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 Rv3517/-:

update plot	correlation	link to info on gene
Rv3694c/-	(cc=0.4981)	info on Rv3694c/-
Rv3689/-	(cc=0.4812)	info on Rv3689/-
Rv3796/-	(cc=0.4794)	info on Rv3796/-
Rv2253/-	(cc=0.4682)	info on Rv2253/-
Rv0831c/-	(cc=0.463)	info on Rv0831c/-
Rv3744/nmtR	(cc=0.4522)	info on Rv3744/nmtR
Rv3695/-	(cc=0.4453)	info on Rv3695/-
Rv1585c/-	(cc=0.4422)	info on Rv1585c/-
Rv3142c/-	(cc=0.4388)	info on Rv3142c/-
Rv3378c/-	(cc=0.4266)	info on Rv3378c/-

Correlation of Rv3517/- with Rv3378c/-

Normalized LFCs for Rv3517/-:
(description and provenance of datasets)

	Rv3517/-	Rv3378c/-
Fe_supp_jason_reseq	0.3	0.09
low_pH_jason_reseq	-1.491	0.0
NO_jason_reseq	-0.541	0.562
B6_jason_reseq	-0.856	-1.175
MHCII_jason_reseq	-0.266	-0.922
Isoniazid02	-0.419	0.188
Rifampicin4	0.65	-0.384
Ethambutol3	0.514	2.745
Meropenem3	1.004	-0.111
Vancomycin16	-0.297	-0.122
Rv2680_day32	-0.576	0.219
H37Rv_KO_MarP	0.016	0.346
hypoxia_3wks	-0.427	0.55
hypoxia_6wks	-0.397	0.288
glycerol	-0.793	-0.791
cholesterol	0.252	-0.435
AJ	1.592	1.356
Bibs02	0.736	-0.123
Bibs02c	0.202	-0.141
BL6	0.556	0.355
BL6a	-0.076	1.004
BXD01	0.731	0.81
BXD010	0.671	2.138
BXD011	0.3	0.362
BXD03	0.891	1.461
BXD04	0.279	0.855
BXD05	0.234	0.736
BXD06	0.218	1.411
BXD07	0.084	0.702
BXD08	1.061	1.308
BXD09	0.589	1.452
CAST	0.14	0.414
CCcont	0.639	0.497
DS01	0.869	0.149
DS02	0.354	0.507
DS04	1.117	1.699
DS0c	0.08	0.506
GP01	0.805	1.723
GP02	-0.124	1.343
GP0c	1.021	0.76
NOD	1.778	0.0
NZO	0.803	0.465
PWK	1.833	0.995
H37Rv_KO_CtpC	1.432	1.423
H37Rv_KO_CtpD	0.683	1.728
H37Rv_KO_Rv1272	1.625	1.589
H37Rv_KO_SugABC	0.39	0.462
H37Rv_KO_MbtN	-0.153	0.391
Trans05	1.08	1.529
macrophage_unactivated	0.698	0.17
IL1	0.036	0.16
Rapamycin	-0.629	-0.945
Tcell	0.948	0.176
GMCSF	0.063	-0.636
IFNab	0.245	-0.729
IFNg	-0.265	-0.644
IFNg_GMCSF1	0.327	-1.191
Rv1432_day32	-0.394	0.0
Rv1565c_day32	-0.357	-0.464
secA2_input	0.332	-0.174
delta_Rv3594	-0.408	-0.85
delta_Rv3717	-0.258	-0.7
delta_Rv3811	0.016	0.0
delta_Rv0954	-0.362	0.074
PonA1	1.154	-0.547
EccD1_KO	0.766	-0.171
EspI_KO	-0.439	0.55
PE35_KO	0.055	-0.475
PPE68_KO	0.358	0.0
glycerol2	0.611	1.334
lignocerate	0.746	-0.751
oleate	0.956	0.044
phosphatidylcholine	0.728	0.209
acetate	0.12	-0.522
glucAc	0.223	-0.638
Rv0950ko	0.036	1.701
Rv1096ko	1.616	1.007
Rv3684ko	1.33	0.757
delta_otsA_trehalose	0.831	0.435