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 Rv1117/-:

update plot	correlation	link to info on gene
Rv2396/PE_PGRS41	(cc=0.5174)	info on Rv2396/PE_PGRS41
Rv1646/PE17	(cc=0.5113)	info on Rv1646/PE17
Rv3065/mmr	(cc=0.5073)	info on Rv3065/mmr
Rv3184/-	(cc=0.4719)	info on Rv3184/-
Rv3884c/eccA2	(cc=0.4637)	info on Rv3884c/eccA2
Rv0830/-	(cc=0.4427)	info on Rv0830/-
Rv2950c/fadD29	(cc=0.4345)	info on Rv2950c/fadD29
Rv2639c/-	(cc=0.4339)	info on Rv2639c/-
Rv2957/-	(cc=0.4316)	info on Rv2957/-
Rv3749c/-	(cc=0.4311)	info on Rv3749c/-

Correlation of Rv1117/- with Rv2396/PE_PGRS41

Normalized LFCs for Rv1117/-:
(description and provenance of datasets)

	Rv1117/-	Rv2396/PE_PGRS41
Fe_supp_jason_reseq	0.325	0.778
low_pH_jason_reseq	0.652	-0.304
NO_jason_reseq	1.302	-0.242
B6_jason_reseq	0.628	0.383
MHCII_jason_reseq	0.89	1.08
Isoniazid02	-1.129	0.019
Rifampicin4	0.249	0.06
Ethambutol3	-0.731	-0.022
Meropenem3	-0.321	-0.331
Vancomycin16	-0.215	-0.109
Rv2680_day32	0.432	-0.576
H37Rv_KO_MarP	-0.058	-0.045
hypoxia_3wks	-0.766	-0.801
hypoxia_6wks	-2.107	-0.432
glycerol	-0.05	0.489
cholesterol	-0.147	-0.292
AJ	1.449	0.576
Bibs02	0.948	0.442
Bibs02c	1.676	1.161
BL6	-0.049	0.0
BL6a	0.967	0.264
BXD01	0.889	-0.145
BXD010	0.198	-0.214
BXD011	-0.323	-0.021
BXD03	0.727	0.214
BXD04	0.692	0.335
BXD05	0.086	0.497
BXD06	0.574	0.079
BXD07	0.525	-0.18
BXD08	0.248	0.309
BXD09	0.195	0.072
CAST	0.906	-0.44
CCcont	0.411	0.122
DS01	0.385	-0.029
DS02	0.11	0.498
DS04	0.429	0.031
DS0c	-0.099	0.497
GP01	0.369	0.028
GP02	2.489	1.743
GP0c	0.316	0.178
NOD	0.251	0.234
NZO	1.211	-0.231
PWK	0.566	-0.04
H37Rv_KO_CtpC	0.98	0.641
H37Rv_KO_CtpD	-0.532	1.276
H37Rv_KO_Rv1272	1.288	1.107
H37Rv_KO_SugABC	1.45	0.494
H37Rv_KO_MbtN	0.819	0.697
Trans05	0.339	0.96
macrophage_unactivated	0.095	-1.316
IL1	-1.818	-0.409
Rapamycin	-1.292	-0.669
Tcell	0.306	-0.655
GMCSF	-1.31	0.135
IFNab	0.163	-0.726
IFNg	-1.686	-0.839
IFNg_GMCSF1	-1.1	0.355
Rv1432_day32	-0.369	0.149
Rv1565c_day32	0.12	0.118
secA2_input	2.365	-0.031
delta_Rv3594	0.587	0.45
delta_Rv3717	0.544	-0.176
delta_Rv3811	0.132	-0.113
delta_Rv0954	0.464	0.129
PonA1	0.542	0.214
EccD1_KO	0.96	0.595
EspI_KO	1.694	0.374
PE35_KO	1.89	0.44
PPE68_KO	1.878	0.688
glycerol2	1.418	1.361
lignocerate	0.784	1.61
oleate	1.448	0.552
phosphatidylcholine	0.98	1.448
acetate	0.741	0.959
glucAc	0.748	1.051
Rv0950ko	-0.425	-0.015
Rv1096ko	-0.495	-0.66
Rv3684ko	-0.57	-0.108
delta_otsA_trehalose	-1.122	-1.153