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 Rv1013/pks16:

update plot	correlation	link to info on gene
Rv1366/-	(cc=0.5409)	info on Rv1366/-
Rv0072/-	(cc=0.5362)	info on Rv0072/-
Rv0643c/mmaA3	(cc=0.5343)	info on Rv0643c/mmaA3
Rv2777c/-	(cc=0.5297)	info on Rv2777c/-
Rv3823c/mmpL8	(cc=0.5196)	info on Rv3823c/mmpL8
Rv0235c/-	(cc=0.5066)	info on Rv0235c/-
Rv3555c/-	(cc=0.494)	info on Rv3555c/-
Rv2444c/rne	(cc=0.4901)	info on Rv2444c/rne
Rv3148/nuoD	(cc=0.4812)	info on Rv3148/nuoD
Rv3421c/-	(cc=0.4794)	info on Rv3421c/-

Correlation of Rv1013/pks16 with Rv2777c/-

Normalized LFCs for Rv1013/pks16:
(description and provenance of datasets)

	Rv1013/pks16	Rv2777c/-
Fe_supp_jason_reseq	0.48	0.396
low_pH_jason_reseq	-0.495	-0.418
NO_jason_reseq	1.533	0.722
B6_jason_reseq	-1.271	0.049
MHCII_jason_reseq	-3.023	0.077
Isoniazid02	-1.756	-0.358
Rifampicin4	0.019	-0.032
Ethambutol3	2.037	0.731
Meropenem3	1.0	-0.436
Vancomycin16	-0.236	-0.252
Rv2680_day32	-0.362	0.619
H37Rv_KO_MarP	0.968	0.086
hypoxia_3wks	-3.334	0.219
hypoxia_6wks	-3.909	-0.04
glycerol	-0.856	0.154
cholesterol	-1.194	0.018
AJ	0.435	-0.316
Bibs02	-0.029	0.827
Bibs02c	-1.15	-0.13
BL6	1.133	0.812
BL6a	0.319	0.848
BXD01	0.994	0.931
BXD010	2.464	0.823
BXD011	1.442	1.104
BXD03	2.47	1.211
BXD04	1.886	1.193
BXD05	1.862	0.725
BXD06	1.863	0.827
BXD07	1.419	0.917
BXD08	1.095	0.947
BXD09	2.209	1.056
CAST	0.0	0.068
CCcont	2.434	0.989
DS01	-0.636	0.322
DS02	-0.106	0.822
DS04	0.561	0.035
DS0c	0.919	0.42
GP01	2.567	0.438
GP02	2.671	1.709
GP0c	1.142	0.17
NOD	-0.185	0.763
NZO	-0.342	-0.415
PWK	1.903	0.533
H37Rv_KO_CtpC	1.227	0.899
H37Rv_KO_CtpD	0.133	0.577
H37Rv_KO_Rv1272	0.656	1.387
H37Rv_KO_SugABC	-0.099	-0.075
H37Rv_KO_MbtN	1.591	0.737
Trans05	0.998	0.778
macrophage_unactivated	-0.552	0.527
IL1	-0.917	-0.095
Rapamycin	-0.853	-0.316
Tcell	0.984	0.391
GMCSF	-1.941	-0.256
IFNab	-2.065	0.275
IFNg	-2.539	0.27
IFNg_GMCSF1	-2.212	-0.251
Rv1432_day32	0.463	0.382
Rv1565c_day32	1.501	0.106
secA2_input	-2.481	-0.175
delta_Rv3594	-1.239	0.315
delta_Rv3717	0.375	-0.047
delta_Rv3811	-2.174	0.055
delta_Rv0954	0.823	0.062
PonA1	0.768	-0.022
EccD1_KO	-0.191	0.28
EspI_KO	0.128	-0.151
PE35_KO	-1.068	0.554
PPE68_KO	-0.218	0.038
glycerol2	-0.073	0.698
lignocerate	4.396	0.679
oleate	6.0	0.679
phosphatidylcholine	2.531	0.903
acetate	1.438	0.294
glucAc	0.923	-0.051
Rv0950ko	-0.956	-0.121
Rv1096ko	-0.323	-0.151
Rv3684ko	1.166	-0.282
delta_otsA_trehalose	-0.506	0.949