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 Rv1033c/trcR:

update plot	correlation	link to info on gene
Rv1429/-	(cc=0.5261)	info on Rv1429/-
Rv3520c/-	(cc=0.5121)	info on Rv3520c/-
Rv1163/narJ	(cc=0.4917)	info on Rv1163/narJ
Rv0886/fprB	(cc=0.4617)	info on Rv0886/fprB
Rv3766/-	(cc=0.4611)	info on Rv3766/-
Rv1646/PE17	(cc=0.4485)	info on Rv1646/PE17
Rv0634c/-	(cc=0.4459)	info on Rv0634c/-
Rv3056/dinP	(cc=0.4436)	info on Rv3056/dinP
Rv3322c/-	(cc=0.4433)	info on Rv3322c/-
Rv3295/-	(cc=0.4414)	info on Rv3295/-

Correlation of Rv1033c/trcR with Rv3322c/-

Normalized LFCs for Rv1033c/trcR:
(description and provenance of datasets)

	Rv1033c/trcR	Rv3322c/-
Fe_supp_jason_reseq	0.638	-0.672
low_pH_jason_reseq	-0.097	-1.981
NO_jason_reseq	0.827	-0.459
B6_jason_reseq	0.15	-0.711
MHCII_jason_reseq	0.557	0.159
Isoniazid02	-0.096	0.298
Rifampicin4	-0.219	-0.376
Ethambutol3	-0.092	-0.229
Meropenem3	-0.151	0.261
Vancomycin16	0.0	0.337
Rv2680_day32	-0.043	-2.622
H37Rv_KO_MarP	0.391	0.673
hypoxia_3wks	-0.108	0.295
hypoxia_6wks	-0.931	-0.395
glycerol	0.199	0.445
cholesterol	0.877	0.496
AJ	1.103	0.145
Bibs02	0.246	-0.121
Bibs02c	0.746	1.126
BL6	-0.694	0.151
BL6a	0.474	0.042
BXD01	-0.088	-0.014
BXD010	-0.299	-0.289
BXD011	-0.165	-0.546
BXD03	0.296	0.111
BXD04	0.273	-0.571
BXD05	0.054	-0.376
BXD06	-0.392	-0.318
BXD07	-0.066	0.232
BXD08	0.068	-0.409
BXD09	0.004	-1.079
CAST	-0.339	-1.026
CCcont	0.168	0.329
DS01	0.45	0.193
DS02	0.25	0.607
DS04	-0.271	0.342
DS0c	0.231	-0.668
GP01	-0.487	-0.78
GP02	0.251	1.469
GP0c	-0.201	0.374
NOD	0.356	-0.174
NZO	1.273	1.124
PWK	-0.567	-0.661
H37Rv_KO_CtpC	-0.292	-1.284
H37Rv_KO_CtpD	-0.036	-0.464
H37Rv_KO_Rv1272	-0.34	-0.455
H37Rv_KO_SugABC	0.324	0.883
H37Rv_KO_MbtN	-0.824	-1.609
Trans05	-0.804	0.744
macrophage_unactivated	0.114	0.451
IL1	-0.362	-2.658
Rapamycin	-0.028	-2.51
Tcell	-0.196	0.274
GMCSF	-0.533	-1.114
IFNab	-0.565	-1.022
IFNg	-0.783	-2.29
IFNg_GMCSF1	0.085	-0.575
Rv1432_day32	0.0	-0.296
Rv1565c_day32	0.332	0.264
secA2_input	-0.535	0.553
delta_Rv3594	0.236	-0.018
delta_Rv3717	-0.549	-0.191
delta_Rv3811	-0.361	-0.391
delta_Rv0954	0.336	-0.416
PonA1	0.04	-1.392
EccD1_KO	0.059	0.5
EspI_KO	0.662	0.73
PE35_KO	0.309	-0.079
PPE68_KO	0.538	-0.31
glycerol2	0.996	0.726
lignocerate	0.654	0.678
oleate	0.936	0.591
phosphatidylcholine	0.766	0.735
acetate	-0.238	0.18
glucAc	0.267	0.223
Rv0950ko	0.814	0.118
Rv1096ko	0.374	-0.29
Rv3684ko	0.262	0.416
delta_otsA_trehalose	0.278	0.667