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 Rv0960/vapC9:

update plot	correlation	link to info on gene
Rv1809/PPE33	(cc=0.5268)	info on Rv1809/PPE33
Rv3238c/-	(cc=0.4467)	info on Rv3238c/-
Rv1591/-	(cc=0.4419)	info on Rv1591/-
Rv2590/fadD9	(cc=0.4385)	info on Rv2590/fadD9
Rv3235/-	(cc=0.427)	info on Rv3235/-
Rv0915c/PPE14	(cc=0.4136)	info on Rv0915c/PPE14
Rv2557/-	(cc=0.4125)	info on Rv2557/-
Rv2024c/-	(cc=0.4118)	info on Rv2024c/-
Rv3736/-	(cc=0.4084)	info on Rv3736/-
Rv3290c/lat	(cc=0.3999)	info on Rv3290c/lat

Correlation of Rv0960/vapC9 with Rv3238c/-

Normalized LFCs for Rv0960/vapC9:
(description and provenance of datasets)

	Rv0960/vapC9	Rv3238c/-
Fe_supp_jason_reseq	-1.844	-0.284
low_pH_jason_reseq	-0.457	-1.181
NO_jason_reseq	-0.362	-0.412
B6_jason_reseq	-1.349	-0.232
MHCII_jason_reseq	-0.342	0.04
Isoniazid02	0.031	0.583
Rifampicin4	0.95	0.412
Ethambutol3	0.303	1.198
Meropenem3	1.523	0.873
Vancomycin16	0.135	0.09
Rv2680_day32	-0.052	-0.093
H37Rv_KO_MarP	0.395	0.426
hypoxia_3wks	-0.49	-0.227
hypoxia_6wks	-0.376	0.019
glycerol	-0.761	-0.834
cholesterol	0.029	-0.074
AJ	0.592	0.282
Bibs02	1.091	-0.57
Bibs02c	-0.058	0.441
BL6	-0.331	-0.079
BL6a	0.04	0.184
BXD01	-0.224	0.159
BXD010	-0.189	-0.315
BXD011	-0.79	0.0
BXD03	0.843	0.249
BXD04	0.776	0.702
BXD05	-0.646	-0.225
BXD06	0.156	0.249
BXD07	0.074	0.174
BXD08	0.139	-0.2
BXD09	0.232	-0.041
CAST	-0.609	0.082
CCcont	-0.162	0.031
DS01	0.498	0.14
DS02	0.173	0.307
DS04	0.627	0.72
DS0c	0.588	0.399
GP01	0.83	0.234
GP02	1.002	0.51
GP0c	-0.045	-0.267
NOD	-0.278	0.519
NZO	-1.74	-0.202
PWK	-0.818	0.59
H37Rv_KO_CtpC	0.033	0.781
H37Rv_KO_CtpD	0.554	-0.056
H37Rv_KO_Rv1272	-0.451	0.424
H37Rv_KO_SugABC	1.658	0.385
H37Rv_KO_MbtN	1.095	0.479
Trans05	-0.467	0.706
macrophage_unactivated	0.455	0.259
IL1	0.899	0.033
Rapamycin	0.663	0.0
Tcell	0.469	0.055
GMCSF	0.85	0.576
IFNab	0.683	0.148
IFNg	-0.257	0.807
IFNg_GMCSF1	1.612	0.437
Rv1432_day32	0.489	-0.137
Rv1565c_day32	-0.325	-0.141
secA2_input	-0.263	-0.507
delta_Rv3594	-0.665	0.401
delta_Rv3717	0.17	-0.059
delta_Rv3811	-0.913	-0.15
delta_Rv0954	-0.636	0.243
PonA1	0.103	-0.34
EccD1_KO	0.434	0.316
EspI_KO	0.961	1.212
PE35_KO	1.103	1.03
PPE68_KO	0.761	1.088
glycerol2	0.993	0.502
lignocerate	0.477	0.514
oleate	0.978	0.625
phosphatidylcholine	0.767	0.501
acetate	-0.452	0.105
glucAc	-0.717	0.016
Rv0950ko	0.473	0.289
Rv1096ko	0.371	-0.166
Rv3684ko	1.117	0.727
delta_otsA_trehalose	0.725	-0.38