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 Rv3669/-:

update plot	correlation	link to info on gene
Rv1404/-	(cc=0.5149)	info on Rv1404/-
Rv2040c/-	(cc=0.4922)	info on Rv2040c/-
Rv1028A/kdpF	(cc=0.4505)	info on Rv1028A/kdpF
Rv1003/-	(cc=0.4431)	info on Rv1003/-
Rv3215/entC	(cc=0.4125)	info on Rv3215/entC
Rv1928c/-	(cc=0.4004)	info on Rv1928c/-
Rv1129c/-	(cc=0.3879)	info on Rv1129c/-
Rv2437/-	(cc=0.3711)	info on Rv2437/-
Rv2316/uspA	(cc=0.3669)	info on Rv2316/uspA
Rv0948c/-	(cc=0.3665)	info on Rv0948c/-

Correlation of Rv3669/- with Rv1404/-

Normalized LFCs for Rv3669/-:
(description and provenance of datasets)

	Rv3669/-	Rv1404/-
Fe_supp_jason_reseq	2.087	2.382
low_pH_jason_reseq	-0.811	-1.328
NO_jason_reseq	-1.273	0.281
B6_jason_reseq	1.973	1.228
MHCII_jason_reseq	-0.474	-0.776
Isoniazid02	0.21	0.332
Rifampicin4	0.912	0.422
Ethambutol3	0.617	0.235
Meropenem3	-0.409	0.395
Vancomycin16	0.0	-0.589
Rv2680_day32	0.0	0.803
H37Rv_KO_MarP	-0.669	0.478
hypoxia_3wks	0.267	0.287
hypoxia_6wks	2.362	-0.159
glycerol	-1.463	-1.862
cholesterol	0.528	-1.612
AJ	-1.487	-0.671
Bibs02	-1.673	-2.035
Bibs02c	-1.914	-2.12
BL6	0.053	0.993
BL6a	-0.088	0.0
BXD01	-0.64	-0.048
BXD010	0.956	1.358
BXD011	1.714	0.968
BXD03	0.92	1.162
BXD04	-0.372	0.167
BXD05	0.682	-0.209
BXD06	1.131	1.229
BXD07	1.2	0.352
BXD08	-0.4	0.729
BXD09	1.787	1.092
CAST	-0.21	-1.018
CCcont	1.049	1.732
DS01	-0.216	-2.178
DS02	-0.531	-0.249
DS04	-1.775	-0.753
DS0c	-1.985	-0.958
GP01	-0.903	-1.099
GP02	-0.761	-0.926
GP0c	-1.19	-1.199
NOD	-0.099	-1.119
NZO	-0.38	-0.994
PWK	0.388	-1.809
H37Rv_KO_CtpC	2.166	-1.808
H37Rv_KO_CtpD	-1.159	-0.787
H37Rv_KO_Rv1272	-1.29	-0.972
H37Rv_KO_SugABC	-0.906	1.453
H37Rv_KO_MbtN	-0.31	-0.348
Trans05	-0.947	-0.812
macrophage_unactivated	0.088	-0.89
IL1	2.334	0.641
Rapamycin	0.252	-0.611
Tcell	0.0	0.433
GMCSF	1.809	0.57
IFNab	2.228	0.889
IFNg	0.69	0.123
IFNg_GMCSF1	2.369	0.55
Rv1432_day32	0.0	-0.961
Rv1565c_day32	0.0	-0.114
secA2_input	-3.131	0.0
delta_Rv3594	1.306	1.326
delta_Rv3717	2.017	0.384
delta_Rv3811	2.411	2.357
delta_Rv0954	-0.792	0.302
PonA1	0.986	0.503
EccD1_KO	0.454	-1.131
EspI_KO	2.852	2.321
PE35_KO	1.263	0.481
PPE68_KO	0.0	0.272
glycerol2	0.0	-0.347
lignocerate	0.32	0.712
oleate	0.0	-2.535
phosphatidylcholine	0.0	-0.618
acetate	1.998	0.459
glucAc	1.306	0.777
Rv0950ko	-1.372	1.683
Rv1096ko	-2.069	-0.941
Rv3684ko	-0.684	-0.134
delta_otsA_trehalose	-0.667	0.239