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 Rv3680/-:

update plot	correlation	link to info on gene
Rv3679/-	(cc=0.6755)	info on Rv3679/-
Rv0505c/serB1	(cc=0.6554)	info on Rv0505c/serB1
Rv1421/-	(cc=0.6354)	info on Rv1421/-
Rv2837c/-	(cc=0.6279)	info on Rv2837c/-
Rv3215/entC	(cc=0.5995)	info on Rv3215/entC
Rv0998/-	(cc=0.5957)	info on Rv0998/-
Rv2966c/-	(cc=0.5688)	info on Rv2966c/-
Rv1821/secA2	(cc=0.5413)	info on Rv1821/secA2
Rv2553c/-	(cc=0.5391)	info on Rv2553c/-
Rv1856c/-	(cc=0.524)	info on Rv1856c/-

Correlation of Rv3680/- with Rv1421/-

Normalized LFCs for Rv3680/-:
(description and provenance of datasets)

	Rv3680/-	Rv1421/-
Fe_supp_jason_reseq	1.689	1.76
low_pH_jason_reseq	1.673	3.244
NO_jason_reseq	0.0	-1.864
B6_jason_reseq	0.0	-0.189
MHCII_jason_reseq	0.0	1.054
Isoniazid02	-1.072	-0.247
Rifampicin4	-0.474	0.355
Ethambutol3	-0.59	-2.404
Meropenem3	-0.21	-1.17
Vancomycin16	-0.464	0.565
Rv2680_day32	0.0	0.0
H37Rv_KO_MarP	-0.766	-3.348
hypoxia_3wks	-0.55	1.934
hypoxia_6wks	-0.288	2.088
glycerol	2.455	2.047
cholesterol	1.612	1.916
AJ	0.0	-0.232
Bibs02	1.015	3.974
Bibs02c	1.822	1.795
BL6	0.0	0.845
BL6a	1.812	1.934
BXD01	0.358	0.0
BXD010	0.128	0.0
BXD011	1.109	0.412
BXD03	0.75	-0.135
BXD04	0.34	0.312
BXD05	0.369	0.768
BXD06	1.035	0.523
BXD07	0.38	0.712
BXD08	0.253	0.121
BXD09	0.69	0.0
CAST	0.0	-0.23
CCcont	1.765	3.297
DS01	0.83	0.595
DS02	0.217	0.199
DS04	1.301	2.513
DS0c	0.413	0.85
GP01	0.0	1.767
GP02	0.0	0.076
GP0c	0.0	0.942
NOD	0.0	-0.225
NZO	0.0	-0.199
PWK	0.0	-0.196
H37Rv_KO_CtpC	0.162	0.739
H37Rv_KO_CtpD	0.445	1.454
H37Rv_KO_Rv1272	0.0	0.457
H37Rv_KO_SugABC	0.768	1.31
H37Rv_KO_MbtN	0.691	1.116
Trans05	0.0	0.228
macrophage_unactivated	0.436	-0.451
IL1	0.0	-1.898
Rapamycin	0.0	0.083
Tcell	0.857	0.424
GMCSF	0.0	0.718
IFNab	0.0	3.105
IFNg	0.0	-0.382
IFNg_GMCSF1	0.0	-0.085
Rv1432_day32	0.0	-0.18
Rv1565c_day32	0.0	0.218
secA2_input	-2.069	-0.595
delta_Rv3594	1.895	2.688
delta_Rv3717	3.237	4.737
delta_Rv3811	2.787	3.169
delta_Rv0954	0.375	1.193
PonA1	1.599	-0.119
EccD1_KO	0.635	-1.266
EspI_KO	0.878	-1.711
PE35_KO	0.735	-0.473
PPE68_KO	1.245	-1.296
glycerol2	-0.193	-2.081
lignocerate	-0.168	-1.808
oleate	-0.196	-2.105
phosphatidylcholine	-0.193	-2.08
acetate	0.743	-0.579
glucAc	0.462	-0.229
Rv0950ko	-1.9	-4.921
Rv1096ko	-2.111	-0.935
Rv3684ko	-2.663	-1.765
delta_otsA_trehalose	0.895	0.564