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 Rv1245c/-:

update plot	correlation	link to info on gene
Rv2088/pknJ	(cc=0.4545)	info on Rv2088/pknJ
Rv0731c/-	(cc=0.4479)	info on Rv0731c/-
Rv1831/-	(cc=0.4248)	info on Rv1831/-
Rv2770c/PPE44	(cc=0.4242)	info on Rv2770c/PPE44
Rv2695/-	(cc=0.418)	info on Rv2695/-
Rv0576/-	(cc=0.4057)	info on Rv0576/-
Rv2495c/bkdC	(cc=0.4046)	info on Rv2495c/bkdC
Rv3521/-	(cc=0.4045)	info on Rv3521/-
Rv2618/-	(cc=0.3913)	info on Rv2618/-
Rv3268/-	(cc=0.3895)	info on Rv3268/-

Correlation of Rv1245c/- with Rv3521/-

Normalized LFCs for Rv1245c/-:
(description and provenance of datasets)

	Rv1245c/-	Rv3521/-
Fe_supp_jason_reseq	-0.677	-0.287
low_pH_jason_reseq	-0.534	-0.927
NO_jason_reseq	-0.084	0.339
B6_jason_reseq	-1.086	-0.667
MHCII_jason_reseq	-0.021	-0.091
Isoniazid02	-0.386	-0.22
Rifampicin4	0.314	0.309
Ethambutol3	0.241	0.666
Meropenem3	0.183	-0.187
Vancomycin16	-0.082	1.059
Rv2680_day32	-0.198	-0.058
H37Rv_KO_MarP	-0.056	0.524
hypoxia_3wks	0.12	0.231
hypoxia_6wks	0.585	-0.025
glycerol	-0.051	0.159
cholesterol	-0.101	-0.219
AJ	-0.203	0.578
Bibs02	-0.886	0.241
Bibs02c	0.53	-0.147
BL6	-0.478	0.325
BL6a	0.352	0.044
BXD01	-0.253	0.424
BXD010	-0.414	0.455
BXD011	-0.369	0.736
BXD03	-0.501	0.672
BXD04	0.764	0.272
BXD05	-0.012	0.415
BXD06	-0.081	0.342
BXD07	-0.401	0.232
BXD08	1.002	1.005
BXD09	-0.36	0.163
CAST	-0.245	0.142
CCcont	-0.305	-0.257
DS01	0.453	0.156
DS02	-0.211	0.566
DS04	1.19	0.804
DS0c	0.141	0.64
GP01	0.677	-0.032
GP02	1.268	0.832
GP0c	0.388	0.296
NOD	-0.303	0.26
NZO	-0.533	0.623
PWK	-0.421	0.179
H37Rv_KO_CtpC	0.368	0.155
H37Rv_KO_CtpD	0.321	0.765
H37Rv_KO_Rv1272	0.179	1.102
H37Rv_KO_SugABC	0.017	0.614
H37Rv_KO_MbtN	-0.179	-0.252
Trans05	0.777	0.759
macrophage_unactivated	0.218	-0.331
IL1	0.178	0.561
Rapamycin	0.184	0.684
Tcell	-0.453	0.283
GMCSF	0.235	0.354
IFNab	0.121	0.166
IFNg	0.08	0.045
IFNg_GMCSF1	0.707	0.421
Rv1432_day32	0.155	-0.005
Rv1565c_day32	-1.632	0.172
secA2_input	-0.798	-0.041
delta_Rv3594	0.106	0.194
delta_Rv3717	0.273	0.167
delta_Rv3811	0.0	0.106
delta_Rv0954	-0.047	0.513
PonA1	0.285	0.16
EccD1_KO	0.668	0.234
EspI_KO	-0.068	0.054
PE35_KO	0.306	-0.146
PPE68_KO	-0.32	-0.048
glycerol2	0.06	-0.149
lignocerate	-0.457	-0.223
oleate	0.411	0.103
phosphatidylcholine	-0.139	0.207
acetate	-0.426	-0.69
glucAc	-0.459	-0.429
Rv0950ko	0.063	0.32
Rv1096ko	0.0	0.365
Rv3684ko	0.233	0.763
delta_otsA_trehalose	-1.386	-0.673