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 Rv2908c/-:

update plot	correlation	link to info on gene
Rv0537c/-	(cc=0.5459)	info on Rv0537c/-
Rv0538/-	(cc=0.4889)	info on Rv0538/-
Rv3060c/-	(cc=0.4787)	info on Rv3060c/-
Rv1178/-	(cc=0.4766)	info on Rv1178/-
Rv0062/celA1	(cc=0.4757)	info on Rv0062/celA1
Rv3075c/-	(cc=0.4744)	info on Rv3075c/-
Rv1081c/-	(cc=0.4638)	info on Rv1081c/-
Rv2506/-	(cc=0.4594)	info on Rv2506/-
Rv3067/-	(cc=0.4353)	info on Rv3067/-
Rv2091c/-	(cc=0.433)	info on Rv2091c/-

Correlation of Rv2908c/- with Rv0537c/-

Normalized LFCs for Rv2908c/-:
(description and provenance of datasets)

	Rv2908c/-	Rv0537c/-
Fe_supp_jason_reseq	0.0	-0.799
low_pH_jason_reseq	0.0	-0.36
NO_jason_reseq	0.0	0.425
B6_jason_reseq	0.0	-0.052
MHCII_jason_reseq	0.0	-1.076
Isoniazid02	0.0	-0.179
Rifampicin4	0.374	-1.828
Ethambutol3	2.247	0.854
Meropenem3	0.165	-0.341
Vancomycin16	0.0	-3.65
Rv2680_day32	0.0	-0.911
H37Rv_KO_MarP	2.492	6.0
hypoxia_3wks	0.0	0.223
hypoxia_6wks	0.0	0.372
glycerol	0.0	0.212
cholesterol	0.145	-0.089
AJ	0.0	-0.407
Bibs02	0.0	0.033
Bibs02c	0.0	-0.435
BL6	0.0	-0.077
BL6a	0.0	-0.293
BXD01	0.0	-0.012
BXD010	0.0	0.212
BXD011	0.0	-0.196
BXD03	0.0	-0.495
BXD04	0.0	-0.017
BXD05	0.0	0.119
BXD06	0.0	-0.018
BXD07	0.0	-0.41
BXD08	0.0	-0.063
BXD09	0.0	-0.128
CAST	0.0	-0.479
CCcont	0.149	0.212
DS01	0.0	-0.642
DS02	0.217	-1.019
DS04	0.0	-1.276
DS0c	0.0	-0.564
GP01	0.0	-0.348
GP02	0.0	-0.638
GP0c	0.0	0.087
NOD	0.0	-0.519
NZO	0.199	-0.415
PWK	0.0	0.027
H37Rv_KO_CtpC	0.0	-0.858
H37Rv_KO_CtpD	0.0	-0.154
H37Rv_KO_Rv1272	0.0	0.0
H37Rv_KO_SugABC	0.0	0.268
H37Rv_KO_MbtN	0.0	-0.293
Trans05	0.0	0.39
macrophage_unactivated	0.0	0.3
IL1	0.0	0.133
Rapamycin	0.0	0.42
Tcell	0.0	0.023
GMCSF	0.0	0.378
IFNab	0.0	0.432
IFNg	0.0	0.684
IFNg_GMCSF1	0.0	0.804
Rv1432_day32	0.0	0.858
Rv1565c_day32	0.0	-0.595
secA2_input	0.0	0.463
delta_Rv3594	-0.176	-0.207
delta_Rv3717	-0.477	0.276
delta_Rv3811	-0.564	-0.211
delta_Rv0954	-0.49	-0.183
PonA1	1.601	0.28
EccD1_KO	0.0	-0.365
EspI_KO	0.0	-0.083
PE35_KO	0.403	-0.974
PPE68_KO	0.0	-0.659
glycerol2	0.0	-0.063
lignocerate	0.0	-0.021
oleate	0.0	0.574
phosphatidylcholine	0.0	0.062
acetate	0.63	0.186
glucAc	0.0	-0.257
Rv0950ko	0.727	0.736
Rv1096ko	0.38	0.461
Rv3684ko	0.789	0.825
delta_otsA_trehalose	0.254	0.558