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 Rv2345/-:

update plot	correlation	link to info on gene
Rv1947/-	(cc=0.6789)	info on Rv1947/-
Rv1000c/-	(cc=0.6093)	info on Rv1000c/-
Rv1899c/lppD	(cc=0.6084)	info on Rv1899c/lppD
Rv1175c/fadH	(cc=0.5897)	info on Rv1175c/fadH
Rv2313c/-	(cc=0.5727)	info on Rv2313c/-
Rv2658c/-	(cc=0.5726)	info on Rv2658c/-
Rv0399c/lpqK	(cc=0.5689)	info on Rv0399c/lpqK
Rv2947c/pks15	(cc=0.5434)	info on Rv2947c/pks15
Rv2639c/-	(cc=0.541)	info on Rv2639c/-
Rv1857/modA	(cc=0.5206)	info on Rv1857/modA

Correlation of Rv2345/- with Rv2639c/-

Normalized LFCs for Rv2345/-:
(description and provenance of datasets)

	Rv2345/-	Rv2639c/-
Fe_supp_jason_reseq	-0.019	0.068
low_pH_jason_reseq	-0.962	-0.085
NO_jason_reseq	-0.053	0.362
B6_jason_reseq	-0.063	0.114
MHCII_jason_reseq	0.065	0.077
Isoniazid02	-1.199	-2.072
Rifampicin4	0.509	0.152
Ethambutol3	-1.019	-2.212
Meropenem3	-1.409	-2.692
Vancomycin16	-0.655	-1.276
Rv2680_day32	-0.466	0.489
H37Rv_KO_MarP	-0.02	0.965
hypoxia_3wks	0.032	0.335
hypoxia_6wks	0.257	0.426
glycerol	0.192	-0.253
cholesterol	-0.086	-0.512
AJ	0.0	1.292
Bibs02	-0.278	-0.623
Bibs02c	-0.205	-0.068
BL6	0.138	-0.797
BL6a	0.118	-0.65
BXD01	0.14	0.011
BXD010	0.141	0.291
BXD011	-0.262	-0.14
BXD03	-0.04	-0.102
BXD04	0.291	0.692
BXD05	0.374	0.194
BXD06	0.147	-0.031
BXD07	0.238	0.037
BXD08	0.434	0.041
BXD09	0.199	-0.126
CAST	-0.225	-0.242
CCcont	0.024	-1.042
DS01	0.0	0.303
DS02	-0.498	-0.071
DS04	-0.142	-0.156
DS0c	-0.057	-0.283
GP01	0.277	0.061
GP02	0.072	1.528
GP0c	0.147	0.714
NOD	0.265	-0.425
NZO	-0.237	0.319
PWK	-0.058	0.558
H37Rv_KO_CtpC	0.373	1.378
H37Rv_KO_CtpD	0.605	-0.976
H37Rv_KO_Rv1272	0.291	0.208
H37Rv_KO_SugABC	0.767	0.621
H37Rv_KO_MbtN	0.628	0.257
Trans05	0.501	0.565
macrophage_unactivated	-0.114	-1.098
IL1	0.338	-0.709
Rapamycin	0.473	-0.282
Tcell	0.039	-1.219
GMCSF	0.599	0.071
IFNab	0.311	-0.484
IFNg	0.216	0.401
IFNg_GMCSF1	0.182	-0.88
Rv1432_day32	0.194	0.81
Rv1565c_day32	0.175	-1.278
secA2_input	0.233	0.283
delta_Rv3594	0.271	0.054
delta_Rv3717	0.055	0.299
delta_Rv3811	0.352	0.442
delta_Rv0954	0.371	0.196
PonA1	-0.321	0.807
EccD1_KO	0.704	1.667
EspI_KO	0.767	0.291
PE35_KO	0.429	0.729
PPE68_KO	0.176	1.334
glycerol2	0.277	0.252
lignocerate	0.284	-0.244
oleate	0.702	0.59
phosphatidylcholine	0.153	0.465
acetate	-0.462	-0.845
glucAc	-0.232	-1.314
Rv0950ko	0.434	0.084
Rv1096ko	-0.567	-0.549
Rv3684ko	-0.54	-0.986
delta_otsA_trehalose	0.582	-0.482