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 Rv2276/cyp121:

update plot	correlation	link to info on gene
Rv3112/moaD1	(cc=0.608)	info on Rv3112/moaD1
Rv2253/-	(cc=0.606)	info on Rv2253/-
Rv2119/-	(cc=0.5777)	info on Rv2119/-
Rv2816c/-	(cc=0.5751)	info on Rv2816c/-
Rv0698/-	(cc=0.5722)	info on Rv0698/-
Rv0596c/vapB4	(cc=0.5715)	info on Rv0596c/vapB4
Rv2267c/-	(cc=0.5628)	info on Rv2267c/-
Rv2562/-	(cc=0.5556)	info on Rv2562/-
Rv0945/-	(cc=0.5409)	info on Rv0945/-
Rv0055/rpsR1	(cc=0.5396)	info on Rv0055/rpsR1

Correlation of Rv2276/cyp121 with Rv2119/-

Normalized LFCs for Rv2276/cyp121:
(description and provenance of datasets)

	Rv2276/cyp121	Rv2119/-
Fe_supp_jason_reseq	0.439	0.362
low_pH_jason_reseq	-0.052	-0.837
NO_jason_reseq	-0.806	0.16
B6_jason_reseq	-0.341	0.739
MHCII_jason_reseq	0.367	0.235
Isoniazid02	-0.042	-0.028
Rifampicin4	-0.241	0.176
Ethambutol3	-0.306	-0.083
Meropenem3	-0.474	-0.787
Vancomycin16	0.223	-0.024
Rv2680_day32	-0.449	-0.497
H37Rv_KO_MarP	-0.26	-0.12
hypoxia_3wks	-0.403	-0.774
hypoxia_6wks	-1.247	0.236
glycerol	0.237	0.155
cholesterol	0.233	-0.227
AJ	1.133	0.034
Bibs02	0.55	-0.498
Bibs02c	-0.277	-0.629
BL6	1.637	0.572
BL6a	0.936	-0.133
BXD01	1.007	-0.109
BXD010	0.564	0.182
BXD011	0.581	0.14
BXD03	1.281	0.573
BXD04	1.013	0.288
BXD05	0.888	0.139
BXD06	1.393	0.231
BXD07	0.491	0.171
BXD08	1.581	0.564
BXD09	1.36	0.031
CAST	0.42	-0.379
CCcont	1.89	0.357
DS01	0.479	0.38
DS02	0.158	-0.096
DS04	0.472	0.042
DS0c	0.693	0.349
GP01	0.678	-0.26
GP02	-0.384	-0.018
GP0c	0.094	-0.33
NOD	1.988	-0.117
NZO	0.097	-0.029
PWK	0.142	-0.072
H37Rv_KO_CtpC	1.918	0.0
H37Rv_KO_CtpD	0.516	0.481
H37Rv_KO_Rv1272	0.931	-0.479
H37Rv_KO_SugABC	1.332	0.457
H37Rv_KO_MbtN	-0.108	0.252
Trans05	1.265	-0.54
macrophage_unactivated	0.859	0.069
IL1	-0.617	-0.75
Rapamycin	-0.338	-0.672
Tcell	0.541	0.701
GMCSF	-0.444	0.383
IFNab	-0.109	-0.686
IFNg	0.045	-0.607
IFNg_GMCSF1	-0.226	-1.046
Rv1432_day32	-0.143	-0.282
Rv1565c_day32	-0.599	-0.158
secA2_input	-1.486	-0.698
delta_Rv3594	-0.623	-0.259
delta_Rv3717	-1.106	-0.293
delta_Rv3811	0.44	-0.085
delta_Rv0954	-0.441	-0.274
PonA1	0.684	-0.171
EccD1_KO	0.21	0.559
EspI_KO	2.193	0.0
PE35_KO	2.129	0.831
PPE68_KO	1.872	0.973
glycerol2	1.864	0.874
lignocerate	2.12	0.997
oleate	0.169	-0.147
phosphatidylcholine	1.84	0.856
acetate	2.369	1.839
glucAc	1.957	1.391
Rv0950ko	0.06	-0.154
Rv1096ko	0.06	-0.311
Rv3684ko	-0.416	-0.337
delta_otsA_trehalose	1.275	-0.682