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 Rv1000c/-:

update plot	correlation	link to info on gene
Rv2345/-	(cc=0.6093)	info on Rv2345/-
Rv1899c/lppD	(cc=0.4895)	info on Rv1899c/lppD
Rv1545/-	(cc=0.4869)	info on Rv1545/-
Rv1857/modA	(cc=0.4858)	info on Rv1857/modA
Rv1947/-	(cc=0.4746)	info on Rv1947/-
Rv1726/-	(cc=0.4718)	info on Rv1726/-
Rv0605/-	(cc=0.4686)	info on Rv0605/-
Rv0399c/lpqK	(cc=0.4606)	info on Rv0399c/lpqK
Rv1141c/echA11	(cc=0.4537)	info on Rv1141c/echA11
Rv2658c/-	(cc=0.4466)	info on Rv2658c/-

Correlation of Rv1000c/- with Rv0605/-

Normalized LFCs for Rv1000c/-:
(description and provenance of datasets)

	Rv1000c/-	Rv0605/-
Fe_supp_jason_reseq	-1.361	-0.995
low_pH_jason_reseq	-2.546	-0.028
NO_jason_reseq	-0.197	-0.215
B6_jason_reseq	-0.576	-0.115
MHCII_jason_reseq	-0.576	0.297
Isoniazid02	-1.963	-0.274
Rifampicin4	0.384	0.195
Ethambutol3	-1.688	-0.371
Meropenem3	-1.517	-0.589
Vancomycin16	-0.584	-0.119
Rv2680_day32	-1.602	-0.777
H37Rv_KO_MarP	0.138	0.391
hypoxia_3wks	0.06	-0.159
hypoxia_6wks	0.566	-0.478
glycerol	0.127	0.127
cholesterol	0.507	0.526
AJ	0.45	-0.207
Bibs02	-0.091	-0.038
Bibs02c	0.073	0.708
BL6	0.353	0.372
BL6a	-0.324	0.194
BXD01	-0.594	0.018
BXD010	0.196	-0.298
BXD011	0.672	1.443
BXD03	0.287	0.08
BXD04	-0.76	-0.205
BXD05	-0.145	0.244
BXD06	-0.125	0.109
BXD07	0.244	0.549
BXD08	-0.345	0.241
BXD09	-0.379	0.128
CAST	-0.229	-0.319
CCcont	-0.888	0.223
DS01	0.542	-0.099
DS02	0.569	0.117
DS04	0.52	-0.115
DS0c	0.608	0.165
GP01	0.172	0.185
GP02	0.497	0.345
GP0c	-0.196	0.099
NOD	0.477	0.22
NZO	0.458	0.152
PWK	-0.345	-0.041
H37Rv_KO_CtpC	0.211	-0.399
H37Rv_KO_CtpD	0.678	1.48
H37Rv_KO_Rv1272	-0.644	-0.807
H37Rv_KO_SugABC	1.463	0.127
H37Rv_KO_MbtN	0.647	-0.069
Trans05	-0.157	-0.126
macrophage_unactivated	-0.199	0.306
IL1	0.789	1.323
Rapamycin	0.657	1.335
Tcell	0.235	0.316
GMCSF	1.751	0.919
IFNab	0.323	0.493
IFNg	1.475	0.583
IFNg_GMCSF1	1.335	0.786
Rv1432_day32	1.551	0.348
Rv1565c_day32	0.607	0.022
secA2_input	-1.032	0.011
delta_Rv3594	-0.413	-0.503
delta_Rv3717	-0.417	0.186
delta_Rv3811	-0.587	-0.778
delta_Rv0954	-0.115	-0.32
PonA1	-0.262	-0.83
EccD1_KO	1.447	0.714
EspI_KO	1.805	0.553
PE35_KO	0.732	1.275
PPE68_KO	1.113	0.733
glycerol2	-0.147	0.502
lignocerate	-0.136	1.359
oleate	0.405	-0.024
phosphatidylcholine	0.21	0.926
acetate	-0.82	0.638
glucAc	-0.624	1.051
Rv0950ko	0.22	0.847
Rv1096ko	0.715	1.056
Rv3684ko	-0.639	1.205
delta_otsA_trehalose	-0.104	-0.234