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 Rv2318/uspC:

update plot	correlation	link to info on gene
Rv1043c/-	(cc=0.4199)	info on Rv1043c/-
Rv3687c/rsfB	(cc=0.4172)	info on Rv3687c/rsfB
Rv0588/yrbE2B	(cc=0.4068)	info on Rv0588/yrbE2B
Rv2514c/-	(cc=0.4034)	info on Rv2514c/-
Rv2392/cysH	(cc=0.3962)	info on Rv2392/cysH
Rv0364/-	(cc=0.3846)	info on Rv0364/-
Rv0943c/-	(cc=0.3815)	info on Rv0943c/-
Rv3523/ltp3	(cc=0.3781)	info on Rv3523/ltp3
Rv0559c/-	(cc=0.3774)	info on Rv0559c/-
Rv1469/ctpD	(cc=0.3758)	info on Rv1469/ctpD

Correlation of Rv2318/uspC with Rv0559c/-

Normalized LFCs for Rv2318/uspC:
(description and provenance of datasets)

	Rv2318/uspC	Rv0559c/-
Fe_supp_jason_reseq	1.013	-0.139
low_pH_jason_reseq	-0.452	-0.882
NO_jason_reseq	0.352	1.315
B6_jason_reseq	0.527	-0.194
MHCII_jason_reseq	0.193	-0.883
Isoniazid02	0.713	-0.151
Rifampicin4	-0.712	-0.068
Ethambutol3	0.82	2.828
Meropenem3	0.0	-0.061
Vancomycin16	0.743	0.114
Rv2680_day32	0.38	0.141
H37Rv_KO_MarP	-0.618	-0.178
hypoxia_3wks	0.311	-0.853
hypoxia_6wks	-0.056	-1.046
glycerol	-0.432	-0.178
cholesterol	-0.057	0.329
AJ	0.296	0.328
Bibs02	0.844	-1.009
Bibs02c	-0.447	1.037
BL6	0.739	0.741
BL6a	0.624	0.677
BXD01	-0.051	0.507
BXD010	1.385	1.101
BXD011	2.132	0.84
BXD03	1.526	1.354
BXD04	-0.207	1.207
BXD05	0.405	0.83
BXD06	0.495	0.716
BXD07	0.152	0.895
BXD08	0.36	1.158
BXD09	0.249	0.833
CAST	0.172	1.133
CCcont	0.265	1.082
DS01	-0.342	0.838
DS02	0.0	-0.309
DS04	-0.998	-3.02
DS0c	-0.984	0.294
GP01	1.43	-0.14
GP02	-0.742	-1.524
GP0c	-0.025	-0.745
NOD	0.675	1.538
NZO	0.629	0.185
PWK	-0.077	0.593
H37Rv_KO_CtpC	0.234	0.105
H37Rv_KO_CtpD	-0.574	1.41
H37Rv_KO_Rv1272	-0.301	-0.008
H37Rv_KO_SugABC	-0.08	0.476
H37Rv_KO_MbtN	-0.633	0.264
Trans05	0.959	0.691
macrophage_unactivated	0.36	1.206
IL1	0.498	0.463
Rapamycin	0.178	0.031
Tcell	0.0	0.433
GMCSF	0.488	0.861
IFNab	0.345	0.457
IFNg	0.588	0.828
IFNg_GMCSF1	-0.255	0.547
Rv1432_day32	-0.314	0.855
Rv1565c_day32	0.595	0.0
secA2_input	-0.852	-0.208
delta_Rv3594	1.028	1.369
delta_Rv3717	0.405	0.26
delta_Rv3811	0.732	1.599
delta_Rv0954	0.22	1.255
PonA1	1.019	0.515
EccD1_KO	0.181	-0.072
EspI_KO	-0.337	0.819
PE35_KO	-0.085	-0.863
PPE68_KO	-0.378	0.141
glycerol2	0.263	1.052
lignocerate	0.392	1.566
oleate	-0.442	-1.155
phosphatidylcholine	0.213	1.035
acetate	0.69	1.797
glucAc	0.903	1.755
Rv0950ko	1.722	0.549
Rv1096ko	1.722	0.736
Rv3684ko	1.392	0.547
delta_otsA_trehalose	0.05	0.904