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 Rv2562/-

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

	Rv2276/cyp121	Rv2562/-
Fe_supp_jason_reseq	0.439	-0.226
low_pH_jason_reseq	-0.052	-0.87
NO_jason_reseq	-0.806	-0.386
B6_jason_reseq	-0.341	-1.875
MHCII_jason_reseq	0.367	-0.528
Isoniazid02	-0.042	0.224
Rifampicin4	-0.241	0.441
Ethambutol3	-0.306	0.045
Meropenem3	-0.474	0.401
Vancomycin16	0.223	0.647
Rv2680_day32	-0.449	0.503
H37Rv_KO_MarP	-0.26	0.422
hypoxia_3wks	-0.403	-0.471
hypoxia_6wks	-1.247	0.044
glycerol	0.237	-1.226
cholesterol	0.233	-0.097
AJ	1.133	-0.022
Bibs02	0.55	0.743
Bibs02c	-0.277	-1.088
BL6	1.637	0.954
BL6a	0.936	-0.293
BXD01	1.007	0.195
BXD010	0.564	0.7
BXD011	0.581	0.647
BXD03	1.281	0.533
BXD04	1.013	0.614
BXD05	0.888	0.613
BXD06	1.393	1.012
BXD07	0.491	0.602
BXD08	1.581	0.675
BXD09	1.36	0.787
CAST	0.42	0.719
CCcont	1.89	0.349
DS01	0.479	-0.44
DS02	0.158	-0.05
DS04	0.472	0.658
DS0c	0.693	0.209
GP01	0.678	0.295
GP02	-0.384	0.362
GP0c	0.094	0.024
NOD	1.988	1.036
NZO	0.097	-0.275
PWK	0.142	0.371
H37Rv_KO_CtpC	1.918	0.923
H37Rv_KO_CtpD	0.516	1.291
H37Rv_KO_Rv1272	0.931	0.843
H37Rv_KO_SugABC	1.332	0.168
H37Rv_KO_MbtN	-0.108	-0.83
Trans05	1.265	1.309
macrophage_unactivated	0.859	1.446
IL1	-0.617	0.528
Rapamycin	-0.338	0.712
Tcell	0.541	0.613
GMCSF	-0.444	0.04
IFNab	-0.109	-0.339
IFNg	0.045	0.858
IFNg_GMCSF1	-0.226	0.575
Rv1432_day32	-0.143	-0.332
Rv1565c_day32	-0.599	-0.423
secA2_input	-1.486	-1.929
delta_Rv3594	-0.623	0.153
delta_Rv3717	-1.106	-0.077
delta_Rv3811	0.44	0.125
delta_Rv0954	-0.441	0.021
PonA1	0.684	0.853
EccD1_KO	0.21	0.441
EspI_KO	2.193	0.476
PE35_KO	2.129	0.825
PPE68_KO	1.872	0.723
glycerol2	1.864	1.247
lignocerate	2.12	1.249
oleate	0.169	0.943
phosphatidylcholine	1.84	1.424
acetate	2.369	1.077
glucAc	1.957	0.617
Rv0950ko	0.06	-0.585
Rv1096ko	0.06	-0.368
Rv3684ko	-0.416	0.079
delta_otsA_trehalose	1.275	-0.634