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 Rv2335/cysE:

update plot	correlation	link to info on gene
Rv2334/cysK1	(cc=0.8197)	info on Rv2334/cysK1
Rv3855/ethR	(cc=0.6071)	info on Rv3855/ethR
Rv2581c/-	(cc=0.5998)	info on Rv2581c/-
Rv2782c/pepR	(cc=0.5932)	info on Rv2782c/pepR
Rv2398c/cysW	(cc=0.5585)	info on Rv2398c/cysW
Rv1239c/corA	(cc=0.5468)	info on Rv1239c/corA
Rv1072/-	(cc=0.5344)	info on Rv1072/-
Rv0805/-	(cc=0.5205)	info on Rv0805/-
Rv2795c/-	(cc=0.5076)	info on Rv2795c/-
Rv0554/bpoC	(cc=0.5047)	info on Rv0554/bpoC

Correlation of Rv2335/cysE with Rv2581c/-

Normalized LFCs for Rv2335/cysE:
(description and provenance of datasets)

	Rv2335/cysE	Rv2581c/-
Fe_supp_jason_reseq	3.268	1.796
low_pH_jason_reseq	3.885	1.282
NO_jason_reseq	-1.935	0.0
B6_jason_reseq	1.467	0.153
MHCII_jason_reseq	-0.842	0.0
Isoniazid02	2.714	0.0
Rifampicin4	0.523	0.0
Ethambutol3	1.018	0.0
Meropenem3	0.0	0.0
Vancomycin16	1.73	0.0
Rv2680_day32	0.0	0.0
H37Rv_KO_MarP	1.274	-0.195
hypoxia_3wks	-1.36	-1.511
hypoxia_6wks	-0.518	-0.24
glycerol	0.0	0.0
cholesterol	2.618	0.0
AJ	1.324	0.0
Bibs02	-0.183	0.0
Bibs02c	-0.209	0.0
BL6	1.125	0.0
BL6a	1.527	0.696
BXD01	2.557	0.0
BXD010	1.915	0.0
BXD011	1.615	0.0
BXD03	1.675	0.0
BXD04	2.008	0.236
BXD05	1.154	0.256
BXD06	2.457	0.0
BXD07	1.675	0.0
BXD08	1.394	0.133
BXD09	1.146	0.386
CAST	4.201	0.0
CCcont	1.565	1.43
DS01	0.216	0.0
DS02	0.704	0.0
DS04	0.0	0.0
DS0c	-0.217	0.0
GP01	-0.099	0.0
GP02	-0.083	0.0
GP0c	-0.13	0.0
NOD	1.282	0.0
NZO	1.537	0.0
PWK	2.646	0.0
H37Rv_KO_CtpC	0.148	0.0
H37Rv_KO_CtpD	0.723	0.537
H37Rv_KO_Rv1272	1.574	0.0
H37Rv_KO_SugABC	-0.099	0.099
H37Rv_KO_MbtN	0.404	0.0
Trans05	0.947	0.0
macrophage_unactivated	-1.196	0.436
IL1	-1.124	0.0
Rapamycin	0.328	0.0
Tcell	-0.785	0.45
GMCSF	-1.001	0.364
IFNab	-0.348	0.417
IFNg	-1.013	0.0
IFNg_GMCSF1	-0.361	0.0
Rv1432_day32	0.611	0.0
Rv1565c_day32	2.631	-0.218
secA2_input	-1.296	0.157
delta_Rv3594	-2.348	-1.649
delta_Rv3717	-3.335	-2.25
delta_Rv3811	-3.324	-1.725
delta_Rv0954	-0.667	-2.31
PonA1	0.537	1.526
EccD1_KO	1.694	2.654
EspI_KO	0.419	0.485
PE35_KO	2.269	0.496
PPE68_KO	2.188	1.677
glycerol2	-1.822	-1.401
lignocerate	-1.877	-1.218
oleate	-2.185	-1.418
phosphatidylcholine	-2.35	-1.401
acetate	0.708	-0.856
glucAc	-0.199	-0.532
Rv0950ko	1.143	1.462
Rv1096ko	1.541	2.045
Rv3684ko	2.577	1.916
delta_otsA_trehalose	0.468	0.0