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 Rv1121/zwf1:

update plot	correlation	link to info on gene
Rv1869c/-	(cc=0.4784)	info on Rv1869c/-
Rv2492/-	(cc=0.4686)	info on Rv2492/-
Rv2435c/-	(cc=0.4466)	info on Rv2435c/-
Rv1519/-	(cc=0.4457)	info on Rv1519/-
Rv1966/mce3A	(cc=0.442)	info on Rv1966/mce3A
Rv3105c/prfB	(cc=0.4244)	info on Rv3105c/prfB
Rv2303c/-	(cc=0.4231)	info on Rv2303c/-
Rv3224/-	(cc=0.4206)	info on Rv3224/-
Rv1428c/-	(cc=0.4193)	info on Rv1428c/-
Rv1336/cysM	(cc=0.419)	info on Rv1336/cysM

Correlation of Rv1121/zwf1 with Rv2303c/-

Normalized LFCs for Rv1121/zwf1:
(description and provenance of datasets)

	Rv1121/zwf1	Rv2303c/-
Fe_supp_jason_reseq	0.234	-0.186
low_pH_jason_reseq	0.408	0.269
NO_jason_reseq	-0.633	0.0
B6_jason_reseq	0.0	0.047
MHCII_jason_reseq	0.579	0.088
Isoniazid02	1.187	0.111
Rifampicin4	-0.284	-0.195
Ethambutol3	1.047	0.507
Meropenem3	2.134	0.864
Vancomycin16	-0.164	0.0
Rv2680_day32	-1.321	0.163
H37Rv_KO_MarP	0.09	0.134
hypoxia_3wks	1.447	0.439
hypoxia_6wks	1.748	0.23
glycerol	-0.36	0.452
cholesterol	-0.367	0.196
AJ	0.353	0.355
Bibs02	0.884	-0.176
Bibs02c	-1.647	-0.056
BL6	-0.784	0.37
BL6a	0.595	0.076
BXD01	0.889	0.184
BXD010	1.479	0.136
BXD011	1.418	0.401
BXD03	1.232	-0.036
BXD04	0.372	0.896
BXD05	0.814	0.786
BXD06	1.097	0.447
BXD07	0.306	0.476
BXD08	0.743	0.101
BXD09	1.142	0.215
CAST	1.023	0.245
CCcont	-0.679	0.019
DS01	0.048	0.121
DS02	-0.046	-0.306
DS04	-0.443	0.394
DS0c	-0.666	0.014
GP01	0.425	0.242
GP02	-0.655	0.977
GP0c	-0.082	0.067
NOD	-0.295	0.74
NZO	1.361	0.977
PWK	0.117	0.429
H37Rv_KO_CtpC	1.02	0.768
H37Rv_KO_CtpD	0.493	0.523
H37Rv_KO_Rv1272	1.866	0.563
H37Rv_KO_SugABC	0.796	0.293
H37Rv_KO_MbtN	0.659	0.825
Trans05	0.665	0.981
macrophage_unactivated	-1.07	-0.638
IL1	0.0	-0.839
Rapamycin	1.439	0.114
Tcell	0.613	0.391
GMCSF	-0.676	-0.401
IFNab	-0.103	-0.587
IFNg	0.219	-0.596
IFNg_GMCSF1	-0.559	-0.544
Rv1432_day32	0.763	0.27
Rv1565c_day32	0.221	-0.178
secA2_input	0.855	-0.088
delta_Rv3594	0.228	0.543
delta_Rv3717	0.438	-0.115
delta_Rv3811	-0.12	-0.497
delta_Rv0954	-0.216	-0.512
PonA1	-0.03	0.495
EccD1_KO	0.27	1.243
EspI_KO	1.417	0.924
PE35_KO	1.21	0.613
PPE68_KO	1.261	0.56
glycerol2	0.076	-0.167
lignocerate	-0.418	-0.46
oleate	0.292	-0.139
phosphatidylcholine	0.0	-0.38
acetate	-0.191	-0.08
glucAc	-0.724	-0.328
Rv0950ko	-0.235	0.066
Rv1096ko	-0.419	-0.718
Rv3684ko	-0.596	0.026
delta_otsA_trehalose	1.71	0.098