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 Rv1043c/-

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

	Rv2318/uspC	Rv1043c/-
Fe_supp_jason_reseq	1.013	-0.267
low_pH_jason_reseq	-0.452	-1.414
NO_jason_reseq	0.352	0.612
B6_jason_reseq	0.527	-0.304
MHCII_jason_reseq	0.193	-0.188
Isoniazid02	0.713	0.281
Rifampicin4	-0.712	-0.157
Ethambutol3	0.82	0.133
Meropenem3	0.0	-0.212
Vancomycin16	0.743	-0.053
Rv2680_day32	0.38	-0.524
H37Rv_KO_MarP	-0.618	0.216
hypoxia_3wks	0.311	0.159
hypoxia_6wks	-0.056	0.008
glycerol	-0.432	-0.908
cholesterol	-0.057	-0.284
AJ	0.296	0.612
Bibs02	0.844	-0.236
Bibs02c	-0.447	-0.48
BL6	0.739	0.462
BL6a	0.624	-0.011
BXD01	-0.051	0.046
BXD010	1.385	0.226
BXD011	2.132	0.117
BXD03	1.526	0.88
BXD04	-0.207	0.177
BXD05	0.405	0.033
BXD06	0.495	0.26
BXD07	0.152	0.088
BXD08	0.36	0.635
BXD09	0.249	0.133
CAST	0.172	0.434
CCcont	0.265	0.0
DS01	-0.342	-0.204
DS02	0.0	0.099
DS04	-0.998	-0.5
DS0c	-0.984	-0.141
GP01	1.43	-0.428
GP02	-0.742	-0.378
GP0c	-0.025	0.042
NOD	0.675	0.218
NZO	0.629	-0.055
PWK	-0.077	0.229
H37Rv_KO_CtpC	0.234	0.209
H37Rv_KO_CtpD	-0.574	0.361
H37Rv_KO_Rv1272	-0.301	-0.263
H37Rv_KO_SugABC	-0.08	0.074
H37Rv_KO_MbtN	-0.633	0.1
Trans05	0.959	-0.398
macrophage_unactivated	0.36	0.556
IL1	0.498	0.214
Rapamycin	0.178	0.012
Tcell	0.0	0.257
GMCSF	0.488	0.681
IFNab	0.345	0.148
IFNg	0.588	-0.214
IFNg_GMCSF1	-0.255	0.185
Rv1432_day32	-0.314	0.107
Rv1565c_day32	0.595	0.592
secA2_input	-0.852	-0.504
delta_Rv3594	1.028	1.146
delta_Rv3717	0.405	0.755
delta_Rv3811	0.732	1.21
delta_Rv0954	0.22	0.318
PonA1	1.019	0.512
EccD1_KO	0.181	-0.21
EspI_KO	-0.337	0.385
PE35_KO	-0.085	0.166
PPE68_KO	-0.378	-0.24
glycerol2	0.263	0.202
lignocerate	0.392	0.581
oleate	-0.442	0.286
phosphatidylcholine	0.213	0.553
acetate	0.69	-0.103
glucAc	0.903	-0.064
Rv0950ko	1.722	0.742
Rv1096ko	1.722	0.938
Rv3684ko	1.392	0.632
delta_otsA_trehalose	0.05	-0.502