv0017c/rodA	(cc=0.3792)	info on Rv0017c/rodA
Rv0589/mce2A	(cc=0.3791)	info on Rv0589/mce2A
Rv1410c/-	(cc=0.3763)	info on Rv1410c/-

Correlation of Rv1254/- with Rv3593/lpqF

Normalized LFCs for Rv1254/-:
(description and provenance of datasets)

	Rv1254/-	Rv3593/lpqF
Fe_supp_jason_reseq	0.0	1.579
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	0.135	0.0
Isoniazid02	-0.183	-0.156
Rifampicin4	-0.341	-0.601
Ethambutol3	-0.32	-0.27
Meropenem3	-0.151	-0.581
Vancomycin16	-0.334	-0.284
Rv2680_day32	0.0	0.0
H37Rv_KO_MarP	-0.684	-3.419
hypoxia_3wks	0.0	-0.55
hypoxia_6wks	0.0	-0.288
glycerol	0.202	1.894
cholesterol	0.398	-0.145
AJ	0.0	0.585
Bibs02	0.0	-0.183
Bibs02c	0.574	-0.209
BL6	0.0	0.781
BL6a	0.0	0.181
BXD01	0.0	0.119
BXD010	0.0	-0.128
BXD011	0.0	0.499
BXD03	0.0	-0.135
BXD04	0.0	0.0
BXD05	0.0	0.235
BXD06	0.0	-0.133
BXD07	0.0	0.126
BXD08	0.0	-0.133
BXD09	0.0	0.0
CAST	0.0	-0.23
CCcont	0.0	0.852
DS01	0.236	-0.236
DS02	0.217	-0.217
DS04	0.533	0.177
DS0c	0.0	-0.217
GP01	0.0	-0.099
GP02	0.0	-0.083
GP0c	0.0	-0.13
NOD	0.0	-0.225
NZO	0.0	0.182
PWK	0.0	-0.196
H37Rv_KO_CtpC	0.0	0.148
H37Rv_KO_CtpD	0.0	0.116
H37Rv_KO_Rv1272	0.0	0.0
H37Rv_KO_SugABC	0.0	0.09
H37Rv_KO_MbtN	0.0	2.067
Trans05	0.0	0.329
macrophage_unactivated	0.0	0.0
IL1	0.0	0.0
Rapamycin	0.0	0.0
Tcell	0.0	0.0
GMCSF	0.0	0.0
IFNab	0.0	0.0
IFNg	0.0	0.0
IFNg_GMCSF1	0.0	0.0
Rv1432_day32	0.0	0.0
Rv1565c_day32	0.218	0.0
secA2_input	-0.412	-2.284
delta_Rv3594	-1.427	0.392
delta_Rv3717	1.258	1.873
delta_Rv3811	-0.454	-0.87
delta_Rv0954	-1.206	-0.835
PonA1	-1.235	-2.133
EccD1_KO	0.0	0.454
EspI_KO	0.0	-0.918
PE35_KO	0.767	-1.353
PPE68_KO	0.442	0.937
glycerol2	0.0	0.0
lignocerate	0.0	0.712
oleate	0.0	0.0
phosphatidylcholine	0.0	0.193
acetate	0.0	0.437
glucAc	0.0	0.605
Rv0950ko	0.0	-3.148
Rv1096ko	0.0	-1.209
Rv3684ko	0.0	0.789
delta_otsA_trehalose	0.133	-0.425