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 Rv2356c/PPE40:

update plot	correlation	link to info on gene
Rv3650/PE33	(cc=0.5562)	info on Rv3650/PE33
Rv3858c/gltD	(cc=0.5221)	info on Rv3858c/gltD
Rv1918c/PPE35	(cc=0.5179)	info on Rv1918c/PPE35
Rv2735c/-	(cc=0.4971)	info on Rv2735c/-
Rv2190c/-	(cc=0.4896)	info on Rv2190c/-
Rv3489/-	(cc=0.4793)	info on Rv3489/-
Rv2067c/-	(cc=0.4614)	info on Rv2067c/-
Rv2678c/hemE	(cc=0.4582)	info on Rv2678c/hemE
Rv1507A/-	(cc=0.4471)	info on Rv1507A/-
Rv3425/PPE57	(cc=0.4463)	info on Rv3425/PPE57

Correlation of Rv2356c/PPE40 with Rv2067c/-

Normalized LFCs for Rv2356c/PPE40:
(description and provenance of datasets)

	Rv2356c/PPE40	Rv2067c/-
Fe_supp_jason_reseq	0.65	0.284
low_pH_jason_reseq	0.139	-0.075
NO_jason_reseq	-0.984	0.572
B6_jason_reseq	-0.202	0.049
MHCII_jason_reseq	0.447	0.0
Isoniazid02	-0.036	0.0
Rifampicin4	0.701	0.393
Ethambutol3	0.102	0.084
Meropenem3	-0.138	0.818
Vancomycin16	0.403	0.159
Rv2680_day32	0.677	0.383
H37Rv_KO_MarP	0.102	-0.138
hypoxia_3wks	-0.471	-0.327
hypoxia_6wks	-0.405	0.033
glycerol	-0.121	0.05
cholesterol	0.105	-0.112
AJ	0.257	0.61
Bibs02	0.147	0.713
Bibs02c	0.456	0.403
BL6	0.519	0.843
BL6a	0.587	0.936
BXD01	-0.225	0.153
BXD010	0.189	0.919
BXD011	0.829	0.54
BXD03	0.435	0.66
BXD04	0.67	0.66
BXD05	0.87	0.646
BXD06	0.547	0.703
BXD07	0.111	0.337
BXD08	-0.177	0.324
BXD09	0.316	0.572
CAST	-0.158	0.444
CCcont	0.049	0.67
DS01	-0.431	0.142
DS02	0.274	0.35
DS04	-0.169	-0.024
DS0c	0.107	0.303
GP01	-0.034	0.426
GP02	0.378	1.662
GP0c	-0.477	0.078
NOD	-0.905	0.633
NZO	0.016	0.12
PWK	-0.499	-0.099
H37Rv_KO_CtpC	0.105	0.06
H37Rv_KO_CtpD	0.384	-0.132
H37Rv_KO_Rv1272	0.847	1.155
H37Rv_KO_SugABC	-0.295	0.241
H37Rv_KO_MbtN	0.957	1.744
Trans05	0.635	0.995
macrophage_unactivated	0.546	0.941
IL1	0.0	0.483
Rapamycin	0.117	0.534
Tcell	-0.293	0.453
GMCSF	0.364	0.552
IFNab	-0.429	0.345
IFNg	0.128	0.465
IFNg_GMCSF1	0.676	0.584
Rv1432_day32	0.018	0.43
Rv1565c_day32	-0.504	0.415
secA2_input	-1.141	-0.538
delta_Rv3594	0.626	0.017
delta_Rv3717	-0.292	-0.176
delta_Rv3811	0.544	0.033
delta_Rv0954	0.686	-0.295
PonA1	0.329	-0.278
EccD1_KO	-0.816	-0.536
EspI_KO	-0.836	-0.103
PE35_KO	-0.802	0.458
PPE68_KO	-0.851	0.074
glycerol2	-0.153	0.333
lignocerate	-0.056	0.666
oleate	-0.109	0.247
phosphatidylcholine	-0.343	0.887
acetate	0.595	0.667
glucAc	0.061	0.246
Rv0950ko	-0.139	-0.154
Rv1096ko	-0.561	-0.941
Rv3684ko	-0.524	-0.236
delta_otsA_trehalose	0.269	0.61