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 Rv2658c/-:

update plot	correlation	link to info on gene
Rv2345/-	(cc=0.5726)	info on Rv2345/-
Rv1947/-	(cc=0.5511)	info on Rv1947/-
Rv1916/aceAb	(cc=0.4909)	info on Rv1916/aceAb
Rv2634c/PE_PGRS46	(cc=0.4838)	info on Rv2634c/PE_PGRS46
Rv3451/cut3	(cc=0.4631)	info on Rv3451/cut3
Rv2791c/-	(cc=0.4541)	info on Rv2791c/-
Rv0078/-	(cc=0.4515)	info on Rv0078/-
Rv1000c/-	(cc=0.4466)	info on Rv1000c/-
Rv2336/-	(cc=0.4412)	info on Rv2336/-
Rv2704/-	(cc=0.4381)	info on Rv2704/-

Correlation of Rv2658c/- with Rv2634c/PE_PGRS46

Normalized LFCs for Rv2658c/-:
(description and provenance of datasets)

	Rv2658c/-	Rv2634c/PE_PGRS46
Fe_supp_jason_reseq	0.387	-0.098
low_pH_jason_reseq	-0.974	-0.97
NO_jason_reseq	0.0	-0.108
B6_jason_reseq	0.034	-0.045
MHCII_jason_reseq	0.572	0.077
Isoniazid02	-0.778	-0.704
Rifampicin4	0.311	0.482
Ethambutol3	-0.143	0.1
Meropenem3	-1.622	-1.533
Vancomycin16	-1.059	-0.44
Rv2680_day32	-0.294	-0.291
H37Rv_KO_MarP	0.78	-0.02
hypoxia_3wks	0.279	0.076
hypoxia_6wks	-0.186	-0.558
glycerol	0.265	-0.369
cholesterol	0.041	-0.02
AJ	-0.655	0.612
Bibs02	0.229	0.37
Bibs02c	0.391	0.808
BL6	-0.702	0.662
BL6a	0.564	0.511
BXD01	-0.257	-0.046
BXD010	-0.135	0.266
BXD011	-0.076	0.19
BXD03	0.005	0.265
BXD04	-0.339	0.404
BXD05	0.775	0.44
BXD06	-0.034	-0.067
BXD07	0.344	0.207
BXD08	-0.109	0.223
BXD09	0.098	-0.019
CAST	0.444	0.344
CCcont	-0.182	-0.199
DS01	0.05	0.25
DS02	0.307	0.203
DS04	-0.197	-0.097
DS0c	0.732	0.284
GP01	-0.697	0.255
GP02	-0.467	0.168
GP0c	-0.551	-0.194
NOD	0.664	0.579
NZO	0.118	0.173
PWK	0.448	0.304
H37Rv_KO_CtpC	-0.272	-0.558
H37Rv_KO_CtpD	0.798	0.181
H37Rv_KO_Rv1272	0.35	0.019
H37Rv_KO_SugABC	0.476	-0.14
H37Rv_KO_MbtN	0.685	-0.214
Trans05	0.346	0.097
macrophage_unactivated	0.309	0.199
IL1	0.653	0.629
Rapamycin	0.715	0.675
Tcell	-0.101	-0.306
GMCSF	0.512	0.475
IFNab	0.435	-0.027
IFNg	0.446	0.259
IFNg_GMCSF1	0.248	0.566
Rv1432_day32	0.037	0.219
Rv1565c_day32	0.125	-0.314
secA2_input	-0.254	0.258
delta_Rv3594	-0.052	-0.292
delta_Rv3717	-0.551	-0.399
delta_Rv3811	-0.425	-0.471
delta_Rv0954	0.133	-0.443
PonA1	-0.97	-0.248
EccD1_KO	0.089	0.701
EspI_KO	0.893	-0.185
PE35_KO	0.939	1.079
PPE68_KO	0.189	0.576
glycerol2	-0.472	-0.111
lignocerate	-0.756	0.443
oleate	0.191	-0.067
phosphatidylcholine	-0.282	0.336
acetate	-0.233	0.545
glucAc	-0.879	0.507
Rv0950ko	0.027	-0.133
Rv1096ko	-0.784	-0.1
Rv3684ko	-0.802	-0.291
delta_otsA_trehalose	1.711	0.576