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 Rv0004/-:

update plot	correlation	link to info on gene
Rv1063c/-	(cc=0.5061)	info on Rv1063c/-
Rv2037c/-	(cc=0.4332)	info on Rv2037c/-
Rv3225c/-	(cc=0.4038)	info on Rv3225c/-
Rv3266c/rmlD	(cc=0.397)	info on Rv3266c/rmlD
Rv0744c/-	(cc=0.3932)	info on Rv0744c/-
Rv3101c/ftsX	(cc=0.3919)	info on Rv3101c/ftsX
Rv2553c/-	(cc=0.3919)	info on Rv2553c/-
Rv0731c/-	(cc=0.3773)	info on Rv0731c/-
Rv1512/epiA	(cc=0.3598)	info on Rv1512/epiA
Rv3258c/-	(cc=0.3588)	info on Rv3258c/-

Correlation of Rv0004/- with Rv1063c/-

Normalized LFCs for Rv0004/-:
(description and provenance of datasets)

	Rv0004/-	Rv1063c/-
Fe_supp_jason_reseq	0.0	-0.021
low_pH_jason_reseq	0.0	-0.912
NO_jason_reseq	0.0	-0.953
B6_jason_reseq	0.0	-0.292
MHCII_jason_reseq	0.0	0.229
Isoniazid02	0.851	1.12
Rifampicin4	-0.712	-0.217
Ethambutol3	0.14	0.815
Meropenem3	0.266	-0.047
Vancomycin16	-0.698	-0.077
Rv2680_day32	0.0	0.393
H37Rv_KO_MarP	-1.865	0.851
hypoxia_3wks	0.0	-0.494
hypoxia_6wks	0.0	-0.852
glycerol	0.385	-0.082
cholesterol	0.0	0.3
AJ	0.0	-0.269
Bibs02	0.0	0.256
Bibs02c	0.0	0.364
BL6	0.0	-0.493
BL6a	0.0	-0.143
BXD01	0.0	-0.108
BXD010	0.0	-0.486
BXD011	0.0	-0.297
BXD03	0.0	-0.041
BXD04	0.0	-0.487
BXD05	0.0	-0.57
BXD06	0.0	-0.713
BXD07	0.0	-0.716
BXD08	0.0	0.541
BXD09	0.0	-0.31
CAST	1.785	0.155
CCcont	0.0	-0.14
DS01	0.0	0.602
DS02	0.0	0.503
DS04	0.533	-0.246
DS0c	0.0	0.085
GP01	2.861	1.423
GP02	1.416	1.24
GP0c	1.663	1.671
NOD	4.852	2.11
NZO	0.0	-0.392
PWK	0.0	-0.162
H37Rv_KO_CtpC	0.0	-0.281
H37Rv_KO_CtpD	0.127	-0.785
H37Rv_KO_Rv1272	0.0	0.159
H37Rv_KO_SugABC	0.55	0.873
H37Rv_KO_MbtN	0.283	-0.131
Trans05	0.0	0.051
macrophage_unactivated	0.0	0.268
IL1	0.0	-0.439
Rapamycin	0.0	-0.221
Tcell	0.0	0.932
GMCSF	0.0	0.137
IFNab	0.0	0.686
IFNg	0.0	0.273
IFNg_GMCSF1	0.826	0.163
Rv1432_day32	0.0	-0.763
Rv1565c_day32	0.0	0.073
secA2_input	1.526	-0.111
delta_Rv3594	0.828	0.961
delta_Rv3717	3.253	0.24
delta_Rv3811	1.387	0.021
delta_Rv0954	-0.178	0.836
PonA1	-0.159	-0.017
EccD1_KO	0.0	-0.164
EspI_KO	0.0	0.462
PE35_KO	0.368	-0.108
PPE68_KO	0.403	0.0
glycerol2	0.0	-0.251
lignocerate	0.0	-0.089
oleate	0.0	-0.401
phosphatidylcholine	0.0	-0.814
acetate	0.0	-0.199
glucAc	0.0	-0.383
Rv0950ko	-0.793	-0.039
Rv1096ko	1.517	1.046
Rv3684ko	1.055	1.513
delta_otsA_trehalose	0.0	-1.127