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 Rv3090/-:

update plot	correlation	link to info on gene
Rv1159A/-	(cc=0.4959)	info on Rv1159A/-
Rv2468A/-	(cc=0.4522)	info on Rv2468A/-
Rv2274c/mazF8	(cc=0.4188)	info on Rv2274c/mazF8
Rv0531/-	(cc=0.3932)	info on Rv0531/-
Rv2865/relF	(cc=0.371)	info on Rv2865/relF
Rv1088/PE9	(cc=0.3666)	info on Rv1088/PE9
Rv3518c/cyp142	(cc=0.3617)	info on Rv3518c/cyp142
Rv3588c/canB	(cc=0.3604)	info on Rv3588c/canB
Rv3764c/tcrY	(cc=0.3588)	info on Rv3764c/tcrY
Rv3843c/-	(cc=0.3551)	info on Rv3843c/-

Correlation of Rv3090/- with Rv1088/PE9

Normalized LFCs for Rv3090/-:
(description and provenance of datasets)

	Rv3090/-	Rv1088/PE9
Fe_supp_jason_reseq	0.156	1.621
low_pH_jason_reseq	-0.412	-2.414
NO_jason_reseq	-0.039	-0.108
B6_jason_reseq	1.177	-0.142
MHCII_jason_reseq	-0.036	-1.374
Isoniazid02	-0.623	0.534
Rifampicin4	0.014	1.037
Ethambutol3	-0.536	0.505
Meropenem3	-0.831	1.364
Vancomycin16	-0.268	0.268
Rv2680_day32	0.415	-3.328
H37Rv_KO_MarP	1.149	-0.277
hypoxia_3wks	0.124	0.299
hypoxia_6wks	-0.449	0.021
glycerol	0.351	-2.147
cholesterol	0.134	-0.961
AJ	0.171	-0.827
Bibs02	-0.146	0.842
Bibs02c	0.418	-0.981
BL6	-0.294	0.674
BL6a	0.727	1.459
BXD01	0.683	1.37
BXD010	0.711	1.021
BXD011	0.205	1.285
BXD03	1.445	1.652
BXD04	0.049	0.061
BXD05	1.162	1.745
BXD06	0.226	1.016
BXD07	0.442	0.866
BXD08	0.564	1.823
BXD09	0.31	1.547
CAST	-0.097	-0.445
CCcont	-0.031	0.882
DS01	-0.378	-1.567
DS02	-0.61	0.21
DS04	0.396	-0.316
DS0c	-0.969	-1.439
GP01	-1.43	-1.37
GP02	0.457	-0.065
GP0c	0.115	0.253
NOD	0.841	-1.189
NZO	0.623	0.87
PWK	0.04	-1.445
H37Rv_KO_CtpC	0.008	0.971
H37Rv_KO_CtpD	0.1	0.683
H37Rv_KO_Rv1272	-0.097	1.354
H37Rv_KO_SugABC	0.005	0.606
H37Rv_KO_MbtN	-0.617	-0.659
Trans05	0.0	2.476
macrophage_unactivated	-0.095	0.707
IL1	0.851	0.406
Rapamycin	-0.242	0.663
Tcell	0.075	1.896
GMCSF	-0.174	0.446
IFNab	0.505	0.106
IFNg	-0.211	0.759
IFNg_GMCSF1	0.057	-0.569
Rv1432_day32	-0.169	0.265
Rv1565c_day32	1.256	0.414
secA2_input	-0.487	-1.772
delta_Rv3594	0.064	-0.278
delta_Rv3717	0.4	0.54
delta_Rv3811	0.354	0.776
delta_Rv0954	0.756	-0.631
PonA1	0.464	-0.248
EccD1_KO	0.5	-0.707
EspI_KO	-0.299	0.0
PE35_KO	-0.385	-1.683
PPE68_KO	-0.25	-1.11
glycerol2	0.098	0.266
lignocerate	0.414	0.911
oleate	-0.198	-0.588
phosphatidylcholine	0.436	0.585
acetate	0.577	0.198
glucAc	0.45	0.484
Rv0950ko	-0.778	-0.992
Rv1096ko	-0.564	-3.016
Rv3684ko	-1.972	-2.738
delta_otsA_trehalose	0.39	0.539