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 Rv3689/-:

update plot	correlation	link to info on gene
Rv1072/-	(cc=0.6562)	info on Rv1072/-
Rv1387/PPE20	(cc=0.6534)	info on Rv1387/PPE20
Rv3694c/-	(cc=0.6327)	info on Rv3694c/-
Rv1386/PE15	(cc=0.62)	info on Rv1386/PE15
Rv3419c/gcp	(cc=0.6172)	info on Rv3419c/gcp
Rv1616/-	(cc=0.6155)	info on Rv1616/-
Rv3142c/-	(cc=0.5926)	info on Rv3142c/-
Rv0932c/pstS2	(cc=0.5862)	info on Rv0932c/pstS2
Rv1488/-	(cc=0.5853)	info on Rv1488/-
Rv2456c/-	(cc=0.5823)	info on Rv2456c/-

Correlation of Rv3689/- with Rv1387/PPE20

Normalized LFCs for Rv3689/-:
(description and provenance of datasets)

	Rv3689/-	Rv1387/PPE20
Fe_supp_jason_reseq	-0.388	-1.71
low_pH_jason_reseq	-1.681	-1.061
NO_jason_reseq	0.105	-0.772
B6_jason_reseq	0.499	0.254
MHCII_jason_reseq	-0.62	-0.581
Isoniazid02	-1.107	-0.93
Rifampicin4	0.495	0.482
Ethambutol3	0.951	-0.393
Meropenem3	-0.364	0.258
Vancomycin16	-0.058	-0.57
Rv2680_day32	-0.811	0.989
H37Rv_KO_MarP	-1.24	-1.185
hypoxia_3wks	0.638	0.028
hypoxia_6wks	0.739	0.72
glycerol	-0.295	-1.504
cholesterol	-0.2	-0.696
AJ	0.576	0.158
Bibs02	-0.311	-0.326
Bibs02c	-0.073	0.65
BL6	0.728	0.692
BL6a	0.844	0.934
BXD01	1.055	1.192
BXD010	0.8	1.342
BXD011	0.852	1.167
BXD03	1.454	1.269
BXD04	1.548	1.003
BXD05	1.047	1.569
BXD06	0.962	1.811
BXD07	1.026	0.98
BXD08	1.004	1.125
BXD09	0.486	1.125
CAST	1.677	1.825
CCcont	0.27	-0.567
DS01	-0.202	-0.587
DS02	0.044	-0.868
DS04	0.225	0.267
DS0c	-0.091	-0.548
GP01	0.821	1.008
GP02	0.096	2.035
GP0c	0.85	0.736
NOD	0.957	0.5
NZO	1.16	0.35
PWK	2.364	2.083
H37Rv_KO_CtpC	0.806	2.061
H37Rv_KO_CtpD	0.981	0.578
H37Rv_KO_Rv1272	0.967	1.045
H37Rv_KO_SugABC	1.067	0.788
H37Rv_KO_MbtN	1.472	1.039
Trans05	0.496	1.611
macrophage_unactivated	0.079	-0.347
IL1	-0.374	-0.825
Rapamycin	-0.997	-1.323
Tcell	0.508	0.336
GMCSF	0.132	-0.312
IFNab	0.206	-0.411
IFNg	0.722	0.706
IFNg_GMCSF1	0.452	0.408
Rv1432_day32	1.172	1.138
Rv1565c_day32	-0.482	-0.455
secA2_input	-0.488	-1.199
delta_Rv3594	-0.58	0.575
delta_Rv3717	-0.205	1.713
delta_Rv3811	-0.21	0.625
delta_Rv0954	-0.979	-0.72
PonA1	-0.099	-1.868
EccD1_KO	0.122	-0.312
EspI_KO	-0.217	-0.405
PE35_KO	0.295	-0.618
PPE68_KO	0.208	-0.71
glycerol2	0.27	-0.38
lignocerate	-0.029	-0.095
oleate	0.717	-0.997
phosphatidylcholine	-0.052	0.028
acetate	0.284	-0.239
glucAc	0.188	0.007
Rv0950ko	0.202	0.024
Rv1096ko	0.85	-0.365
Rv3684ko	0.799	0.111
delta_otsA_trehalose	-0.482	0.083