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 Rv1366/-

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

	Rv1013/pks16	Rv1366/-
Fe_supp_jason_reseq	0.48	-0.884
low_pH_jason_reseq	-0.495	-0.172
NO_jason_reseq	1.533	-0.294
B6_jason_reseq	-1.271	-0.871
MHCII_jason_reseq	-3.023	-0.267
Isoniazid02	-1.756	0.148
Rifampicin4	0.019	-0.376
Ethambutol3	2.037	0.269
Meropenem3	1.0	0.237
Vancomycin16	-0.236	0.172
Rv2680_day32	-0.362	-0.969
H37Rv_KO_MarP	0.968	0.518
hypoxia_3wks	-3.334	-0.235
hypoxia_6wks	-3.909	-0.048
glycerol	-0.856	-0.78
cholesterol	-1.194	-0.44
AJ	0.435	0.134
Bibs02	-0.029	-0.823
Bibs02c	-1.15	0.656
BL6	1.133	0.376
BL6a	0.319	0.397
BXD01	0.994	0.834
BXD010	2.464	1.115
BXD011	1.442	0.35
BXD03	2.47	-0.278
BXD04	1.886	0.315
BXD05	1.862	0.231
BXD06	1.863	0.323
BXD07	1.419	0.476
BXD08	1.095	0.506
BXD09	2.209	-0.012
CAST	0.0	-0.142
CCcont	2.434	0.646
DS01	-0.636	0.301
DS02	-0.106	-0.254
DS04	0.561	0.263
DS0c	0.919	0.525
GP01	2.567	1.227
GP02	2.671	1.296
GP0c	1.142	0.54
NOD	-0.185	0.148
NZO	-0.342	0.839
PWK	1.903	0.406
H37Rv_KO_CtpC	1.227	0.467
H37Rv_KO_CtpD	0.133	-0.907
H37Rv_KO_Rv1272	0.656	0.341
H37Rv_KO_SugABC	-0.099	0.902
H37Rv_KO_MbtN	1.591	0.392
Trans05	0.998	0.557
macrophage_unactivated	-0.552	0.107
IL1	-0.917	-0.739
Rapamycin	-0.853	-0.681
Tcell	0.984	0.694
GMCSF	-1.941	-1.117
IFNab	-2.065	-0.593
IFNg	-2.539	-1.384
IFNg_GMCSF1	-2.212	-1.628
Rv1432_day32	0.463	-0.55
Rv1565c_day32	1.501	0.175
secA2_input	-2.481	-0.188
delta_Rv3594	-1.239	-0.249
delta_Rv3717	0.375	0.371
delta_Rv3811	-2.174	-0.665
delta_Rv0954	0.823	0.813
PonA1	0.768	0.726
EccD1_KO	-0.191	-0.276
EspI_KO	0.128	0.262
PE35_KO	-1.068	0.379
PPE68_KO	-0.218	0.534
glycerol2	-0.073	1.188
lignocerate	4.396	1.47
oleate	6.0	0.387
phosphatidylcholine	2.531	1.27
acetate	1.438	1.549
glucAc	0.923	1.226
Rv0950ko	-0.956	0.856
Rv1096ko	-0.323	0.32
Rv3684ko	1.166	0.534
delta_otsA_trehalose	-0.506	1.077