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 Rv1366/-:

update plot	correlation	link to info on gene
Rv3749c/-	(cc=0.6056)	info on Rv3749c/-
Rv2078/-	(cc=0.5622)	info on Rv2078/-
Rv1913/-	(cc=0.5434)	info on Rv1913/-
Rv1013/pks16	(cc=0.5409)	info on Rv1013/pks16
Rv2287/yjcE	(cc=0.5232)	info on Rv2287/yjcE
Rv1751/-	(cc=0.5193)	info on Rv1751/-
Rv3697c/vapC48	(cc=0.5103)	info on Rv3697c/vapC48
Rv3819/-	(cc=0.4989)	info on Rv3819/-
Rv0226c/-	(cc=0.4983)	info on Rv0226c/-
Rv0235c/-	(cc=0.4943)	info on Rv0235c/-

Correlation of Rv1366/- with Rv1913/-

Normalized LFCs for Rv1366/-:
(description and provenance of datasets)

	Rv1366/-	Rv1913/-
Fe_supp_jason_reseq	-0.884	1.913
low_pH_jason_reseq	-0.172	0.952
NO_jason_reseq	-0.294	0.583
B6_jason_reseq	-0.871	-0.571
MHCII_jason_reseq	-0.267	0.457
Isoniazid02	0.148	-0.116
Rifampicin4	-0.376	0.203
Ethambutol3	0.269	0.035
Meropenem3	0.237	-0.236
Vancomycin16	0.172	-0.212
Rv2680_day32	-0.969	0.985
H37Rv_KO_MarP	0.518	-0.797
hypoxia_3wks	-0.235	0.327
hypoxia_6wks	-0.048	2.543
glycerol	-0.78	-0.629
cholesterol	-0.44	-1.144
AJ	0.134	-0.876
Bibs02	-0.823	-2.188
Bibs02c	0.656	-1.725
BL6	0.376	0.896
BL6a	0.397	-0.032
BXD01	0.834	1.136
BXD010	1.115	-0.455
BXD011	0.35	2.06
BXD03	-0.278	0.374
BXD04	0.315	0.216
BXD05	0.231	0.68
BXD06	0.323	1.098
BXD07	0.476	0.752
BXD08	0.506	-0.414
BXD09	-0.012	0.815
CAST	-0.142	0.464
CCcont	0.646	0.694
DS01	0.301	-0.406
DS02	-0.254	-0.217
DS04	0.263	0.204
DS0c	0.525	-0.585
GP01	1.227	0.499
GP02	1.296	0.468
GP0c	0.54	-0.432
NOD	0.148	-1.175
NZO	0.839	-1.383
PWK	0.406	-0.23
H37Rv_KO_CtpC	0.467	0.805
H37Rv_KO_CtpD	-0.907	-0.316
H37Rv_KO_Rv1272	0.341	2.984
H37Rv_KO_SugABC	0.902	2.071
H37Rv_KO_MbtN	0.392	0.56
Trans05	0.557	1.699
macrophage_unactivated	0.107	-0.802
IL1	-0.739	-6.0
Rapamycin	-0.681	-6.0
Tcell	0.694	4.027
GMCSF	-1.117	-6.0
IFNab	-0.593	-6.0
IFNg	-1.384	-6.0
IFNg_GMCSF1	-1.628	-6.0
Rv1432_day32	-0.55	-0.897
Rv1565c_day32	0.175	0.28
secA2_input	-0.188	-0.848
delta_Rv3594	-0.249	0.217
delta_Rv3717	0.371	0.836
delta_Rv3811	-0.665	-0.125
delta_Rv0954	0.813	-0.501
PonA1	0.726	-0.291
EccD1_KO	-0.276	-0.872
EspI_KO	0.262	-1.366
PE35_KO	0.379	-0.893
PPE68_KO	0.534	-0.979
glycerol2	1.188	0.963
lignocerate	1.47	1.388
oleate	0.387	-0.22
phosphatidylcholine	1.27	1.004
acetate	1.549	1.142
glucAc	1.226	1.034
Rv0950ko	0.856	0.715
Rv1096ko	0.32	-0.407
Rv3684ko	0.534	0.36
delta_otsA_trehalose	1.077	1.073