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 Rv2345/-

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

	Rv1000c/-	Rv2345/-
Fe_supp_jason_reseq	-1.361	-0.019
low_pH_jason_reseq	-2.546	-0.962
NO_jason_reseq	-0.197	-0.053
B6_jason_reseq	-0.576	-0.063
MHCII_jason_reseq	-0.576	0.065
Isoniazid02	-1.963	-1.199
Rifampicin4	0.384	0.509
Ethambutol3	-1.688	-1.019
Meropenem3	-1.517	-1.409
Vancomycin16	-0.584	-0.655
Rv2680_day32	-1.602	-0.466
H37Rv_KO_MarP	0.138	-0.02
hypoxia_3wks	0.06	0.032
hypoxia_6wks	0.566	0.257
glycerol	0.127	0.192
cholesterol	0.507	-0.086
AJ	0.45	0.0
Bibs02	-0.091	-0.278
Bibs02c	0.073	-0.205
BL6	0.353	0.138
BL6a	-0.324	0.118
BXD01	-0.594	0.14
BXD010	0.196	0.141
BXD011	0.672	-0.262
BXD03	0.287	-0.04
BXD04	-0.76	0.291
BXD05	-0.145	0.374
BXD06	-0.125	0.147
BXD07	0.244	0.238
BXD08	-0.345	0.434
BXD09	-0.379	0.199
CAST	-0.229	-0.225
CCcont	-0.888	0.024
DS01	0.542	0.0
DS02	0.569	-0.498
DS04	0.52	-0.142
DS0c	0.608	-0.057
GP01	0.172	0.277
GP02	0.497	0.072
GP0c	-0.196	0.147
NOD	0.477	0.265
NZO	0.458	-0.237
PWK	-0.345	-0.058
H37Rv_KO_CtpC	0.211	0.373
H37Rv_KO_CtpD	0.678	0.605
H37Rv_KO_Rv1272	-0.644	0.291
H37Rv_KO_SugABC	1.463	0.767
H37Rv_KO_MbtN	0.647	0.628
Trans05	-0.157	0.501
macrophage_unactivated	-0.199	-0.114
IL1	0.789	0.338
Rapamycin	0.657	0.473
Tcell	0.235	0.039
GMCSF	1.751	0.599
IFNab	0.323	0.311
IFNg	1.475	0.216
IFNg_GMCSF1	1.335	0.182
Rv1432_day32	1.551	0.194
Rv1565c_day32	0.607	0.175
secA2_input	-1.032	0.233
delta_Rv3594	-0.413	0.271
delta_Rv3717	-0.417	0.055
delta_Rv3811	-0.587	0.352
delta_Rv0954	-0.115	0.371
PonA1	-0.262	-0.321
EccD1_KO	1.447	0.704
EspI_KO	1.805	0.767
PE35_KO	0.732	0.429
PPE68_KO	1.113	0.176
glycerol2	-0.147	0.277
lignocerate	-0.136	0.284
oleate	0.405	0.702
phosphatidylcholine	0.21	0.153
acetate	-0.82	-0.462
glucAc	-0.624	-0.232
Rv0950ko	0.22	0.434
Rv1096ko	0.715	-0.567
Rv3684ko	-0.639	-0.54
delta_otsA_trehalose	-0.104	0.582