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 Rv3760/-:

update plot	correlation	link to info on gene
Rv0351/grpE	(cc=0.4979)	info on Rv0351/grpE
Rv2129c/-	(cc=0.4871)	info on Rv2129c/-
Rv3379c/dxs2	(cc=0.4539)	info on Rv3379c/dxs2
Rv2530c/vapC39	(cc=0.4343)	info on Rv2530c/vapC39
Rv1949c/-	(cc=0.428)	info on Rv1949c/-
Rv1116/-	(cc=0.4277)	info on Rv1116/-
Rv1664/pks9	(cc=0.4275)	info on Rv1664/pks9
Rv1984c/cfp21	(cc=0.4244)	info on Rv1984c/cfp21
Rv2757c/vapC21	(cc=0.421)	info on Rv2757c/vapC21
Rv0469/umaA	(cc=0.4209)	info on Rv0469/umaA

Correlation of Rv3760/- with Rv0469/umaA

Normalized LFCs for Rv3760/-:
(description and provenance of datasets)

	Rv3760/-	Rv0469/umaA
Fe_supp_jason_reseq	2.259	1.002
low_pH_jason_reseq	1.4	0.125
NO_jason_reseq	1.754	0.039
B6_jason_reseq	-0.799	-0.616
MHCII_jason_reseq	-2.059	-0.862
Isoniazid02	0.252	-0.34
Rifampicin4	0.593	-0.558
Ethambutol3	-0.314	0.193
Meropenem3	-0.031	0.291
Vancomycin16	0.034	-0.403
Rv2680_day32	-3.356	-1.846
H37Rv_KO_MarP	0.569	0.119
hypoxia_3wks	1.487	0.12
hypoxia_6wks	0.054	0.157
glycerol	-0.622	0.565
cholesterol	-0.404	0.048
AJ	0.711	0.397
Bibs02	-0.735	-0.411
Bibs02c	0.135	0.297
BL6	-2.023	-0.021
BL6a	0.854	1.129
BXD01	0.899	0.624
BXD010	0.186	1.099
BXD011	0.894	0.879
BXD03	-1.357	0.588
BXD04	0.781	1.348
BXD05	-0.375	0.997
BXD06	0.293	0.761
BXD07	-0.512	0.856
BXD08	-0.061	0.705
BXD09	0.626	0.815
CAST	-1.246	0.292
CCcont	-2.416	0.379
DS01	0.602	-0.482
DS02	-1.942	0.744
DS04	-0.541	0.663
DS0c	-1.524	-0.355
GP01	0.67	1.709
GP02	-0.098	0.189
GP0c	2.098	0.803
NOD	0.833	-0.197
NZO	-1.402	0.425
PWK	-1.968	0.718
H37Rv_KO_CtpC	1.982	0.812
H37Rv_KO_CtpD	-0.784	1.551
H37Rv_KO_Rv1272	1.778	2.299
H37Rv_KO_SugABC	1.55	1.213
H37Rv_KO_MbtN	-0.558	0.693
Trans05	1.302	1.456
macrophage_unactivated	0.931	0.426
IL1	-1.783	-0.258
Rapamycin	-0.534	-0.457
Tcell	1.215	0.44
GMCSF	-2.308	0.288
IFNab	-0.641	0.127
IFNg	0.414	0.361
IFNg_GMCSF1	0.0	0.465
Rv1432_day32	-0.793	0.162
Rv1565c_day32	0.16	-0.027
secA2_input	0.028	-1.124
delta_Rv3594	-0.951	0.75
delta_Rv3717	-2.154	0.367
delta_Rv3811	-1.862	0.568
delta_Rv0954	-1.771	0.18
PonA1	-1.08	1.236
EccD1_KO	-2.43	-0.339
EspI_KO	-1.406	-0.756
PE35_KO	-1.12	-1.178
PPE68_KO	-0.493	-0.806
glycerol2	-0.219	-0.02
lignocerate	-1.533	-0.218
oleate	-0.774	0.461
phosphatidylcholine	0.197	0.204
acetate	-2.668	-0.244
glucAc	-3.998	-0.555
Rv0950ko	0.585	0.311
Rv1096ko	0.175	-0.41
Rv3684ko	-0.888	-0.799
delta_otsA_trehalose	-0.274	0.097