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 Rv3379c/dxs2

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

	Rv3760/-	Rv3379c/dxs2
Fe_supp_jason_reseq	2.259	0.745
low_pH_jason_reseq	1.4	0.47
NO_jason_reseq	1.754	0.081
B6_jason_reseq	-0.799	-0.107
MHCII_jason_reseq	-2.059	-0.462
Isoniazid02	0.252	-0.374
Rifampicin4	0.593	0.233
Ethambutol3	-0.314	1.671
Meropenem3	-0.031	0.307
Vancomycin16	0.034	0.04
Rv2680_day32	-3.356	-0.452
H37Rv_KO_MarP	0.569	1.095
hypoxia_3wks	1.487	0.415
hypoxia_6wks	0.054	-0.205
glycerol	-0.622	0.492
cholesterol	-0.404	-0.315
AJ	0.711	0.659
Bibs02	-0.735	-0.201
Bibs02c	0.135	-0.112
BL6	-2.023	0.11
BL6a	0.854	0.356
BXD01	0.899	0.396
BXD010	0.186	0.158
BXD011	0.894	0.448
BXD03	-1.357	0.597
BXD04	0.781	0.912
BXD05	-0.375	0.767
BXD06	0.293	0.53
BXD07	-0.512	0.513
BXD08	-0.061	0.516
BXD09	0.626	0.467
CAST	-1.246	0.414
CCcont	-2.416	0.184
DS01	0.602	0.318
DS02	-1.942	0.618
DS04	-0.541	-0.55
DS0c	-1.524	0.292
GP01	0.67	0.328
GP02	-0.098	0.715
GP0c	2.098	0.408
NOD	0.833	0.404
NZO	-1.402	0.15
PWK	-1.968	0.374
H37Rv_KO_CtpC	1.982	0.122
H37Rv_KO_CtpD	-0.784	0.36
H37Rv_KO_Rv1272	1.778	0.804
H37Rv_KO_SugABC	1.55	0.845
H37Rv_KO_MbtN	-0.558	0.903
Trans05	1.302	0.318
macrophage_unactivated	0.931	0.35
IL1	-1.783	0.501
Rapamycin	-0.534	0.853
Tcell	1.215	0.124
GMCSF	-2.308	0.354
IFNab	-0.641	0.405
IFNg	0.414	1.04
IFNg_GMCSF1	0.0	0.839
Rv1432_day32	-0.793	-0.043
Rv1565c_day32	0.16	0.269
secA2_input	0.028	0.495
delta_Rv3594	-0.951	-0.153
delta_Rv3717	-2.154	-0.624
delta_Rv3811	-1.862	-1.002
delta_Rv0954	-1.771	-0.545
PonA1	-1.08	-0.284
EccD1_KO	-2.43	-0.214
EspI_KO	-1.406	0.0
PE35_KO	-1.12	-0.391
PPE68_KO	-0.493	0.16
glycerol2	-0.219	0.481
lignocerate	-1.533	-0.347
oleate	-0.774	-0.295
phosphatidylcholine	0.197	0.102
acetate	-2.668	-0.304
glucAc	-3.998	-0.714
Rv0950ko	0.585	-0.145
Rv1096ko	0.175	0.314
Rv3684ko	-0.888	0.0
delta_otsA_trehalose	-0.274	-0.749