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 Rv0943c/-

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

	Rv2318/uspC	Rv0943c/-
Fe_supp_jason_reseq	1.013	-0.636
low_pH_jason_reseq	-0.452	0.283
NO_jason_reseq	0.352	-0.058
B6_jason_reseq	0.527	-0.556
MHCII_jason_reseq	0.193	-0.54
Isoniazid02	0.713	1.331
Rifampicin4	-0.712	0.69
Ethambutol3	0.82	0.67
Meropenem3	0.0	0.2
Vancomycin16	0.743	0.703
Rv2680_day32	0.38	-1.037
H37Rv_KO_MarP	-0.618	0.195
hypoxia_3wks	0.311	-0.116
hypoxia_6wks	-0.056	0.117
glycerol	-0.432	-0.328
cholesterol	-0.057	0.236
AJ	0.296	-0.015
Bibs02	0.844	0.625
Bibs02c	-0.447	-0.246
BL6	0.739	0.304
BL6a	0.624	-0.013
BXD01	-0.051	0.098
BXD010	1.385	0.332
BXD011	2.132	0.854
BXD03	1.526	0.519
BXD04	-0.207	0.345
BXD05	0.405	0.473
BXD06	0.495	0.611
BXD07	0.152	0.386
BXD08	0.36	1.259
BXD09	0.249	0.089
CAST	0.172	-0.652
CCcont	0.265	0.158
DS01	-0.342	0.719
DS02	0.0	0.203
DS04	-0.998	-1.057
DS0c	-0.984	0.042
GP01	1.43	-0.215
GP02	-0.742	0.371
GP0c	-0.025	-0.653
NOD	0.675	-0.199
NZO	0.629	0.09
PWK	-0.077	-0.607
H37Rv_KO_CtpC	0.234	0.265
H37Rv_KO_CtpD	-0.574	0.0
H37Rv_KO_Rv1272	-0.301	-0.474
H37Rv_KO_SugABC	-0.08	-1.462
H37Rv_KO_MbtN	-0.633	-0.72
Trans05	0.959	0.205
macrophage_unactivated	0.36	-0.095
IL1	0.498	0.569
Rapamycin	0.178	0.282
Tcell	0.0	-0.072
GMCSF	0.488	-0.343
IFNab	0.345	0.088
IFNg	0.588	0.564
IFNg_GMCSF1	-0.255	0.091
Rv1432_day32	-0.314	-0.28
Rv1565c_day32	0.595	-0.104
secA2_input	-0.852	-0.412
delta_Rv3594	1.028	0.0
delta_Rv3717	0.405	-0.454
delta_Rv3811	0.732	-0.537
delta_Rv0954	0.22	-0.395
PonA1	1.019	0.519
EccD1_KO	0.181	0.612
EspI_KO	-0.337	-0.071
PE35_KO	-0.085	0.143
PPE68_KO	-0.378	0.157
glycerol2	0.263	-0.115
lignocerate	0.392	0.485
oleate	-0.442	0.302
phosphatidylcholine	0.213	0.325
acetate	0.69	0.482
glucAc	0.903	0.21
Rv0950ko	1.722	1.107
Rv1096ko	1.722	0.832
Rv3684ko	1.392	1.297
delta_otsA_trehalose	0.05	-0.766