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 Rv1622c/cydB:

update plot	correlation	link to info on gene
Rv1623c/cydA	(cc=0.8667)	info on Rv1623c/cydA
Rv1621c/cydD	(cc=0.8409)	info on Rv1621c/cydD
Rv1620c/cydC	(cc=0.6724)	info on Rv1620c/cydC
Rv2190c/-	(cc=0.4989)	info on Rv2190c/-
Rv0647c/-	(cc=0.4879)	info on Rv0647c/-
Rv1836c/-	(cc=0.4816)	info on Rv1836c/-
Rv3207c/-	(cc=0.461)	info on Rv3207c/-
Rv3044/fecB	(cc=0.454)	info on Rv3044/fecB
Rv3823c/mmpL8	(cc=0.4515)	info on Rv3823c/mmpL8
Rv1780/-	(cc=0.4514)	info on Rv1780/-

Correlation of Rv1622c/cydB with Rv1623c/cydA

Normalized LFCs for Rv1622c/cydB:
(description and provenance of datasets)

	Rv1622c/cydB	Rv1623c/cydA
Fe_supp_jason_reseq	0.218	2.363
low_pH_jason_reseq	0.811	1.506
NO_jason_reseq	-1.63	-4.702
B6_jason_reseq	-1.11	-0.759
MHCII_jason_reseq	-0.977	-1.292
Isoniazid02	0.0	-0.183
Rifampicin4	0.0	-0.341
Ethambutol3	0.0	0.0
Meropenem3	0.0	-0.151
Vancomycin16	0.0	-0.334
Rv2680_day32	0.584	0.728
H37Rv_KO_MarP	-1.576	-2.253
hypoxia_3wks	0.0	0.0
hypoxia_6wks	0.0	-0.464
glycerol	0.0	1.138
cholesterol	0.398	0.381
AJ	0.0	0.324
Bibs02	0.0	-0.642
Bibs02c	0.0	1.593
BL6	0.125	0.254
BL6a	0.696	2.593
BXD01	0.358	0.416
BXD010	0.859	0.88
BXD011	1.05	1.938
BXD03	0.135	0.875
BXD04	0.0	1.837
BXD05	0.135	1.118
BXD06	0.566	1.719
BXD07	0.138	1.555
BXD08	0.253	1.274
BXD09	0.386	1.542
CAST	0.0	-0.581
CCcont	1.606	2.556
DS01	0.0	-0.38
DS02	0.0	-0.764
DS04	0.194	0.916
DS0c	0.0	0.157
GP01	3.382	3.382
GP02	2.044	3.182
GP0c	3.233	4.011
NOD	0.0	-0.566
NZO	0.0	-0.503
PWK	0.0	0.0
H37Rv_KO_CtpC	0.901	1.865
H37Rv_KO_CtpD	0.445	0.405
H37Rv_KO_Rv1272	0.0	0.0
H37Rv_KO_SugABC	0.099	0.37
H37Rv_KO_MbtN	4.101	5.071
Trans05	0.0	0.0
macrophage_unactivated	0.83	0.303
IL1	2.011	3.111
Rapamycin	0.807	0.571
Tcell	0.0	-0.166
GMCSF	0.694	2.297
IFNab	0.417	0.0
IFNg	0.369	1.694
IFNg_GMCSF1	0.434	0.584
Rv1432_day32	3.687	4.133
Rv1565c_day32	0.766	1.579
secA2_input	0.0	-1.082
delta_Rv3594	0.34	0.0
delta_Rv3717	1.472	1.664
delta_Rv3811	-0.187	-0.348
delta_Rv0954	0.416	2.017
PonA1	1.154	3.713
EccD1_KO	-0.635	-0.286
EspI_KO	-0.55	0.77
PE35_KO	-0.271	-1.467
PPE68_KO	0.0	0.634
glycerol2	0.0	0.14
lignocerate	0.0	0.235
oleate	0.0	0.0
phosphatidylcholine	0.0	0.14
acetate	0.0	0.603
glucAc	0.0	0.74
Rv0950ko	-2.723	-3.986
Rv1096ko	-1.022	-1.24
Rv3684ko	1.163	0.986
delta_otsA_trehalose	-2.127	-2.142